% This file was created with JabRef 2.10. % Encoding: UTF8 @Book{Alon:2006, Title = {{A}n introduction to systems biology: design principles of biological circuits}, Author = {Alon, Uri}, Publisher = {CRC press}, Year = {2006} } @Book{azhari2010basics, Title = {{B}asics of biomedical ultrasound for engineers}, Author = {Azhari, Haim}, Publisher = {John Wiley \& Sons}, Year = {2010} } @Article{Baizabal-Carvallo2016, Title = {{L}ow-frequency deep brain stimulation for movement disorders}, Author = {Baizabal-Carvallo, Jos{\'e} Fidel and Alonso-Juarez, Marlene}, Journal = {Parkinsonism \& Related Disorders}, Year = {2016}, Pages = {14--22}, Volume = {31}, Publisher = {Elsevier} } @Article{Bellisario:1972, Title = {{I}solation and properties of luciferase, a non-heme peroxidase, from the bioluminescent earthworm, {D}iplocardia longa}, Author = {Bellisario, Ronald and Spencer, Terry E and Cormier, Milton J}, Journal = {Biochemistry}, Year = {1972}, Number = {12}, Pages = {2256--2266}, Volume = {11}, Owner = {lidija}, Publisher = {ACS Publications}, Timestamp = {2016.05.11} } @Article{Beudel2015, Title = {{Adaptive deep brain stimulation in Parkinson's disease.}}, Author = {Beudel, M. and Brown, P.}, Journal = {Parkinsonism {\&} related disorders}, Year = {2015}, Pages = {1--4}, Volume = {22}, Doi = {10.1016/j.parkreldis.2015.09.028}, File = {:Users/Samo/Downloads/1-s2.0-S1353802015004174-main.pdf:pdf}, ISBN = {1873-5126 (Electronic)$\backslash$r1353-8020 (Linking)}, ISSN = {1873-5126}, Keywords = {Brain-computer interface,Deep brain stimulation,Parkinson's disease}, Pmid = {26411502}, Publisher = {Elsevier Ltd} } @Article{Cesaratto2015, Title = {{E}ngineered tobacco etch virus ({TEV}) protease active in the secretory pathway of mammalian cells.}, Author = {Cesaratto, Francesca and L{\'{o}}pez-Requena, Alejandro and Burrone, Oscar R. and Petris, Gianluca}, Journal = {J Biotechnol}, Year = {2015}, Month = {Oct}, Pages = {159--166}, Volume = {212}, __markedentry = {[lidija:6]}, Abstract = {Tobacco etch virus protease (TEVp) is a unique endopeptidase with stringent substrate specificity. TEVp has been widely used as a purified protein for in vitro applications, but also as a biological tool directly expressing it in living cells. To adapt the protease to diverse applications, several TEVp mutants with different stability and enzymatic properties have been reported. Herein we describe the development of a novel engineered TEVp mutant designed to be active in the secretory pathway. While wild type TEVp targeted to the secretory pathway of mammalian cells is synthetized as an N-glycosylated and catalytically inactive enzyme, a TEVp mutant with selected mutations at two verified N-glycosylation sites and at an exposed cysteine was highly efficient. This mutant was very active in the endoplasmic reticulum (ER) of living cells and can be used as a biotechnological tool to cleave proteins within the secretory pathway. As an immediate practical application we report the expression of a complete functional monoclonal antibody expressed from a single polypeptide, which was cleaved by our TEVp mutant into the two antibody chains and secreted as an assembled and functional molecule. In addition, we show active TEVp mutants lacking auto-cleavage activity.}, Doi = {10.1016/j.jbiotec.2015.08.026}, Institution = {International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy. Electronic address: burrone@icgeb.org.}, Keywords = {Antibodies, Monoclonal, metabolism; Cytosol, metabolism; Endopeptidases, genetics/metabolism; Endoplasmic Reticulum, metabolism; HEK293 Cells; Humans; Immunoglobulin G, immunology; Mutation; Peptides, metabolism; Secretory Pathway}, Language = {eng}, Medline-pst = {ppublish}, Owner = {lidija}, Pii = {S0168-1656(15)30105-X}, Pmid = {26327323}, Timestamp = {2016.10.16}, Url = {http://dx.doi.org/10.1016/j.jbiotec.2015.08.026} } @Article{Darzacq:2007, Title = {{I}n vivo dynamics of {RNA} polymerase {II} transcription}, Author = {Darzacq, Xavier and Shav-Tal, Yaron and de Turris, Valeria and Brody, Yehuda and Shenoy, Shailesh M and Phair, Robert D and Singer, Robert H}, Journal = {Nature Structural \& Molecular Biology}, Year = {2007}, Month = {Aug}, Number = {9}, Pages = {796–806}, Volume = {14}, Doi = {10.1038/nsmb1280}, ISSN = {1545-9985}, Owner = {lidija}, Publisher = {Nature Publishing Group}, Timestamp = {2016.08.04}, Url = {http://dx.doi.org/10.1038/nsmb1280} } @Article{DeCrescenzo:2003, Title = {{R}eal-time monitoring of the interactions of two-stranded de novo designed coiled-coils: effect of chain length on the kinetic and thermodynamic constants of binding.}, Author = {{De Crescenzo}, Gregory and Litowski, Jennifer R. and Hodges, Robert S. and O'Connor-McCourt, Maureen D.}, Journal = {Biochemistry}, Year = {2003}, Month = {Feb}, Number = {6}, Pages = {1754--1763}, Volume = {42}, Abstract = {We have de novo designed a heterodimeric coiled-coil formed by two peptides as a capture/delivery system that can be used in applications such as affinity tag purification, immobilization in biosensors, etc. The two strands are designated as K coil (KVSALKE heptad sequence) and E coil (EVSALEK heptad sequence), where positively charged or negatively charged residues occupy positions e and g of the heptad repeat. In this study, for each E coil or K coil, three peptides were synthesized with lengths varying from three to five heptads. The effect of the chain length of each partner upon the kinetic and thermodynamic constants of interaction were determined using a surface plasmon resonance-based biosensor. Global fitting of the interactions revealed that the E5 coil interacted with the K5 coil according to a simple binding model. All the other interactions involving shorter coils were better described by a more complex kinetic model involving a rate-limiting reorganization of the coiled-coil structure. The affinities of these de novo designed coiled-coil interactions were found to range from 60 pM (E5/K5) to 30 microM (E3/K3). From these K(d) values, we were able to determine the free energy contribution of each heptad, depending on its relative position within the coiled-coils. We found that the free energy contribution of a heptad occupying a central position was 3-fold higher than that of a heptad at either end of the coiled-coil. The wide range of stabilities and affinities for the E/K coil system provides considerable flexibility for protein engineering and biotechnological applications.}, Doi = {10.1021/bi0268450}, Institution = {Cell Surface Receptor Group, Health Sector, Biotechnology Research Institute, National Research Council (Canada), 6100, Royalmount Avenue, Montreal, Quebec, Canada H4P 2R2.}, Keywords = {Amino Acid Sequence; Computer Simulation; Dimerization; Hydrophobic and Hydrophilic Interactions; Kinetics; Models, Molecular; Molecular Sequence Data; Peptide Biosynthesis; Peptides, chemistry/isolation /&/ purification; Protein Binding; Protein Conformation; Protein Folding; Protein Structure, Secondary; Static Electricity; Structure-Activity Relationship; Surface Plasmon Resonance, methods; Thermodynamics}, Language = {eng}, Medline-pst = {ppublish}, Owner = {lidija}, Pmid = {12578390}, Timestamp = {2016.08.06}, Url = {http://dx.doi.org/10.1021/bi0268450} } @Article{Dietmair:2012, Title = {{A} multi-omics analysis of recombinant protein production in {H}ek293 cells}, Author = {Dietmair, Stefanie and Hodson, Mark P and Quek, Lake-Ee and Timmins, Nicholas E and Gray, Peter and Nielsen, Lars K}, Journal = {PLoS one}, Year = {2012}, Number = {8}, Pages = {e43394}, Volume = {7}, Owner = {lidija}, Publisher = {Public Library of Science}, Timestamp = {2016.05.07} } @Article{Donahue:1987, Title = {{F}ree diffusion coefficient of ionic calcium in cytoplasm}, Author = {Donahue, Brian S and Abercrombie, RF}, Journal = {Cell calcium}, Year = {1987}, Number = {6}, Pages = {437--448}, Volume = {8}, Owner = {lidija}, Publisher = {Elsevier}, Timestamp = {2016.05.14} } @Article{Eden:2011, Title = {{P}roteome {H}alf-{L}ife {D}ynamics in {L}iving {H}uman {C}ells}, Author = {Eden, E. and Geva-Zatorsky, N. and Issaeva, I. and Cohen, A. and Dekel, E. and Danon, T. and Cohen, L. and Mayo, A. and Alon, U.}, Journal = {Science}, Year = {2011}, Month = {Jan}, Number = {6018}, Pages = {764–768}, Volume = {331}, Doi = {10.1126/science.1199784}, ISSN = {1095-9203}, Owner = {lidija}, Publisher = {American Association for the Advancement of Science (AAAS)}, Timestamp = {2016.08.04}, Url = {http://dx.doi.org/10.1126/science.1199784} } @Book{escoffre2016therapeutic, Title = {{T}herapeutic ultrasound}, Author = {Escoffre, Jean-Michel and Bouakaz, Ayache}, Publisher = {Springer}, Year = {2016} } @Book{Fall:2002, Title = {{C}omputational {C}ell {B}iology}, Author = {Fall, Christopher P}, Publisher = {Springer-Verlag New York Incorporated}, Year = {2002}, Journal = {Interdisciplinary Applied Mathematics; V. 20}, Owner = {lidija}, Timestamp = {2016.05.11} } @Article{Fischer:2016, Title = {{T}ropomyosin diffusion over actin subunits facilitates thin filament assembly}, Author = {Fischer, Stefan and Rynkiewicz, Michael J and Moore, Jeffrey R and Lehman, William}, Journal = {Structural Dynamics}, Year = {2016}, Number = {1}, Pages = {012002}, Volume = {3}, Owner = {lidija}, Publisher = {American Crystallographic Association, Inc.}, Timestamp = {2016.05.11} } @Article{Gaber:2014, Title = {{D}esignable {DNA}-binding domains enable construction of logic circuits in mammalian cells.}, Author = {Gaber, Rok and Lebar, Tina and Majerle, Andreja and Šter, Branko and Dobnikar, Andrej and Benčina, Mojca and Jerala, Roman}, Journal = {Nat Chem Biol}, Year = {2014}, Month = {Mar}, Number = {3}, Pages = {203--208}, Volume = {10}, __markedentry = {[lidija:]}, Abstract = {Electronic computer circuits consisting of a large number of connected logic gates of the same type, such as NOR, can be easily fabricated and can implement any logic function. In contrast, designed genetic circuits must employ orthogonal information mediators owing to free diffusion within the cell. Combinatorial diversity and orthogonality can be provided by designable DNA- binding domains. Here, we employed the transcription activator-like repressors to optimize the construction of orthogonal functionally complete NOR gates to construct logic circuits. We used transient transfection to implement all 16 two-input logic functions from combinations of the same type of NOR gates within mammalian cells. Additionally, we present a genetic logic circuit where one input is used to select between an AND and OR function to process the data input using the same circuit. This demonstrates the potential of designable modular transcription factors for the construction of complex biological information-processing devices.}, Doi = {10.1038/nchembio.1433}, Institution = { EN-FIST Centre of Excellence, Ljubljana, Slovenia.}, Keywords = {Amino Acid Motifs; Animals; Binding Sites; DNA, chemistry/metabolism; Flow Cytometry; HEK293 Cells; Humans; Logic; Protein Structure, Tertiary; Synthetic Biology}, Language = {eng}, Medline-pst = {ppublish}, Owner = {lidija}, Pii = {nchembio.1433}, Pmid = {24413461}, Timestamp = {2016.10.08}, Url = {http://dx.doi.org/10.1038/nchembio.1433} } @Article{Gann:1991, Title = {{U}ltrasound: current concepts}, Author = {Gann, Nancy}, Journal = {Clin Manage}, Year = {1991}, Number = {4}, Pages = {64--69}, Volume = {11} } @Article{Hsiao:2015, Title = {{D}esign and implementation of a biomolecular concentration tracker.}, Author = {Hsiao, Victoria and {de los Santos}, Emmanuel L C. and Whitaker, Weston R. and Dueber, John E. and Murray, Richard M.}, Journal = {ACS Synth Biol}, Year = {2015}, Month = {Feb}, Number = {2}, Pages = {150--161}, Volume = {4}, Abstract = {As a field, synthetic biology strives to engineer increasingly complex artificial systems in living cells. Active feedback in closed loop systems offers a dynamic and adaptive way to ensure constant relative activity independent of intrinsic and extrinsic noise. In this work, we use synthetic protein scaffolds as a modular and tunable mechanism for concentration tracking through negative feedback. Input to the circuit initiates scaffold production, leading to colocalization of a two-component system and resulting in the production of an inhibitory antiscaffold protein. Using a combination of modeling and experimental work, we show that the biomolecular concentration tracker circuit achieves dynamic protein concentration tracking in Escherichia coli and that steady state outputs can be tuned.}, Doi = {10.1021/sb500024b}, Institution = {Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, California United States.}, Keywords = {Escherichia coli Proteins, chemistry/metabolism; Escherichia coli, metabolism; Feedback, Physiological; Kinetics; Leucine Zippers; Models, Molecular; Phosphoric Monoester Hydrolases, chemistry/metabolism; Protein Kinases, chemistry/metabolism}, Language = {eng}, Medline-pst = {ppublish}, Owner = {lidija}, Pmid = {24847683}, Timestamp = {2016.08.06}, Url = {http://dx.doi.org/10.1021/sb500024b} } @Article{Ingolia:2011, Title = {{R}ibosome {P}rofiling of {M}ouse {E}mbryonic {S}tem {C}ells {R}eveals the {C}omplexity and {D}ynamics of {M}ammalian {P}roteomes}, Author = {Ingolia, Nicholas T. and Lareau, Liana F. and Weissman, Jonathan S.}, Journal = {Cell}, Year = {2011}, Month = {Nov}, Number = {4}, Pages = {789–802}, Volume = {147}, Doi = {10.1016/j.cell.2011.10.002}, ISSN = {0092-8674}, Owner = {lidija}, Publisher = {Elsevier BV}, Timestamp = {2016.08.04}, Url = {http://dx.doi.org/10.1016/j.cell.2011.10.002} } @Book{Keener:2009, Title = {{M}athematical {P}hysiology: {C}ellular {P}hysiology. {I}}, Author = {James P.. Keener and Sneyd, James}, Publisher = {Springer}, Year = {2009}, Owner = {lidija}, Timestamp = {2016.05.11} } @Article{Kiani:2014, Title = {{CRISPR} transcriptional repression devices and layered circuits in mammalian cells.}, Author = {Kiani, Samira and Beal, Jacob and Ebrahimkhani, Mohammad R. and Huh, Jin and Hall, Richard N. and Xie, Zhen and Li, Yinqing and Weiss, Ron}, Journal = {Nat Methods}, Year = {2014}, Month = {Jul}, Number = {7}, Pages = {723--726}, Volume = {11}, Abstract = {A key obstacle to creating sophisticated genetic circuits has been the lack of scalable device libraries. Here we present a modular transcriptional repression architecture based on clustered regularly interspaced palindromic repeats (CRISPR) system and examine approaches for regulated expression of guide RNAs in human cells. Subsequently we demonstrate that CRISPR regulatory devices can be layered to create functional cascaded circuits, which provide a valuable toolbox for engineering purposes.}, Doi = {10.1038/nmeth.2969}, Institution = { Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.}, Keywords = {Clustered Regularly Interspaced Short Palindromic Repeats, genetics; Gene Expression Regulation; Gene Targeting; Genetic Engineering, instrumentation/methods; HEK293 Cells; Humans; Promoter Regions, Genetic; RNA Polymerase II, genetics; RNA Polymerase III, genetics; RNA, Guide, biosynthesis/metabolism; Transcription, Genetic, drug effects}, Language = {eng}, Medline-pst = {ppublish}, Owner = {lidija}, Pii = {nmeth.2969}, Pmid = {24797424}, Timestamp = {2016.10.08}, Url = {http://dx.doi.org/10.1038/nmeth.2969} } @Article{Kim:2008, Title = {{CENP}-{E} combines a slow, processive motor and a flexible coiled coil to produce an essential motile kinetochore tether}, Author = {Kim, Yumi and Heuser, John E and Waterman, Clare M and Cleveland, Don W}, Journal = {The Journal of cell biology}, Year = {2008}, Number = {3}, Pages = {411--419}, Volume = {181}, Owner = {lidija}, Publisher = {Rockefeller Univ Press}, Timestamp = {2016.05.12} } @Article{Kruszynska:1987f, Title = {{B}asal and 24-h {C}-peptide and insulin secretion rate in normal man.}, Author = {Kruszynska, Y. T. and Home, P. D. and Hanning, I. and Alberti, K. G.}, Journal = {Diabetologia}, Year = {1987}, Month = {Jan}, Number = {1}, Pages = {16--21}, Volume = {30}, Abstract = {An understanding of the metabolic abnormalities rising from inappropriate insulin delivery in diabetic patients demands a knowledge of 24-h and basal insulin secretion rates in normal man. We have used biosynthetic human C-peptide to determine its kinetic parameters in 10 normal subjects and applied these to measurements of plasma concentrations in the same subjects to determine pancreatic secretion rate. Metabolic clearance rate measured by stepped primed infusion of biosynthetic human C-peptide at rates of 10, 19 and 26 nmol/h was 4.7 +/- 0.7 (+/- SD) ml X kg-1 X min-1, and was independent of infusion rate. Fractional clearance (T1/2, 26 +/- 3 min) and distribution volume (0.178 +/- 0.039 l/kg) were calculated from the decline in concentration after cessation of the highest rate infusion. Basal insulin secretion calculated from the C-peptide metabolic clearance rate and plasma concentrations for the period 02.00 to 07.00 hours was 1.3 +/- 0.4 U/h. Over 24 h total insulin secretion on a standard high carbohydrate diet was 63 +/- 15 U, calculated from the area under the C-peptide concentration curve. Basal insulin secretion, therefore, accounted for 50 +/- 8\% of total insulin secretion. Although only 5.6 +/- 1.1\% of C-peptide was detected in 24-h urine collections, urinary C-peptide excretion was significantly related to 24-h C-peptide secretion (r = 0.74, p less than 0.02).}, Keywords = {Adult; C-Peptide, metabolism/secretion; Circadian Rhythm; Female; Humans; Insulin, blood/secretion; Kinetics; Male}, Language = {eng}, Medline-pst = {ppublish}, Owner = {lidija}, Pmid = {3552817}, Timestamp = {2016.09.25} } @Book{kumar2014robbins, Title = {{R}obbins and {C}otran pathologic basis of disease}, Author = {Kumar, Vinay and Abbas, Abul K and Fausto, Nelson and Aster, Jon C}, Publisher = {Elsevier Health Sciences}, Year = {2014} } @Article{Li2016, Title = {{T}herapies for {P}arkinson’s diseases: alternatives to current pharmacological interventions}, Author = {Li, Song and Dong, Jie and Cheng, Cheng and Le, Weidong}, Journal = {Journal of Neural Transmission}, Year = {2016}, Pages = {1--21}, Publisher = {Springer} } @Article{Mariani:2010, Title = {{S}hort-term memory in gene induction reveals the regulatory principle behind stochastic {IL}-4 expression.}, Author = {Mariani, Luca and Schulz, Edda G. and Lexberg, Maria H. and Helmstetter, Caroline and Radbruch, Andreas and Löhning, Max and Höfer, Thomas}, Journal = {Mol Syst Biol}, Year = {2010}, Month = {Apr}, Pages = {359}, Volume = {6}, Abstract = {Although cell-to-cell variability has been recognized as an unavoidable consequence of stochasticity in gene expression, it may also serve a functional role for tuning physiological responses within a cell population. In the immune system, remarkably large variability in the expression of cytokine genes has been observed in homogeneous populations of lymphocytes, but the underlying molecular mechanisms are incompletely understood. Here, we study the interleukin-4 gene (il4) in T-helper lymphocytes, combining mathematical modeling with the experimental quantification of expression variability and critical parameters. We show that a stochastic rate-limiting step upstream of transcription initiation, but acting at the level of an individual allele, controls il4 expression. Only a fraction of cells reaches an active, transcription-competent state in the transient time window determined by antigen stimulation. We support this finding by experimental evidence of a previously unknown short-term memory that was predicted by the model to arise from the long lifetime of the active state. Our analysis shows how a stochastic mechanism acting at the chromatin level can be integrated with transcriptional regulation to quantitatively control cell-to-cell variability.}, Doi = {10.1038/msb.2010.13}, Institution = {Research Group Modeling of Biological Systems, German Cancer Research Center, Heidelberg, Germany. luca.mariani@ifom-ieo-campus.it}, Keywords = {Animals; Chromatin, metabolism; Flow Cytometry; GATA3 Transcription Factor, metabolism; Gene Expression Regulation; Interleukin-4, biosynthesis/genetics; Mice; Models, Genetic; NFATC Transcription Factors, metabolism; RNA, Messenger, genetics/metabolism; Stochastic Processes; Th2 Cells, metabolism; Transcriptional Activation}, Language = {eng}, Medline-pst = {ppublish}, Owner = {lidija}, Pii = {msb201013}, Pmid = {20393579}, Timestamp = {2016.10.08}, Url = {http://dx.doi.org/10.1038/msb.2010.13} } @Article{Melnik:2003, Title = {{S}hift of fibril-forming ability of the designed $\alpha$-helical coiled-coil peptides into the physiological p{H} region}, Author = {Melnik, TN and Villard, V and Vasiliev, V and Corradin, G and Kajava, AV and Potekhin, SA}, Journal = {Protein engineering}, Year = {2003}, Number = {12}, Pages = {1125--1130}, Volume = {16}, Owner = {lidija}, Publisher = {Oxford Univ Press}, Timestamp = {2016.05.12} } @Misc{Murray:2002, Title = {{M}athematical biology {I}: an introduction, {V}ol. 17 of interdisciplinary applied mathematics}, Author = {Murray, James D}, Year = {2002}, Owner = {lidija}, Publisher = {Springer, New York, NY, USA,}, Timestamp = {2016.07.20} } @Article{Oertel2016, Title = {{C}urrent and experimental treatments of {P}arkinson disease: {A} guide for neuroscientists}, Author = {Oertel, Wolfgang and Schulz, J{\"o}rg B}, Journal = {Journal of Neurochemistry}, Year = {2016}, Publisher = {Wiley Online Library} } @Article{Paehler:2012, Title = {{C}oiled-{C}oil {F}ormation on {L}ipid {B}ilayers—{I}mplications for {D}ocking and {F}usion {E}fficiency}, Author = {P{\"a}hler, Gesa and Panse, Cornelia and Diederichsen, Ulf and Janshoff, Andreas}, Journal = {Biophysical journal}, Year = {2012}, Number = {11}, Pages = {2295--2303}, Volume = {103}, Owner = {lidija}, Publisher = {Elsevier}, Timestamp = {2016.05.11} } @Article{Peersen:1997, Title = {{I}ntermolecular tuning of calmodulin by target peptides and proteins: differential effects on {C}a2+ binding and implications for kinase activation}, Author = {Peersen, Olve B and Madsen, Travis S and Falke, Joseph J}, Journal = {Protein Science}, Year = {1997}, Number = {4}, Pages = {794--807}, Volume = {6}, Owner = {lidija}, Publisher = {Wiley Online Library}, Timestamp = {2016.07.20} } @Article{Saisho:2007a, Title = {{P}ancreas volumes in humans from birth to age one hundred taking into account sex, obesity, and presence of type-2 diabetes.}, Author = {Saisho, Y. and Butler, A. E. and Meier, J. J. and Monchamp, T. and Allen-Auerbach, M. and Rizza, R. A. and Butler, P. C.}, Journal = {Clin Anat}, Year = {2007}, Month = {Nov}, Number = {8}, Pages = {933--942}, Volume = {20}, Abstract = {Our aims were (1) by computed tomography (CT) to establish a population database for pancreas volume (parenchyma and fat) from birth to age 100 years, (2) in adults, to establish the impact of gender, obesity, and the presence or absence of type-2 diabetes on pancreatic volume (parenchyma and fat), and (3) to confirm the latter histologically from pancreatic tissue obtained at autopsy with a particular emphasis on whether pancreatic fat is increased in type-2 diabetes. We measured pancreas volume in 135 children and 1,886 adults (1,721 nondiabetic and 165 with type-2 diabetes) with no history of pancreas disease who had undergone abdominal CT scan between 2003 and 2006. Pancreas volume was computed from the contour of the pancreas on each CT image. In addition to total pancreas volume, parenchymal volume, fat volume, and fat/parenchyma ratio (F/P ratio) were determined by CT density. We also quantified pancreatic fat in autopsy tissue of 47 adults (24 nondiabetic and 23 with type-2 diabetes). During childhood and adolescence, the volumes of total pancreas, pancreatic parenchyma, and fat increase linearly with age. From age 20-60 years, pancreas volume reaches a plateau (72.4 +/- 25.8 cm(3) total; 44.5 +/- 16.5 cm(3) parenchyma) and then declines thereafter. In adults, total ( approximately 32\%), parenchymal ( approximately 13\%), and fat ( approximately 68\%) volumes increase with obesity. Pancreatic fat content also increases with aging but is not further increased in type-2 diabetes. We provide lifelong population data for total pancreatic, parenchymal, and fat volumes in humans. Although pancreatic fat increases with aging and obesity, it is not increased in type-2 diabetes.}, Doi = {10.1002/ca.20543}, Institution = {Larry Hillblom Islet Research Center, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-7073, USA.}, Keywords = {Adolescent; Adult; Aged; Aged, 80 and over; Aging; Autopsy; Body Mass Index; Child; Child, Preschool; Diabetes Mellitus, Type 2, physiopathology; Female; Humans; Infant; Infant, Newborn; Male; Middle Aged; Obesity, physiopathology; Organ Size; Pancreas, anatomy /&/ histology; Phantoms, Imaging; Sex Characteristics; Thinness, physiopathology; Tomography, X-Ray Computed}, Language = {eng}, Medline-pst = {ppublish}, Owner = {lidija}, Pmid = {17879305}, Timestamp = {2016.09.25}, Url = {http://dx.doi.org/10.1002/ca.20543} } @Article{Sanabria:2008, Title = {{S}patial diffusivity and availability of intracellular calmodulin}, Author = {Sanabria, Hugo and Digman, Michelle A and Gratton, Enrico and Waxham, M Neal}, Journal = {Biophysical journal}, Year = {2008}, Number = {12}, Pages = {6002--6015}, Volume = {95}, Owner = {lidija}, Publisher = {Elsevier}, Timestamp = {2016.05.11} } @Article{Shapiro:2007, Title = {{M}athematica platforms for modeling in systems biology: {R}ecent developments in {M}ath{SBML} and {C}ellerator.}, Author = {Shapiro BE, Lu J, Hucka M, Mjolsness E.}, Year = {2007} } @Article{Taggart:2007, Title = {{U}ltrasonic characterization of whole cells and isolated nuclei}, Author = {Taggart, Linda R and Baddour, Ralph E and Giles, Anoja and Czarnota, Gregory J and Kolios, Michael C}, Journal = {Ultrasound in medicine \& biology}, Year = {2007}, Number = {3}, Pages = {389--401}, Volume = {33}, Owner = {lidija}, Publisher = {Elsevier}, Timestamp = {2016.05.07} } @Article{Tarcsa:2000, Title = {{C}a2+-free {C}almodulin and {C}almodulin {D}amaged byin {V}itro {A}ging {A}re {S}electively {D}egraded by 26 {S} {P}roteasomes without {U}biquitination}, Author = {Tarcsa, Edit and Szymanska, Grazyna and Lecker, Stewart and O'Connor, Clare M and Goldberg, Alfred L}, Journal = {Journal of Biological Chemistry}, Year = {2000}, Number = {27}, Pages = {20295--20301}, Volume = {275}, Owner = {lidija}, Publisher = {ASBMB}, Timestamp = {2016.07.20} } @Article{Taslimi:2016, Title = {{O}ptimized second-generation {CRY}2-{CIB} dimerizers and photoactivatable {C}re recombinase.}, Author = {Taslimi, Amir and Zoltowski, Brian and Miranda, Jose G. and Pathak, Gopal P. and Hughes, Robert M. and Tucker, Chandra L.}, Journal = {Nat Chem Biol}, Year = {2016}, Month = {Jun}, Number = {6}, Pages = {425--430}, Volume = {12}, Abstract = {Arabidopsis thaliana cryptochrome 2 (AtCRY2), a light-sensitive photosensory protein, was previously adapted for use in controlling protein-protein interactions through light-dependent binding to a partner protein, CIB1. While the existing CRY2-CIB dimerization system has been used extensively for optogenetic applications, some limitations exist. Here, we set out to optimize function of the CRY2-CIB system by identifying versions of CRY2-CIB that are smaller, show reduced dark interaction, and maintain longer or shorter signaling states in response to a pulse of light. We describe minimal functional CRY2 and CIB1 domains maintaining light-dependent interaction and new signaling mutations affecting AtCRY2 photocycle kinetics. The latter work implicates an α13-α14 turn motif within plant CRYs whose perturbation alters signaling-state lifetime. Using a long-lived L348F photocycle mutant, we engineered a second-generation photoactivatable Cre recombinase, PA-Cre2.0, that shows five-fold improved dynamic range, allowing robust recombination following exposure to a single, brief pulse of light.}, Doi = {10.1038/nchembio.2063}, Institution = {Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA.}, Language = {eng}, Medline-pst = {ppublish}, Owner = {lidija}, Pii = {nchembio.2063}, Pmid = {27065233}, Timestamp = {2016.09.04}, Url = {http://dx.doi.org/10.1038/nchembio.2063} } @Article{Vasquez:2014, Title = {{E}ffect of pulsed and continuous therapeutic ultrasound on healthy skeletal muscle in rats.}, Author = {Vásquez, Bélgica and Navarrete, Javiera and Farfán, Emilio and Cantín, Mario}, Journal = {Int J Clin Exp Pathol}, Year = {2014}, Number = {2}, Pages = {779--783}, Volume = {7}, Abstract = {Ultrasound therapy is used to treat injuries in joints, nerves and tendons. Part of the radiation generated is absorbed by nearby undamaged tissues, such as muscles. The aim was to evaluate histomorphological changes in the healthy gastrocnemius muscle in rats irradiated with continuous ultrasound (CUS) and pulsed ultrasound (PUS). Healthy adult rats were used, separated into two groups: CUS and PUS. Both were irradiated in the gastrocnemius muscle for 10 days: the CUS group in continuous mode (3 MHz, 1.0 W/cm(2), 1 min/session) and the PUS group in pulsed mode (3 MHz, 1.0 W/cm(2), 100 Hz, 50\% duty cycle, 1 min/session). The contralateral muscles were used as a control. Their histological characteristics were analyzed, and the area and perimeter of the muscle fibers were measured. The connective tissue showed no histological changes. The area of muscle fibers of the irradiated groups was significantly greater (CUS 1325.2 ± 182.1 μm(2), p=0.0278 and PUS 1019.4 ± 125.3 μm(2), p=0.0398) than the control, and the CUS area was greater than the PUS (p=0.0383). The perimeter of muscle fibers showed significant differences between the irradiated groups (CUS 148 ± 11.12 μm, p=0.0178 and PUS 129.3 ± 8.83 μm, p=0.0236) compared to the control, as well as differences between CUS and PUS (p=0.0319). The application of ultrasound on healthy muscle produces hypertrophy of the muscle fibers, greater when continuous mode is used. It is advisable to apply pulsed, focused ultrasound therapies with sound heads sufficient for the tissue or zone to be treated, thereby reducing the risk of altering the adjacent healthy tissue.}, Institution = {CIMA Research Group, Faculty of Dentistry, Doctoral Program in Morphological Science, Universidad de La Frontera Temuco, Chile ; Center of Research in Biomedical Sciences, Universidad Autónoma de Chile Temuco, Chile.}, Keywords = {Animals; Hypertrophy; Male; Muscle Fibers, Skeletal, pathology; Rats; Rats, Sprague-Dawley; Time Factors; Ultrasonic Therapy, adverse effects/methods}, Language = {eng}, Medline-pst = {epublish}, Owner = {lidija}, Pmid = {24551303}, Timestamp = {2016.09.30} } @Article{Wagner:2005, Title = {{T}oward the development of peptide nanofilaments and nanoropes as smart materials}, Author = {Wagner, Daniel E and Phillips, Charles L and Ali, Wasif M and Nybakken, Grant E and Crawford, Emily D and Schwab, Alexander D and Smith, Walter F and Fairman, Robert}, Journal = {Proceedings of the National Academy of Sciences of the United States of America}, Year = {2005}, Number = {36}, Pages = {12656--12661}, Volume = {102}, Owner = {lidija}, Publisher = {National Acad Sciences}, Timestamp = {2016.05.12} } @Article{Waldhaeusl:1979a, Title = {{I}nsulin production rate following glucose ingestion estimated by splanchnic {C}-peptide output in normal man.}, Author = {Waldh{\"{a}}usl, W. and Bratusch-Marrain, P. and Gasic, S. and Korn, A. and Nowotny, P.}, Journal = {Diabetologia}, Year = {1979}, Month = {Oct}, Number = {4}, Pages = {221--227}, Volume = {17}, Abstract = {Insulin production rate has been estimated in healthy male volunteers (n = 16), and evaluated with respect to splanchnic glucose exchange. Insulin production rate was calculated from splanchnic immunoreactive C-peptide output. C-peptide secretion was estimated by the hepatic venous catheter technique both in the basal state and for 2 h following ingestion of various glucose loads (0, 12.5, 25, 50, 75, and 100 g). The results demonstrate a basal insulin production rate of 0.017 +/- 0.002 U/min (mean +/- SEM) or 2.04 U/2 h. Values rose in a dose dependent manner from 2.6 +/- 1.1 U/2 h after ingestion of 12.5 g of glucose to 10.8 +/- 1.1 U/2 h following a glucose load of 100 g. Insulin retention by the liver was estimated at 0.012 +/- 0.001 U/min in the basal state, and ranged from 47-85\% (70 +/- 2\%) of production following an oral glucose load. It was also demonstrated 1) that the relative splanchnic glucose output was inversely related to the amount of ingested glucose, and reached a minimum when glucose in excess of 50 g was ingested; and 2) that hepatic glucose retention was directly proportional to insulin production rate (r = 0.83; p less than 0.001; n = 15). It is suggested that the adaptive capacity of the splanchnic bed to retain glucose depending on the amount of ingested glucose guarantees that splanchnic glucose output fluctuates in healthy man only within a narrow range.}, Keywords = {Adult; Blood Glucose, analysis; C-Peptide, blood; Glucose, metabolism; Humans; Insulin, blood/secretion; Male; Peptides, blood}, Language = {eng}, Medline-pst = {ppublish}, Owner = {lidija}, Pmid = {499682}, Timestamp = {2016.09.25} } @Article{Yang:2003, Title = {{D}ecay rates of human m{RNA}s: correlation with functional characteristics and sequence attributes.}, Author = {Yang, Edward and {van Nimwegen}, Erik and Zavolan, Mihaela and Rajewsky, Nikolaus and Schroeder, Mark and Magnasco, Marcelo and Darnell, Jr, James E}, Journal = {Genome Res}, Year = {2003}, Month = {Aug}, Number = {8}, Pages = {1863--1872}, Volume = {13}, Abstract = {Although mRNA decay rates are a key determinant of the steady-state concentration for any given mRNA species, relatively little is known, on a population level, about what factors influence turnover rates and how these rates are integrated into cellular decisions. We decided to measure mRNA decay rates in two human cell lines with high-density oligonucleotide arrays that enable the measurement of decay rates simultaneously for thousands of mRNA species. Using existing annotation and the Gene Ontology hierarchy of biological processes, we assign mRNAs to functional classes at various levels of resolution and compare the decay rate statistics between these classes. The results show statistically significant organizational principles in the variation of decay rates among functional classes. In particular, transcription factor mRNAs have increased average decay rates compared with other transcripts and are enriched in "fast-decaying" mRNAs with half-lives <2 h. In contrast, we find that mRNAs for biosynthetic proteins have decreased average decay rates and are deficient in fast-decaying mRNAs. Our analysis of data from a previously published study of Saccharomyces cerevisiae mRNA decay shows the same functional organization of decay rates, implying that it is a general organizational scheme for eukaryotes. Additionally, we investigated the dependence of decay rates on sequence composition, that is, the presence or absence of short mRNA motifs in various regions of the mRNA transcript. Our analysis recovers the positive correlation of mRNA decay with known AU-rich mRNA motifs, but we also uncover further short mRNA motifs that show statistically significant correlation with decay. However, we also note that none of these motifs are strong predictors of mRNA decay rate, indicating that the regulation of mRNA decay is more complex and may involve the cooperative binding of several RNA-binding proteins at different sites.}, Doi = {10.1101/gr.1272403}, Institution = {Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10021-6399, USA.}, Keywords = {Base Composition; Carcinoma, Hepatocellular, genetics/pathology; Cell Line; Fibroblasts, chemistry/cytology/metabolism; Genetic Variation; Half-Life; Humans; Liver Neoplasms, genetics/pathology; Oligonucleotide Array Sequence Analysis, methods/statistics /&/ numerical data; RNA, Messenger, chemistry/genetics/metabolism/physiology; RNA, Neoplasm, classification/genetics/metabolism/physiology; Tumor Cells, Cultured}, Language = {eng}, Medline-pst = {ppublish}, Owner = {lidija}, Pii = {13/8/1863}, Pmid = {12902380}, Timestamp = {2016.08.06}, Url = {http://dx.doi.org/10.1101/gr.1272403} } @Article{Yi:2013, Title = {{E}ngineering of {TEV} protease variants by yeast {ER} sequestration screening ({YESS}) of combinatorial libraries}, Author = {Yi, L. and Gebhard, M. C. and Li, Q. and Taft, J. M. and Georgiou, G. and Iverson, B. L.}, Journal = {Proceedings of the National Academy of Sciences}, Year = {2013}, Month = {Apr}, Number = {18}, Pages = {7229–7234}, Volume = {110}, Doi = {10.1073/pnas.1215994110}, ISSN = {1091-6490}, Owner = {lidija}, Publisher = {Proc Natl Acad Sci U S A}, Timestamp = {2016.07.25}, Url = {http://dx.doi.org/10.1073/pnas.1215994110} } @Article{Yu:2007, Title = {{A}rabidopsis cryptochrome 2 completes its posttranslational life cycle in the nucleus}, Author = {Yu, Xuhong and Klejnot, John and Zhao, Xiaoying and Shalitin, Dror and Maymon, Maskit and Yang, Hongyun and Lee, Janet and Liu, Xuanming and Lopez, Javier and Lin, Chentao}, Journal = {The Plant Cell}, Year = {2007}, Number = {10}, Pages = {3146--3156}, Volume = {19}, Owner = {lidija}, Publisher = {Am Soc Plant Biol}, Timestamp = {2016.07.20} } @Article{Zhu:2004, Title = {{C}alcium binding sequences in calmyrin regulates interaction with presenilin-2}, Author = {Zhu, Jingsong and Stabler, Stacy M and Ames, James B and Baskakov, Ilia and Monteiro, Mervyn J}, Journal = {Experimental cell research}, Year = {2004}, Number = {2}, Pages = {440--454}, Volume = {300}, Owner = {lidija}, Publisher = {Elsevier}, Timestamp = {2016.07.20} } @article{Evans2009, abstract = {Calmodulin (CaM) is an essential eukaryotic calcium receptor that regulates many kinases, including CaMKII. Calcium-depleted CaM does not bind to CaMKII under physiological conditions. However, binding of (Ca(2+))(4)-CaM to a basic amphipathic helix in CaMKII releases auto-inhibition of the kinase. The crystal structure of CaM bound to CaMKIIp, a peptide representing the CaM-binding domain (CaMBD) of CaMKII, shows an antiparallel interface: the C-domain of CaM primarily contacts the N-terminal half of the CaMBD. The two domains of calcium-saturated CaM are believed to play distinct roles in releasing auto-inhibition. To investigate the underlying mechanism of activation, calcium-dependent titrations of isolated domains of CaM binding to CaMKIIp were monitored using fluorescence anisotropy. The binding affinity of CaMKIIp for the domains of CaM increased upon saturation with calcium, with the C-domain having a 35-fold greater affinity than the N-domain. Because the interdomain linker of CaM regulates calcium-binding affinity and contribute to conformational change, the role of each CaM domain was explored further by investigating effects of CaMKIIp on site-knockout mutants affecting the calcium-binding sites of a single domain. Investigation of the thermodynamic linkage between saturation of individual calcium-binding sites and CaM-domain binding to CaMKIIp showed that calcium binding to Sites III and IV was sufficient to recapitulate the behavior of (Ca(2+))(4)-CaM. The magnitude of favorable interdomain cooperativity varied depending on which of the four calcium-binding sites were mutated, emphasizing differential regulatory roles for the domains of CaM, despite the high degree of homology among the four EF-hands of CaM.}, author = {Evans, T. Idil Apak and Shea, Madeline A.}, doi = {10.1002/prot.22317}, isbn = {1097-0134 (Electronic)}, issn = {08873585}, journal = {Proteins: Structure, Function and Bioinformatics}, number = {1}, pages = {47--61}, pmid = {19089983}, title = {{Energetics of calmodulin domain interactions with the calmodulin binding domain of CaMKII}}, volume = {76}, year = {2009} } @article{Miyawaki1997, abstract = {Important Ca2+ signals in the cytosol and organelles are often extremely localized and hard to measure. To overcome this problem we have constructed new fluorescent indicators for Ca2+ that are genetically encoded without cofactors and are targetable to specific intracellular locations. We have dubbed these fluorescent indicators 'cameleons'. They consist of tandem fusions of a blue- or cyan-emitting mutant of the green fluorescent protein (GFP)1,2, calmodulin3, 4, 5, the calmodulin-binding peptide M13 (ref. 6), and an enhanced green- or yellow-emitting GFP7, 8, 9. Binding of Ca2+ makes calmodulin wrap around the M13 domain, increasing the fluorescence resonance energy transfer (FRET) between the flanking GFPs2. Calmodulin mutations can tune the Ca2+ affinities to measure free Ca2+ concentrations in the range 10-8 to 10-2 M. We have visualized free Ca2+ dynamics in the cytosol, nucleus and endoplasmic reticulum of single HeLa cells transfected with complementary DNAs encoding chimaeras bearing appropriate localization signals. Ca2+ concentration in the endoplasmic reticulum of individual cells ranged from 60 to 400 M at rest, and 1 to 50 M after Ca2+ mobilization. FRET is also an indicator of the reversible intermolecular association of cyan-GFP-labelled calmodulin with yellow-GFP-labelled M13. Thus FRET between GFP mutants can monitor localized Ca2+ signals and protein heterodimerization in individual live cells.}, author = {Miyawaki, Atsushi and Llopis, Juan and Heim, Roger and McCaffery, J. Michael and Adams, Joseph A. and Ikura, Mitsuhiko and Tsien, Roger Y.}, doi = {10.1038/42264}, isbn = {0028-0836 (Print)}, issn = {0028-0836}, journal = {Nature}, number = {6645}, pages = {882--887}, pmid = {9278050}, title = {{Fluorescent indicators for Ca2+based on green fluorescent proteins and calmodulin}}, volume = {388}, year = {1997} } @article{Whitaker2010, abstract = {Small, fluorescent, calcium-sensing molecules have been enormously useful in mapping intracellular calcium signals in time and space, as chapters in this volume attest. Despite their widespread adoption and utility, they suffer some disadvantages. Genetically-encoded calcium sensors that can by expressed inside cells by transfection or transgenesis are desirable. The last ten years have been marked by a rapid evolution in the laboratory of genetically encoded calcium sensors two families both figuratively and literally, resulting in11distinct configurations of fluorescent proteins and their attendant calcium sensor modules. Here, I described the design logic and performance of this abundant collection of sensors and describe their use and performance in intro and in vivo. Genetically-encoded calcium sensors have proved valuable in the measurement of calcium concentration in cellular organelles, for the most part in single cells in vitro. Their success as quantitative calcium sensors in tissues in vitro and in vivo is qualified, but they have proved valuable in imaging the pattern of calcium signals within tissues in whole animals. Some branches of the calcium sensor evolutionary tree continue to evolve rapidly and the steady progress in optimising sensor parameters leads to the certain hope that these drawbacks will eventually be overcome by further genetic engineering. 1.}, author = {Whitaker, Michael}, doi = {10.1016/B978-0-12-374841-6.00006-2.Genetically-encoded}, isbn = {9780123748416}, issn = {0091-679X}, journal = {Methods in cell biology}, pages = {153--182}, pmid = {21035686}, title = {{Genetically-encoded probes for measurement of intracellular calcium}}, volume = {99}, year = {2010} } @article{Wilms2014, author = {Wilms, Christian D and Häusser, Michael}, doi = {10.1038/nmeth.2814}, issn = {1548-7105}, journal = {Nature methods}, month = {feb}, number = {2}, pages = {139--40}, pmid = {24481218}, title = {{Twitching towards the ideal calcium sensor}}, volume = {11}, year = {2014} } @article{Shapiro2014, author = {Shapiro, Mikhail G. and Goodwill, Patrick W. and Neogy, Arkosnato and Yin, Melissa and Foster, F. Stuart and Schaffer, David V. and Conolly, Steven M.}, doi = {10.1038/nnano.2014.32}, issn = {1748-3387}, journal = {Nature Nanotechnology}, month = {mar}, number = {4}, pages = {311--316}, publisher = {Nature Research}, title = {{Biogenic gas nanostructures as ultrasonic molecular reporters}}, url = {http://www.nature.com/doifinder/10.1038/nnano.2014.32}, volume = {9}, year = {2014} } @article{Bourne1982, abstract = {Gadolinium (Gd3+) is a trivalent ion of the lanthanide series which has a high charge density and a similar ionic radius to Ca2+. The effects of gadolinium ions on [3H]noradrenaline output and 45Ca fluxes during resting conditions and stimulation were investigated in cultured bovine chromaffin cells. Chromaffin cells isolated from bovine adrenal medullae were plated on collagen-coated dishes (106 cells/dish) in a medium containing 10{\%} fetal calf serum. Seven-day-old cells were used in all studies. Exposure of chromaffin cells to 0.05mM Gd3+ produced 80 ± 5{\%} and 81 ± 4{\%} inhibition of the secretory responses to 10-4M acetylcholine and 56 mM K+ respectively. Doubling of the extracellular concentration of Gd3+ produced an 87 ± 3{\%} and 100 ± 2{\%} inhibition of the acetylcholine-induced and K+-induced release of [3H]noradrenaline. Gd3+ (0.05 mM) also produced a parallel shift to the right in the dose-response relationship between extracellular Ca2+ concentrations and [3H]noradrenaline output during acetylcholine stimulation. This observation suggests a competitive antagonism between Ca2+ and Gd3+ in stimulus-secretion coupling. Gd3+ (0.05 mM) was an effective inhibitor (92.3 ± 0.7{\%}) of the uptake of 45Ca into chromaffin cells induced by a depolarizing concentration (56 mM) of K+. Furthermore, Gd3+ also inhibited the increase in both Ca2+ - Ca2+ exchange mechanism and [3H]noradrenaline output observed in chromaffin cells upon the reintroduction of Ca2+ into a Ca2+]-free incubation medium. The results, which were obtained using low concentrations of Gd3+, indicate that gadolinium is a powerful inhibitor of the Ca2+ movements which are required for triggering amine release from chromaffin cells by different secretagogues. Moreover, the results also suggest that Gd3+ might be a useful tool for release and electrophysiological studies in other Ca2+-dependent systems. © 1982.}, author = {Bourne, G. W. and Trifaró, J. M.}, doi = {10.1016/0306-4522(82)90019-7}, isbn = {0306-4522}, issn = {03064522}, journal = {Neuroscience}, number = {7}, pages = {1615--1622}, pmid = {6289176}, title = {{The gadolinium ion: A potent blocker of calcium channels and catecholamine release from cultured chromaffin cells}}, volume = {7}, year = {1982} } @article{Hayes1986, abstract = {Gas vesicles of cyanobacteria are formed by a protein called 'gas-vesicle protein' (GVP). The complete amino acid sequence has been determined of GVP from Anabaena flos-aquae. It is 70 residues long and has an Mr of 7388. This corresponds to the size of the repeating unit cell demonstrated by X-ray crystallography of intact gas vesicles. Details of the sequence are related to the secondary beta-sheet structure of the protein and its contrasting hydrophilic and hydrophobic surfaces. Extensive amino acid sequences have also been determined for GVPs from two other cyanobacteria, species of Calothrix and Microcystis; they are highly homologous with that of Anabaena GVP. Electrophoretic analysis indicates that GVPs of different cyanobacteria form a variety of stable oligomers.}, author = {Hayes, P K and Walsby, A E and Walker, J E}, doi = {10.1042/BJ2360031}, issn = {0264-6021}, journal = {The Biochemical journal}, month = {may}, number = {1}, pages = {31--6}, pmid = {3098234}, title = {{Complete amino acid sequence of cyanobacterial gas-vesicle protein indicates a 70-residue molecule that corresponds in size to the crystallographic unit cell}}, volume = {236}, year = {1986} } @article{Buchholz1993, abstract = {Previous studies have shown that gas vesicles isolated from the cyanobacterium Anabaena flos-aquae contain two types of protein, GvpA, a small hydrophobic protein that forms the main ribbed structure, and GvpC, a protein comprising five repeats of a 33-amino-acid-residue motif, which is located on the outer surface of the GvpA shell. GvpC was shown to increase the critical collapse pressure of the gas vesicles; it was thought to do this by forming a series of molecular ties that bind the ribs together. We now show that antibodies raised against GvpC label both the central cylinders and the conical end caps of native gas vesicles but fail to bind to gas vesicles that have been stripped of GvpC. The molar ratio of GvpA to GvpC has been calculated from amino acid analyses of gas vesicle hydrolysates by reference to the abundance of amino acids that occur predominantly or exclusively in one protein or the other; the molar ratio was found to be 25:1 in freshly isolated gas vesicles and 23:1 in gas vesicles saturated with GvpC. We have considered three ways in which the 33-residue repeats of GvpC might interact with the crystallographic unit cell of GvpA molecules in the ribs. The Anabaena GvpC will bind to and restore the strength of gas vesicles isolated from Aphanizomenon and Microcystis that lack their native GvpC.}, author = {Buchholz, B E and Hayes, P K and a E Walsby}, doi = {10.1099/00221287-139-10-2353}, isbn = {0022-1287 (Print)$\backslash$r0022-1287 (Linking)}, issn = {0022-1287}, journal = {Journal of general microbiology}, number = {10}, pages = {2353--63}, pmid = {8254305}, title = {{The distribution of the outer gas vesicle protein, GvpC, on the Anabaena gas vesicle, and its ratio to GvpA}}, volume = {139}, year = {1993} } @article{Blomley2001, abstract = {Contrast agents are widely used in imaging, but until recently they had little place in ultrasonography. This has changed with the introduction of microbubbles—small (typically 3 $\mu$m in diameter) gas filled bubbles that are usually injected intravenously. Injecting a gas into the circulation may seem potentially hazardous, but extensive clinical experience has shown that the tiny volume of air or gas given (under 200 $\mu$l) is not dangerous, and the safety of microbubbles compares well to that of conventional agents in radiography and magnetic resonance imaging.1 Although microbubbles were originally designed simply to improve conventional ultrasound scanning, recent discoveries have opened up powerful emerging applications. This article describes some of these applications in radiology and cardiology and discusses the potential of microbubbles for therapy.}, author = {Blomley, Martin J K and Cooke, Jennifer C and Unger, Evan C and Monaghan, Mark J and Cosgrove, David O}, doi = {10.1136/bmj.322.7296.1222}, isbn = {0959-8138 (Print)}, issn = {09598138}, journal = {Bmj}, number = {7296}, pages = {1222--1225}, pmid = {11358777}, title = {{Science, medicine, and the future: Microbubble contrast agents: a new era in ultrasound}}, volume = {322}, year = {2001} } @article{Ibsen2015, abstract = {A major challenge in neuroscience is to reliably activate individual neurons, particularly those in deeper brain regions. Current optogenetic approaches require invasive surgical procedures to deliver light of specific wavelengths to target cells to activate or silence them. Here, we demonstrate the use of low-pressure ultrasound as a non-invasive trigger to activate specific ultrasonically sensitized neurons in the nematode, Caenorhabditis elegans. We first show that wild-type animals are insensitive to low-pressure ultrasound and require gas-filled microbubbles to transduce the ultrasound wave. We find that neuron-specific misexpression of TRP-4, the pore-forming subunit of a mechanotransduction channel, sensitizes neurons to ultrasound stimulus, resulting in behavioural outputs. Furthermore, we use this approach to manipulate the function of sensory neurons and interneurons and identify a role for PVD sensory neurons in modifying locomotory behaviours. We suggest that this method can be broadly applied to manipulate cellular functions in vivo.}, author = {Ibsen, Stuart and Tong, Ada and Schutt, Carolyn and Esener, Sadik and Chalasani, Sreekanth H}, doi = {10.1038/ncomms9264}, isbn = {2041-1723}, issn = {2041-1723}, journal = {Nature Communications}, pages = {1--12}, pmid = {26372413}, publisher = {Nature Publishing Group}, title = {{Sonogenetics is a non-invasive approach to activating neurons in Caenorhabditis elegans}}, volume = {6}, year = {2015} } @article{Shekhawat2009, author = {Shekhawat, Sujan S and Porter, Jason R and Sriprasad, Akshay and Ghosh, Indraneel}, journal = {Jacs}, number = {42}, pages = {15284--15290}, title = {{An Autoinhibited Coiled-Coil Design Strategy for Split-Protein Protease Sensors}}, volume = {131}, year = {2009} } @article{Konermann2013, author = {Konermann, Silvana and Brigham, Mark D. and Trevino, Alexandro and Hsu, Patrick D. and Heidenreich, Matthias and {Le Cong}, Le and Platt, Randall J. and Scott, David A. and Church, George M. and Zhang, Feng}, doi = {10.1038/nature12466}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Konermann et al. - 2013 - Optical control of mammalian endogenous transcription and epigenetic states(2).pdf:pdf}, issn = {0028-0836}, journal = {Nature}, month = {jul}, publisher = {Nature Research}, title = {{Optical control of mammalian endogenous transcription and epigenetic states}}, url = {http://www.nature.com/doifinder/10.1038/nature12466}, year = {2013} } @article{Lin2012, author = {Lin, George Guan-hua and Scott, Jeffrey G}, doi = {10.1016/j.pestbp.2011.02.012.Investigations}, isbn = {8585348585}, issn = {15378276}, number = {2}, pages = {130--134}, pmid = {1000000221}, title = {{NIH Public Access}}, volume = {100}, year = {2012} } @article{He2015, author = {He, Qiye and Johnston, Jeff and Zeitlinger, Julia and City, Kansas and City, Kansas}, doi = {10.1038/nbt.3121.ChIP-nexus}, isbn = {0000000000000}, issn = {1527-5418}, number = {4}, pages = {395--401}, pmid = {24655651}, title = {{HHS Public Access}}, volume = {33}, year = {2015} } @article{Wend2014, abstract = {Light-dependent dimerization is the basis for recently developed noninvasive optogenetic tools. Here we present a novel tool combining optogenetics with the control of protein kinase activity to investigate signal transduction pathways. Mediated by Arabidopsis thaliana photoreceptor cryptochrome 2, we activated the protein kinase C-RAF by blue light-dependent dimerization, allowing for decoupling from upstream signaling events induced by surface receptors. The activation by light is fast, reversible, and not only time but also dose dependent as monitored by phosphorylation of ERK1/2. Additionally, light-activated C-RAF controls serum response factor-mediated gene expression. Light-induced heterodimerization of C-RAF with a kinase-dead mutant of B-RAF demonstrates the enhancing role of B-RAF as a scaffold for C-RAF activity, which leads to the paradoxical activation of C-RAF found in human cancers. This optogenetic tool enables reversible control of protein kinase activity in signal duration and strength. These properties can help to shed light onto downstream signaling processes of protein kinases in living cells. © 2013 American Chemical Society.}, author = {Wend, S. and Wagner, H.J. and Muller, K. and Zurbriggen, M.D. and Weber, W. and Radziwill, G.}, doi = {10.1021/sb400090s}, issn = {21615063}, journal = {ACS Synthetic Biology}, number = {5}, pages = {280--285}, title = {{Optogenetic control of protein kinase activity in mammalian cells}}, volume = {3}, year = {2014} } @article{Muller2014, abstract = {Optogenetic gene switches allow gene expression control at an unprecedented spatiotemporal resolution. Recently, light-responsive transgene expression systems that are activated by UV-B, blue, or red light have been developed. These systems perform well on their own, but their integration into genetic networks has been hampered by the overlapping absorbance spectra of the photoreceptors. We identified a lack of orthogonality between UV-B and blue light-controlled gene expression as the bottleneck and employed a model-based approach that identified the need for a blue light-responsive gene switch that is insensitive to low-intensity light. Based on this prediction, we developed a blue light-responsive and rapidly reversible expression system. Finally, we employed this expression system to demonstrate orthogonality between UV-B, blue, and red/far-red light-responsive gene switches in a single mammalian cell culture. We expect this approach to enable the spatiotemporal control of gene networks and to expand the applications of optogenetics in synthetic biology.}, author = {Müller, Konrad and Engesser, Raphael and Timmer, Jens and Zurbriggen, Matias D. and Weber, Wilfried}, doi = {10.1021/sb500305v}, isbn = {2161-5063 (Electronic)$\backslash$r2161-5063 (Linking)}, issn = {21615063}, journal = {ACS Synthetic Biology}, number = {11}, pages = {796--801}, pmid = {25343333}, title = {{Orthogonal optogenetic triple-gene control in mammalian cells}}, volume = {3}, year = {2014} } @article{Kennedy2010, abstract = {Dimerizers allowing inducible control of protein-protein interactions are powerful tools for manipulating biological processes. Here we describe genetically encoded light-inducible protein-interaction modules based on Arabidopsis thaliana cryptochrome 2 and CIB1 that require no exogenous ligands and dimerize on blue-light exposure with subsecond time resolution and subcellular spatial resolution. We demonstrate the utility of this system by inducing protein translocation, transcription and Cre recombinase-mediated DNA recombination using light.}, author = {Kennedy, Matthew J and Hughes, Robert M and Peteya, Leslie A and Schwartz, Joel W and Ehlers, Michael D and Tucker, Chandra L}, doi = {10.1038/nmeth.1524.Rapid}, isbn = {1548-7105 (Electronic)$\backslash$r1548-7091 (Linking)}, issn = {1548-7105}, journal = {Nature Methods}, number = {12}, pages = {973--975}, pmid = {21037589}, title = {{Rapid blue light induction of protein interaction in living cells}}, volume = {7}, year = {2010} } @article{Zhang2015, abstract = {Cells employ a plethora of signaling pathways to make their life-and-death decisions. Extensive genetic, biochemical, and physiological studies have led to the accumulation of knowledge about signaling components and their interactions within signaling networks. These conventional approaches, although useful, lack the ability to control the spatial and temporal aspects of signaling processes. The recently emerged optogenetic tools open exciting opportunities by enabling signaling regulation with superior temporal and spatial resolution, easy delivery, rapid reversibility, fewer off-target side effects, and the ability to dissect complex signaling networks. Here we review recent achievements in using light to control intracellular signaling pathways and discuss future prospects for the field, including integration of new genetic approaches into optogenetics.}, author = {Zhang, Kai and Cui, Bianxiao}, doi = {10.1016/j.tibtech.2014.11.007}, isbn = {1879-3096 (Electronic)$\backslash$r0167-7799 (Linking)}, issn = {18793096}, journal = {Trends in Biotechnology}, number = {2}, pages = {92--100}, pmid = {25529484}, publisher = {Elsevier Ltd}, title = {{Optogenetic control of intracellular signaling pathways}}, volume = {33}, year = {2015} } @article{Stricklandetal.2012, author = {Strickland et al.}, doi = {10.1038/nmeth.1904.TULIPs}, number = {4}, pages = {379--384}, title = {{Biology}}, volume = {9}, year = {2012} } @article{Guntas2015, abstract = {The discovery of light-inducible protein–protein interactions has allowed for the spatial and temporal control of a variety of bi- ological processes. To be effective, a photodimerizer should have several characteristics: it should show a large change in binding affinity upon light stimulation, it should not cross-react with other molecules in the cell, and it should be easily used in a variety of organisms to recruit proteins of interest to each other. To create a switch that meets these criteria we have embedded the bacterial SsrA peptide in the C-terminal helix of a naturally occurring photo- switch, the light-oxygen-voltage 2 (LOV2) domain from Avena sativa. In the dark the SsrA peptide is sterically blocked from binding its natural binding partner, SspB. When activated with blue light, the C-terminal helix of the LOV2 domain undocks from the protein, allowing the SsrA peptide to bind SspB. Without optimization, the switch exhibited a twofold change in binding affinity for SspB with light stimulation. Here, we describe the use of computational protein design, phage display, and high-throughput binding assays to create an improved light inducible dimer (iLID) that changes its affinity for SspB by over 50-fold with light stimulation. A crystal structure of iLID shows a critical interaction between the surface of the LOV2 domain and a phenylalanine engineered tomore tightly pin the SsrA peptide against the LOV2 domain in the dark. We demonstrate the functional utility of the switch through light- mediated subcellular localization in mammalian cell culture and reversible control of small GTPase signaling.}, author = {Guntas, Gurkan and Hallett, Ryan a. and Zimmerman, Seth P. and Williams, Tishan and Yumerefendi, Hayretin and Bear, James E. and Kuhlman, Brian}, doi = {10.1073/pnas.1417910112}, isbn = {1009056107}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {1}, pages = {112--117}, pmid = {25535392}, title = {{Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins}}, volume = {112}, year = {2015} } @article{Schmidt2015, abstract = {The ability to perturb living systems is essential to understand how cells sense, integrate, and exchange information, to comprehend how pathologic changes in these processes relate to disease, and to provide insights into therapeutic points of intervention. Several molecular technologies based on natural photoreceptor systems have been pioneered that allow distinct cellular signaling pathways to be modulated with light in a temporally and spatially precise manner. In this review, we describe and discuss the underlying design principles of natural photoreceptors that have emerged as fundamental for the rational design and implementation of synthetic light-controlled signaling systems. Furthermore, we examine the unique challenges that synthetic protein technologies face when applied to the study of neural dynamics at the cellular and network level.}, author = {Schmidt, Daniel and Cho, Yong Ku}, doi = {10.1016/j.tibtech.2014.10.007}, isbn = {0167-7799}, issn = {18793096}, journal = {Trends in Biotechnology}, number = {2}, pages = {80--91}, pmid = {25466878}, publisher = {Elsevier Ltd}, title = {{Natural photoreceptors and their application to synthetic biology}}, volume = {33}, year = {2015} } @article{Niopek2014, abstract = {The function of many eukaryotic proteins is regulated by highly dynamic changes in their nucleocytoplasmic distribution. The ability to precisely and reversibly control nuclear translocation would, therefore, allow dissecting and engineering cellular networks. Here we develop a genetically encoded, light-inducible nuclear localization signal (LINuS) based on the LOV2 domain of Avena sativa phototropin 1. LINuS is a small, versatile tag, customizable for different proteins and cell types. LINuS-mediated nuclear import is fast and reversible, and can be tuned at different levels, for instance, by introducing mutations that alter AsLOV2 domain photo-caging properties or by selecting nuclear localization signals (NLSs) of various strengths. We demonstrate the utility of LINuS in mammalian cells by controlling gene expression and entry into mitosis with blue light.}, author = {Niopek, D and Benzinger, D and Roensch, J and Draebing, T and Wehler, P and Eils, R and {Di Ventura}, B}, doi = {10.1038/ncomms5404}, isbn = {2041-1723 (Electronic)$\backslash$r2041-1723 (Linking)}, issn = {2041-1723}, journal = {Nat Commun}, pages = {4404}, pmid = {25019686}, publisher = {Nature Publishing Group}, title = {{Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells}}, volume = {5}, year = {2014} } @book{Zimmerman2016, abstract = {Cellular optogenetic switches, a novel class of biological tools, have improved our understanding of biological phenomena that were previously intractable. While the design and engineering of these proteins has historically varied, they are all based on borrowed elements from plant and bacterial photoreceptors. In general terms, each of the optogenetic switches designed to date exploits the endogenous light-induced change in photoreceptor conformation while repurposing its effect to target a different biological phenomenon. We focus on the well-characterized light???oxygen???voltage 2 (LOV2) domain from Avena sativa phototropin 1 as our cornerstone for design. While the function of the LOV2 domain in the context of the phototropin protein is not fully elucidated, its thorough biophysical characterization as an isolated domain has created a strong foundation for engineering of photoswitches. In this chapter, we examine the biophysical characteristics of the LOV2 domain that may be exploited to produce an optogenetic switch and summarize previous design efforts to provide guidelines for an effective design. Furthermore, we provide protocols for assays including fluorescence polarization, phage display, and microscopy that are optimized for validating, improving, and using newly designed photoswitches.}, author = {Zimmerman, S. P. and Kuhlman, B. and Yumerefendi, H.}, booktitle = {Methods in Enzymology}, doi = {10.1016/bs.mie.2016.05.058}, edition = {1}, isbn = {9780128053805}, issn = {15577988}, pages = {169--190}, publisher = {Elsevier Inc.}, title = {{Engineering and Application of LOV2-Based Photoswitches}}, volume = {580}, year = {2016} } @article{Speed2001, abstract = {Therapeutic ultrasound is one of the most common treatments used in the management of soft tissue lesions, which constitute the majority of rheumatic complaints. Although many laboratory-based research studies have demonstrated a number of physiological effects of ultrasound upon living tissue, there is remarkably little evidence for benefit in the treatment of soft tissue injuries. This may be related to several confounding factors, including technical variables, the complexity and variety of underlying pathologies in soft tissue lesions, methodological limitations of clinical studies, or true lack of effect. In this review the scientific basis for the use of therapeutic ultrasound in soft tissue lesions and the existing evidence relating to its clinical effect are detailed.}, author = {Speed, C A}, doi = {10.1093/RHEUMATOLOGY/40.12.1331}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Speed - 2001 - Therapeutic ultrasound in soft tissue lesions.pdf:pdf}, issn = {1462-0324}, journal = {Rheumatology (Oxford, England)}, month = {dec}, number = {12}, pages = {1331--6}, pmid = {11752501}, publisher = {Oxford University Press}, title = {{Therapeutic ultrasound in soft tissue lesions}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/11752501}, volume = {40}, year = {2001} } @article{Vasquez2014, abstract = {Ultrasound therapy is used to treat injuries in joints, nerves and tendons. Part of the radiation generated is absorbed by nearby undamaged tissues, such as muscles. The aim was to evaluate histomorphological changes in the healthy gastrocnemius muscle in rats irradiated with continuous ultrasound (CUS) and pulsed ultrasound (PUS). Healthy adult rats were used, separated into two groups: CUS and PUS. Both were irradiated in the gastrocnemius muscle for 10 days: the CUS group in continuous mode (3 MHz, 1.0 W/cm(2), 1 min/session) and the PUS group in pulsed mode (3 MHz, 1.0 W/cm(2), 100 Hz, 50{\%} duty cycle, 1 min/session). The contralateral muscles were used as a control. Their histological characteristics were analyzed, and the area and perimeter of the muscle fibers were measured. The connective tissue showed no histological changes. The area of muscle fibers of the irradiated groups was significantly greater (CUS 1325.2 ± 182.1 $\mu$m(2), p=0.0278 and PUS 1019.4 ± 125.3 $\mu$m(2), p=0.0398) than the control, and the CUS area was greater than the PUS (p=0.0383). The perimeter of muscle fibers showed significant differences between the irradiated groups (CUS 148 ± 11.12 $\mu$m, p=0.0178 and PUS 129.3 ± 8.83 $\mu$m, p=0.0236) compared to the control, as well as differences between CUS and PUS (p=0.0319). The application of ultrasound on healthy muscle produces hypertrophy of the muscle fibers, greater when continuous mode is used. It is advisable to apply pulsed, focused ultrasound therapies with sound heads sufficient for the tissue or zone to be treated, thereby reducing the risk of altering the adjacent healthy tissue.}, author = {Vásquez, Bélgica and Navarrete, Javiera and Farfán, Emilio and Cantín, Mario}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/V{\'{a}}squez et al. - 2014 - Effect of pulsed and continuous therapeutic ultrasound on healthy skeletal muscle in rats.pdf:pdf}, issn = {1936-2625}, journal = {International journal of clinical and experimental pathology}, keywords = {Therapeutic ultrasound,continuous ultrasound,health muscle,muscle tissue,pulsed ultrasound}, number = {2}, pages = {779--83}, pmid = {24551303}, publisher = {e-Century Publishing Corporation}, title = {{Effect of pulsed and continuous therapeutic ultrasound on healthy skeletal muscle in rats}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24551303 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3925927}, volume = {7}, year = {2014} } @article{Carrington1988, abstract = {Mature viral-encoded proteins of tobacco etch virus (TEV) arise by proteolytic processing of a large precursor. The proteinase responsible for most of these cleavages is a viral-encoded 49-kDa protein. All known or predicted cleavage sites in the TEV polyprotein are flanked by the conserved sequence motif Glu-Xaa-Xaa-Tyr-Xaa-Gln-Ser or Gly, with the scissile bond located between the Gln-Ser or Gly dipeptide. By using cell-free systems to manipulate and express cloned cDNA sequences, a 25-amino acid segment containing a putative proteolytic cleavage site of the TEV polyprotein has been introduced into the TEV capsid protein sequence. This recombinant protein is cleaved by the 49-kDa proteinase at the introduced cleavage site, thus demonstrating portability of a functional cleavage site. The role of the conserved amino acid sequence in determining substrate activity was tested by construction of engineered proteins that contained part or all of this motif. A protein that harbored an insertion of the conserved 7-amino acid segment was cleaved by the 49-kDa TEV proteinase. Cleavage of the synthetic precursor was shown to occur accurately between the expected Gln-Ser dipeptide by microsequence analysis. Proteins containing insertions that generated only the Gln-Ser, or only the serine moiety of the conserved sequence, were insensitive to the 49-kDa proteinase.}, author = {Carrington, J C and Dougherty, W G}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, month = {may}, number = {10}, pages = {3391--5}, pmid = {3285343}, publisher = {National Academy of Sciences}, title = {{A viral cleavage site cassette: identification of amino acid sequences required for tobacco etch virus polyprotein processing.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/3285343 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC280215}, volume = {85}, year = {1988} } @article{Phan2002, abstract = {Because of its stringent sequence specificity, the 3C-type protease from tobacco etch virus (TEV) is frequently used to remove affinity tags from recombinant proteins. It is unclear, however, exactly how TEV protease recognizes its substrates with such high selectivity. The crystal structures of two TEV protease mutants, inactive C151A and autolysis-resistant S219D, have now been solved at 2.2- and 1.8-A resolution as complexes with a substrate and product peptide, respectively. The enzyme does not appear to have been perturbed by the mutations in either structure, and the modes of binding of the product and substrate are virtually identical. Analysis of the protein-ligand interactions helps to delineate the structural determinants of substrate specificity and provides guidance for reengineering the enzyme to further improve its utility for biotechnological applications.}, author = {Phan, Jason and Zdanov, Alexander and Evdokimov, Artem G and Tropea, Joseph E and Peters, Howard K and Kapust, Rachel B and Li, Mi and Wlodawer, Alexander and Waugh, David S}, doi = {10.1074/jbc.M207224200}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Phan et al. - 2002 - Structural basis for the substrate specificity of tobacco etch virus protease.pdf:pdf}, issn = {0021-9258}, journal = {The Journal of biological chemistry}, month = {dec}, number = {52}, pages = {50564--72}, pmid = {12377789}, publisher = {American Society for Biochemistry and Molecular Biology}, title = {{Structural basis for the substrate specificity of tobacco etch virus protease.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12377789}, volume = {277}, year = {2002} } @article{Merzlyak2007, abstract = {Fluorescent proteins have become extremely popular tools for in vivo imaging and especially for the study of localization, motility and interaction of proteins in living cells. Here we report TagRFP, a monomeric red fluorescent protein, which is characterized by high brightness, complete chromophore maturation, prolonged fluorescence lifetime and high pH-stability. These properties make TagRFP an excellent tag for protein localization studies and fluorescence resonance energy transfer (FRET) applications.}, author = {Merzlyak, Ekaterina M and Goedhart, Joachim and Shcherbo, Dmitry and Bulina, Mariya E and Shcheglov, Aleksandr S and Fradkov, Arkady F and Gaintzeva, Anna and Lukyanov, Konstantin A and Lukyanov, Sergey and Gadella, Theodorus W J and Chudakov, Dmitriy M}, doi = {10.1038/nmeth1062}, issn = {1548-7091}, journal = {Nature methods}, month = {jul}, number = {7}, pages = {555--7}, pmid = {17572680}, title = {{Bright monomeric red fluorescent protein with an extended fluorescence lifetime.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17572680}, volume = {4}, year = {2007} } @unpublished{Farrar2000, abstract = {The coumermycin-GyrB system is a useful strategy for regulating protein homodimerization and activation both in cell extracts and in intact cell culture systems. Coumermycin-based dimerization strategies are currently being used to identify biological responses (such as changes in gene transcription) induced by the Raf and Jak/signal transducers and activators of transcription (STAT) signal transduction pathways. As the utility of dimerization-based strategies becomes evident, they are applied to an increasing number of signal transduction pathways. An important development in this process is the generation of heterodimeric reagents incorporating GyrB-binding groups. The relative ease by which novobiocin can be synthetically modified to incorporate novel chemical entities should permit facile development of such reagents. It is interesting to investigate how specific pathways interact by using chemically distinct dimerization methods to regulate the activity of each independently. Such approaches provide important insights into the overall regulation of cell signaling.}, author = {Farrar, Michael A. and Olson, Steven H. and Perlmutter, Roger M.}, booktitle = {Methods in Enzymology}, doi = {10.1016/S0076-6879(00)27293-5}, isbn = {9780121822286}, issn = {00766879}, pages = {421--IN5}, title = {{[31] Coumermycin-induced dimerization of GyrB-containing fusion proteins}}, volume = {327}, year = {2000} } @article{Banaszynski, abstract = {Rapamycin is an important immunosuppressant, a possible anticancer therapeutic, and a widely used research tool. Essential to its various functions is its ability to bind simultaneously to two different proteins, FKBP and mTOR. Despite its widespread use, a thorough analysis of the interactions between FKBP, rapamycin, and the rapamycin-binding domain of mTOR, FRB, is lacking. To probe the affinities involved in the formation of the FKBP‚rapamycin‚FRB complex, we used fluorescence polarization, surface plasmon resonance, and NMR spectroscopy. Analysis of the data shows that rapamycin binds to FRB with moderate affinity (K d) 26 (0.8 µM). The FKBP12‚rapamycin complex, however, binds to FRB 2000-fold more tightly (Kd) 12 (0.8 nM) than rapamycin alone. No interaction between FKBP and FRB was detected in the absence of rapamycin. These studies suggest that rapamycin's ability to bind to FRB, and by extension to mTOR, in the absence of FKBP is of little consequence under physiological conditions. Furthermore, protein-protein interactions at the FKBP12-FRB interface play a role in the stability of the ternary complex.}, author = {Banaszynski, Laura A and Liu, Corey W and Wandless, Thomas J}, doi = {10.1021/ja043277y}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Banaszynski, Liu, Wandless - Unknown - Characterization of the FKBP‚Rapamycin‚FRB Ternary Complex.pdf:pdf}, title = {{Characterization of the FKBP‚Rapamycin‚FRB Ternary Complex}}, journal = {J Am Chem Soc} } @article{Gibson2009, author = {Gibson, Daniel G and Young, Lei and Chuang, Ray-Yuan and Venter, J Craig and Hutchison, Clyde A and Smith, Hamilton O}, doi = {10.1038/nmeth.1318}, issn = {1548-7091}, journal = {Nature Methods}, month = {may}, number = {5}, pages = {343--345}, publisher = {Nature Publishing Group}, title = {{Enzymatic assembly of DNA molecules up to several hundred kilobases}}, url = {http://www.nature.com/doifinder/10.1038/nmeth.1318}, volume = {6}, year = {2009} } @article{Henrich2003, abstract = {In eukaryotes, many essential secreted proteins and peptide hormones are excised from larger precursors by members of a class of calcium-dependent endoproteinases, the prohormone-proprotein convertases (PCs). Furin, the best-characterized member of the mammalian PC family, has essential functions in embryogenesis and homeostasis but is also implicated in various pathologies such as tumor metastasis, neurodegeneration and various bacterial and viral diseases caused by such pathogens as anthrax and pathogenic Ebola virus strains. Furin cleaves protein precursors with narrow specificity following basic Arg-Xaa-Lys/Arg-Arg-like motifs. The 2.6 A crystal structure of the decanoyl-Arg-Val-Lys-Arg-chloromethylketone (dec-RVKR-cmk)-inhibited mouse furin ectodomain, the first PC structure, reveals an eight-stranded jelly-roll P domain associated with the catalytic domain. Contoured surface loops shape the active site by cleft, thus explaining furin's stringent requirement for arginine at P1 and P4, and lysine at P2 sites by highly charge-complementary pockets. The structure also explains furin's preference for basic residues at P3, P5 and P6 sites. This structure will aid in the rational design of antiviral and antibacterial drugs.}, author = {Henrich, Stefan and Cameron, Angus and Bourenkov, Gleb P and Kiefersauer, Reiner and Huber, Robert and Lindberg, Iris and Bode, Wolfram and Than, Manuel E}, doi = {10.1038/nsb941}, issn = {1072-8368}, journal = {Nature structural biology}, month = {jul}, number = {7}, pages = {520--6}, pmid = {12794637}, title = {{The crystal structure of the proprotein processing proteinase furin explains its stringent specificity.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12794637}, volume = {10}, year = {2003} } @article{Cesaratto2015, abstract = {Tobacco etch virus protease (TEVp) is a unique endopeptidase with stringent substrate specificity. TEVp has been widely used as a purified protein for in vitro applications, but also as a biological tool directly expressing it in living cells. To adapt the protease to diverse applications, several TEVp mutants with different stability and enzymatic properties have been reported. Herein we describe the development of a novel engineered TEVp mutant designed to be active in the secretory pathway. While wild type TEVp targeted to the secretory pathway of mammalian cells is synthetized as an N-glycosylated and catalytically inactive enzyme, a TEVp mutant with selected mutations at two verified N-glycosylation sites and at an exposed cysteine was highly efficient. This mutant was very active in the endoplasmic reticulum (ER) of living cells and can be used as a biotechnological tool to cleave proteins within the secretory pathway. As an immediate practical application we report the expression of a complete functional monoclonal antibody expressed from a single polypeptide, which was cleaved by our TEVp mutant into the two antibody chains and secreted as an assembled and functional molecule. In addition, we show active TEVp mutants lacking auto-cleavage activity.}, author = {Cesaratto, Francesca and L{\'{o}}pez-Requena, Alejandro and Burrone, Oscar R and Petris, Gianluca}, doi = {10.1016/j.jbiotec.2015.08.026}, issn = {1873-4863}, journal = {Journal of biotechnology}, keywords = {ER,ERAD,Glycosylation,Sec-TEV,Secretory pathway,TEV protease}, month = {oct}, pages = {159--66}, pmid = {26327323}, title = {{Engineered tobacco etch virus (TEV) protease active in the secretory pathway of mammalian cells.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26327323}, volume = {212}, year = {2015} } @article{Letourneur1994, abstract = {Dilysine motifs in cytoplasmic domains of transmembrane proteins are signals for their continuous retrieval from the Golgi back to the endoplasmic reticulum (ER). We describe a system to assess retrieval to the ER in yeast cells making use of a dilysine-tagged Ste2 protein. Whereas retrieval was unaffected in most sec mutants tested (sec7, sec12, sec13, sec16, sec17, sec18, sec19, sec22, and sec23), a defect in retrieval was observed in previously characterized coatomer mutants (sec21-1, sec27-1), as well as in newly isolated retrieval mutants (sec21-2, ret1-1). RET1 was cloned by complementation and found to encode the $\alpha$ subunit of coatomer. While temperature-sensitive for growth, the newly isolated coatomer mutants exhibited a very modest defect in secretion at the nonpermissive temperature. Coatomer from $\beta$'-COP (sec27-1) and $\alpha$-COP (ret1-1) mutants, but not from $\gamma$-COP (sec21) mutants, had lost the ability to bind dilysine motifs in vitro. Together, these results suggest that coatomer plays an essential role in retrograde Golgi-to-ER transport and retrieval of dilysine-tagged proteins back to the ER.}, author = {Letourneur, François and Gaynor, Erin C. and Hennecke, Silke and Démollière, Corinne and Duden, Rainer and Emr, Scott D. and Riezman, Howard and Cosson, Pierre}, doi = {10.1016/0092-8674(94)90011-6}, issn = {00928674}, journal = {Cell}, number = {7}, pages = {1199--1207}, publisher = {Cell Press}, title = {{Coatomer is essential for retrieval of dilysine-tagged proteins to the endoplasmic reticulum}}, volume = {79}, year = {1994} } @article{Munro1987, abstract = {Proteins that permanently reside in the lumen of the endoplasmic reticulum (ER) must somehow be distinguished from newly synthesized secretory proteins, which pass through this compartment on their way out of the cell. Three luminal ER proteins whose sequence is known, grp78 ("BiP"), grp94, and protein disulphide isomerase, share the carboxy-terminal sequence Lys-Asp-Glu-Leu (KDEL). We show that deletion (or extension) of the carboxyl terminus of grp78 results in secretion of this protein when it is expressed in COS cells. Conversely, a derivative of chicken lysozyme containing the last six amino acids of grp78 fails to be secreted and instead accumulates in the ER. We propose that the KDEL sequence marks proteins that are to be retained in the ER and discuss possible retention mechanisms.}, author = {Munro, S and Pelham, H R}, issn = {0092-8674}, journal = {Cell}, month = {mar}, number = {5}, pages = {899--907}, pmid = {3545499}, title = {{A C-terminal signal prevents secretion of luminal ER proteins}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/3545499}, volume = {48}, year = {1987} } @article{Jackson1990, abstract = {Several families of transmembrane endoplasmic reticulum (ER) proteins contain retention motifs in their cytoplasmically exposed tails. Mutational analyses demonstrated that two lysines positioned three and four or five residues from the C-terminus represent the retention motif. The introduction of a lysine preceding the lysine that occurs three residues from the terminus of Lyt2 renders this cell surface protein a resident of the ER. Likewise, the appropriate positioning of two lysine residues in a poly-serine sequence confines marker proteins to the ER. Arginines or histidines cannot replace lysines, suggesting that simple charge interactions are not sufficient to explain the retention. The identified consensus motif may serve as a retrieval signal that brings proteins back from a sorting compartment adjacent to the ER.}, author = {Jackson, M R and Nilsson, T and Peterson, P A}, issn = {0261-4189}, journal = {The EMBO journal}, month = {oct}, number = {10}, pages = {3153--62}, pmid = {2120038}, publisher = {European Molecular Biology Organization}, title = {{Identification of a consensus motif for retention of transmembrane proteins in the endoplasmic reticulum.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2120038 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC552044}, volume = {9}, year = {1990} } @article{Chen2013, abstract = {Optical control of protein interactions has emerged as a powerful experimental paradigm for manipulating and studying various cellular processes. Tools are now available for controlling a number of cellular functions, but some fundamental processes, such as protein secretion, have been difficult to engineer using current optical tools. Here we use UVR8, a plant photoreceptor protein that forms photolabile homodimers, to engineer the first light-triggered protein secretion system. UVR8 fusion proteins were conditionally sequestered in the endoplasmic reticulum, and a brief pulse of light triggered robust forward trafficking through the secretory pathway to the plasma membrane. UVR8 was not responsive to excitation light used to image cyan, green, or red fluorescent protein variants, allowing multicolor visualization of cellular markers and secreted protein cargo as it traverses the cellular secretory pathway. We implemented this novel tool in neurons to demonstrate restricted, local trafficking of secretory cargo near dendritic branch points.}, author = {Chen, Daniel and Gibson, Emily S and Kennedy, Matthew J}, doi = {10.1083/jcb.201210119}, issn = {1540-8140}, journal = {The Journal of cell biology}, month = {may}, number = {4}, pages = {631--40}, pmid = {23671313}, title = {{A light-triggered protein secretion system}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23671313 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3653365}, volume = {201}, year = {2013} } @article{Rivera2000, abstract = {A system for direct pharmacologic control of protein secretion was developed to allow rapid and pulsatile delivery of therapeutic proteins. A protein was engineered so that it accumulated as aggregates in the endoplasmic reticulum. Secretion was then stimulated by a synthetic small-molecule drug that induces protein disaggregation. Rapid and transient secretion of growth hormone and insulin was achieved in vitro and in vivo. A regulated pulse of insulin secretion resulted in a transient correction of serum glucose concentrations in a mouse model of hyperglycemia. This approach may make gene therapy a viable method for delivery of polypeptides that require rapid and regulated delivery.}, author = {Rivera, V M and Wang, X and Wardwell, S and Courage, N L and Volchuk, A and Keenan, T and Holt, D A and Gilman, M and Orci, L and Cerasoli, F and Rothman, J E and Clackson, T}, issn = {0036-8075}, journal = {Science (New York, N.Y.)}, month = {feb}, number = {5454}, pages = {826--30}, pmid = {10657290}, title = {{Regulation of protein secretion through controlled aggregation in the endoplasmic reticulum}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10657290}, volume = {287}, year = {2000} } @article{Fernandez-Rodriguez2016, abstract = {Genetic engineering projects often require control over when a protein is degraded. To this end, we use a fusion between a degron and an inactivating peptide that can be added to the N-terminus of a protein. When the corresponding protease is expressed, it cleaves the peptide and the protein is degraded. Three protease:cleavage site pairs from Potyvirus are shown to be orthogonal and active in exposing degrons, releasing inhibitory domains and cleaving polyproteins. This toolbox is applied to the design of genetic circuits as a means to control regulator activity and degradation. First, we demonstrate that a gate can be constructed by constitutively expressing an inactivated repressor and having an input promoter drive the expression of the protease. It is also shown that the proteolytic release of an inhibitory domain can improve the dynamic range of a transcriptional gate (200-fold repression). Next, we design polyproteins containing multiple repressors and show that their cleavage can be used to control multiple outputs. Finally, we demonstrate that the dynamic range of an output can be improved (8-fold to 190-fold) with the addition of a protease-cleaved degron. Thus, controllable proteolysis offers a powerful tool for modulating and expanding the function of synthetic gene circuits.}, author = {Fernandez-Rodriguez, Jesus and Voigt, Christopher A}, doi = {10.1093/nar/gkw537}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Fernandez-Rodriguez, Voigt - 2016 - Post-translational control of genetic circuits using Potyvirus proteases.pdf:pdf}, issn = {1362-4962}, journal = {Nucleic acids research}, month = {jul}, number = {13}, pages = {6493--502}, pmid = {27298256}, publisher = {Oxford University Press}, title = {{Post-translational control of genetic circuits using Potyvirus proteases}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/27298256}, volume = {44}, year = {2016} } @article{Seo2016, author = {Seo, Jang-Kyun and Choi, Hong-Soo and Kim, Kook-Hyung and Lee, M. W. and Yang, Y. and Schob, H. and Kunc, C. and Meins, F. and Vaghchhipawala, Z. and Rojas, C. M. and Senthil-Kumar, M. and Mysore, K. S. and Annamalai, P. and Rao, A. L. and Zhang, C. and Ghabrial, S. A. and Zhang, C. and Bradshaw, J. D. and Whitham, S. A. and Hill, J. H. and Seo, J. K. and Lee, H. G. and Kim, K. H. and Gleba, Y. and Klimyuk, V. and Marillonnet, S. and Matsuo, K. and Bedoya, L. and Martinez, F. and Rubio, L. and Daros, J. A. and Kelloniemi, J. and Makinen, K. and Valkonen, J. P. and Seo, J. K. and Kang, S. H. and Seo, B. Y. and Jung, J. K. and Kim, K. H. and Walter, M. and Chen, Y. and Mills, J. D. and Periasamy, A. and Fields, S. and Song, O. K. and Tsuda, K. and Kerppola, T. K. and Seo, J. K. and Kwon, S. J. and Rao, A. L. and Ho, Y. and Mann, M. and Hendrickson, R. C. and Pandey, A. and Vasilescu, J. and Figeys, D. and Maia, I. G. and Haenni, A. L. and Bernardi, F. and Roudet-Tavert, G. and Blanc, S. and Ruiz-Ferrer, V. and Sirover, M. A. and Glaser, P. E. and Han, X. L. and Gross, R. W. and Ishitani, R. and Chuang, D. M. and Berry, M. D. and Boulton, A. A. and Sirover, M. A. and Yang, S. H. and Liu, M. L. and Tien, C. F. and Chou, S. J. and Chang, R. Y. and Prasanth, K. R. and Kishimoto, N. and Sakamoto, W. and Kindle, K. L. and Stern, D. B. and Wroblewski, T. and Tomczak, A. and Michelmore, R. and King, J. L. and Finer, J. J. and McHale, L. K. and Schmutz, J. and Kim, M. Y. and Severin, A. J. and Kim, K. H. and Jones, S. I. and Vodkin, L. O. and Vidal, R. O. and do Nascimento, L. C. and Mondego, J. M. and Pereira, G. A. and Carazzolle, M. F. and Seo, J. K. and Kwon, S. J. and Cho, W. K. and Choi, H. S. and Kim, K. H. and Pogue, G. P. and Lindbo, J. A. and Garger, S. J. and Fitzmaurice, W. P. and Urcuqui-Inchima, S. and Haenni, A. L. and Bernardi, F. and Arazi, T. and Dolja, V. V. and McBride, H. J. and Carrington, J. C. and Beauchemin, C. and Bougie, V. and Laliberte, J. F. and Yu, J. H. and Park, M.}, doi = {10.1038/srep22436}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Seo et al. - 2016 - Engineering of soybean mosaic virus as a versatile tool for studying protein–protein interactions in soybean(2).pdf:pdf}, issn = {2045-2322}, journal = {Scientific Reports}, month = {feb}, pages = {22436}, publisher = {Nature Publishing Group}, title = {{Engineering of soybean mosaic virus as a versatile tool for studying protein–protein interactions in soybean}}, url = {http://www.nature.com/articles/srep22436}, volume = {6}, year = {2016} } @article{Garcia1991, abstract = {Plasmids encoding chimeric NIa-type proteases made of sequences from the polyviruses plum pox virus (PPV) and tobacco etch virus (TEV) have been constructed. Their proteolytic activity on the large nuclear inclusion protein (NIa)-capsid protein (CP) junction of each virus was assayed in Escherichia coli cells. The amino half of the protease seemed to be involved neither in the enzymatic catalysis nor in substrate recognition. In spite of the large homology among the PPV and TEV NIa-type proteases, the exchange of fragments from the carboxyl halves of the molecules usually caused a drastic decrease in the enzymatic activity. Inactive chimeric proteases did not interfere with cleavage by PPV wild type protease expressed from a second plasmid. The results suggest that the recognition and catalytic sites of the NIa proteases are closely interlinked and, although residues relevant for the correct interaction with the substrate could be present in other parts of the protein, a main determinant for substrate specificity should lie in a region situated, approximately, between positions 30 and 90 from the carboxyl end. This region includes the conserved His at position 360 of PPV or 355 of TEV, which has been postulated to interact with the Gin at position −1 of the cleavage sites.}, author = {Garcia, Juan Antonio and Lain, Sonia}, doi = {10.1016/0014-5793(91)80360-F}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Garcia, Lain - 1991 - Proteolytic activity of plum pox virus—tobacco etch virus chimeric NIa proteases(2).pdf:pdf}, issn = {00145793}, journal = {FEBS Letters}, number = {1}, pages = {67--72}, publisher = {No longer published by Elsevier}, title = {{Proteolytic activity of plum pox virus—tobacco etch virus chimeric NIa proteases}}, volume = {281}, year = {1991} } @article{Zheng2008, abstract = {Site-specific proteases are the most popular kind of enzymes for removing the fusion tags from fused target proteins. Nuclear inclusion protein a (NIa) proteases obtained from the family Potyviridae have become promising due to their high activities and stringencies of sequences recognition. NIa proteases from tobacco etch virus (TEV) and tomato vein mottling virus (TVMV) have been shown to process recombinant proteins successfully in vitro. In this report, recombinant PPV (plum pox virus) NIa protease was employed to process fusion proteins with artificial cleavage site in vitro. Characteristics such as catalytic ability and affecting factors (salt, temperature, protease inhibitors, detergents, and denaturing reagents) were investigated. Recombinant PPV NIa protease expressed and purified from Escherichia coli demonstrated efficient and specific processing of recombinant GFP and SARS-CoV nucleocapsid protein, with site F (N V V V H Q black triangle down A) for PPV NIa protease artificially inserted between the fusion tags and the target proteins. Its catalytic capability is similar to those of TVMV and TEV NIa protease. Recombinant PPV NIa protease reached its maximal proteolytic activity at approximately 30 degrees C. Salt concentration and only one of the tested protease inhibitors had minor influences on the proteolytic activity of PPV NIa protease. Recombinant PPV NIa protease was resistant to self-lysis for at least five days.}, author = {Zheng, Nuoyan and Pérez, José de Jesús and Zhang, Zhonghui and Domínguez, Elvira and Garcia, Juan Antonio and Xie, Qi}, doi = {10.1016/j.pep.2007.10.008}, issn = {1046-5928}, journal = {Protein expression and purification}, month = {feb}, number = {2}, pages = {153--62}, pmid = {18024078}, title = {{Specific and efficient cleavage of fusion proteins by recombinant plum pox virus NIa protease}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18024078}, volume = {57}, year = {2008} } @article{Nunn2005, abstract = {Tobacco etch virus (TEV) protease is a cysteine protease exhibiting stringent sequence specificity. The enzyme is widely used in biotechnology for the removal of the affinity tags from recombinant fusion proteins. Crystal structures of two TEV protease mutants as complexes with a substrate and a product peptide provided the first insight into the mechanism of substrate specificity of this enzyme. We now report a 2.7A crystal structure of a full-length inactive C151A mutant protein crystallised in the absence of peptide. The structure reveals the C terminus of the protease bound to the active site. In addition, we determined dissociation constants of TEV protease substrate and product peptides using isothermal titration calorimetry for various forms of this enzyme. Data suggest that TEV protease could be inhibited by the peptide product of autolysis. Separate modes of recognition for native substrates and the site of TEV protease self-cleavage are proposed.}, author = {Nunn, Christine M and Jeeves, Mark and Cliff, Matthew J and Urquhart, Gillian T and George, Roger R and Chao, Luke H and Tscuchia, Yugo and Djordjevic, Snezana}, doi = {10.1016/j.jmb.2005.04.013}, issn = {0022-2836}, journal = {Journal of molecular biology}, month = {jul}, number = {1}, pages = {145--55}, pmid = {15919091}, title = {{Crystal structure of tobacco etch virus protease shows the protein C terminus bound within the active site}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15919091}, volume = {350}, year = {2005} } @article{Yoon2000, author = {Yoon, Hyun Yee and Hwang, Duk Chul and Choi, Kwan Yong and Song, Byeong Doo}, doi = {10.1007/s10059-000-0213-3}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Yoon et al. - 2000 - Proteolytic Processing of Oligopeptides Containing the Target Sequences by the Recombinant Tobacco Vein Mottling Vi.pdf:pdf}, issn = {1016-8478}, journal = {Molecules and Cells}, month = {apr}, number = {2}, pages = {213--219}, publisher = {Springer-Verlag}, title = {{Proteolytic Processing of Oligopeptides Containing the Target Sequences by the Recombinant Tobacco Vein Mottling Virus NIa Proteinase}}, url = {http://link.springer.com/10.1007/s10059-000-0213-3}, volume = {10}, year = {2000} } @article{Yi2013, abstract = {Myriad new applications of proteases would be enabled by an ability to fine-tune substrate specificity and activity. Herein we present a general strategy for engineering protease selectivity and activity by capitalizing on sequestration of the protease to be engineered within the yeast endoplasmic reticulum (ER). A substrate fusion protein composed of yeast adhesion receptor subunit Aga2, selection and counterselection substrate sequences, multiple intervening epitope tag sequences, and a C-terminal ER retention sequence is coexpressed with a protease library. Cleavage of the substrate fusion protein by the protease eliminates the ER retention sequence, facilitating transport to the yeast surface. Yeast cells that display Aga2 fusions in which only the selection substrate is cleaved are isolated by multicolor FACS with fluorescently labeled antiepitope tag antibodies. Using this system, the Tobacco Etch Virus protease (TEV-P), which strongly prefers Gln at P1 of its canonical ENLYFQ↓S substrate, was engineered to recognize selectively Glu or His at P1. Kinetic analysis indicated an overall 5,000-fold and 1,100-fold change in selectivity, respectively, for the Glu- and His-specific TEV variants, both of which retained high catalytic turnover. Human granzyme K and the hepatitis C virus protease were also shown to be amenable to this unique approach. Further, by adjusting the signaling strategy to identify phosphorylated as opposed to cleaved sequences, this unique system was shown to be compatible with the human Abelson tyrosine kinase.}, author = {Yi, Li and Gebhard, Mark C and Li, Qing and Taft, Joseph M and Georgiou, George and Iverson, Brent L}, doi = {10.1073/pnas.1215994110}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, month = {apr}, number = {18}, pages = {7229--34}, pmid = {23589865}, title = {{Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23589865 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3645551}, volume = {110}, year = {2013} } @article{Parks1994, abstract = {An improved method for the production, cleavage, and purification of fusion proteins and peptides is described. The unique aspect of this method is dependent on the use of a proteinase from tobacco etch virus (TEV). The proteinase used is a recombinant TEV proteinase produced with a polyhistidine tract positioned at the amino terminus. The proteinase recognizes a specific, extended cleavage site sequence. The peptide or protein of interest is purified as a fusion protein with a TEV proteinase cleavage site sequence located between it and an affinity carrier portion of the fusion. Incubation with the recombinant TEV proteinase mediates release of the peptide or protein of interest. Use of the recombinant TEV proteinase to cleave fusion proteins is an improvement over use of other proteinases for several reasons, including its high degree of specificity, its insensitivity to many proteinase inhibitors generally used in protein purification, and the ready separation of both the affinity tag and the proteinase from the cleaved product of interest.}, author = {Parks, T D and Leuther, K K and Howard, E D and Johnston, S A and Dougherty, W G}, doi = {10.1006/abio.1994.1060}, issn = {0003-2697}, journal = {Analytical biochemistry}, month = {feb}, number = {2}, pages = {413--7}, pmid = {8179197}, title = {{Release of proteins and peptides from fusion proteins using a recombinant plant virus proteinase.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/8179197}, volume = {216}, year = {1994} } @article{Cesaratto2015, abstract = {Tobacco etch virus protease (TEVp) is a unique endopeptidase with stringent substrate specificity. TEVp has been widely used as a purified protein for in vitro applications, but also as a biological tool directly expressing it in living cells. To adapt the protease to diverse applications, several TEVp mutants with different stability and enzymatic properties have been reported. Herein we describe the development of a novel engineered TEVp mutant designed to be active in the secretory pathway. While wild type TEVp targeted to the secretory pathway of mammalian cells is synthetized as an N-glycosylated and catalytically inactive enzyme, a TEVp mutant with selected mutations at two verified N-glycosylation sites and at an exposed cysteine was highly efficient. This mutant was very active in the endoplasmic reticulum (ER) of living cells and can be used as a biotechnological tool to cleave proteins within the secretory pathway. As an immediate practical application we report the expression of a complete functional monoclonal antibody expressed from a single polypeptide, which was cleaved by our TEVp mutant into the two antibody chains and secreted as an assembled and functional molecule. In addition, we show active TEVp mutants lacking auto-cleavage activity.}, author = {Cesaratto, Francesca and L{\'{o}}pez-Requena, Alejandro and Burrone, Oscar R and Petris, Gianluca}, doi = {10.1016/j.jbiotec.2015.08.026}, issn = {1873-4863}, journal = {Journal of biotechnology}, keywords = {ER,ERAD,Glycosylation,Sec-TEV,Secretory pathway,TEV protease}, month = {oct}, pages = {159--66}, pmid = {26327323}, title = {{Engineered tobacco etch virus (TEV) protease active in the secretory pathway of mammalian cells.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26327323}, volume = {212}, year = {2015} } @article{Berger1988, author = {Berger, Joel and Hauber, Joachim and Hauber, Regina and Geiger, Reinhard and Cullen, Bryan R.}, doi = {10.1016/0378-1119(88)90219-3}, issn = {03781119}, journal = {Gene}, month = {jun}, number = {1}, pages = {1--10}, title = {{Secreted placental alkaline phosphatase: a powerful new quantitative indicator of gene expression in eukaryotic cells}}, volume = {66}, year = {1988} } @article{Merzlyak2007, author = {Merzlyak, Ekaterina M and Goedhart, Joachim and Shcherbo, Dmitry and Bulina, Mariya E and Shcheglov, Aleksandr S and Fradkov, Arkady F and Gaintzeva, Anna and Lukyanov, Konstantin A and Lukyanov, Sergey and Gadella, Theodorus W J and Chudakov, Dmitriy M}, doi = {10.1038/nmeth1062}, issn = {1548-7091}, journal = {Nature Methods}, month = {jul}, number = {7}, pages = {555--557}, title = {{Bright monomeric red fluorescent protein with an extended fluorescence lifetime}}, volume = {4}, year = {2007} } @article{Kanno2007, author = {Kanno, Akira and Yamanaka, Yuko and Hirano, Hisashi and Umezawa, Yoshio and Ozawa, Takeaki}, doi = {10.1002/anie.200700538}, issn = {1433-7851}, journal = {Angewandte Chemie (International ed. in English)}, month = {jan}, number = {40}, pages = {7595--7599}, pmid = {17722214}, title = {{Cyclic luciferase for real-time sensing of caspase-3 activities in living mammals.}}, volume = {46}, year = {2007} } @article{Fan2008, abstract = {Genetically encoded biosensors have proven valuable for real-time monitoring of intracellular phenomena, particularly FRET-based sensors incorporating variants of green fluorescent protein. To increase detection sensitivity and response dynamics, we genetically engineered firefly luciferase to detect specific intermolecular interactions through modulation of its luminescence activity. This concept has been applied in covalent, noncovalent, and allosteric design configurations. The covalent design gives sensitive detection of protease activity through a cleavage-dependent increase in luminescence. The noncovalent and allosteric designs allow reversible detection of the small molecules rapamycin and cAMP, respectively. These sensors allow detection of molecular processes within living cells following addition of the luciferin substrate to the growth medium. For example, the cAMP sensor allows monitoring of intracellular signal transduction associated with G-protein coupled receptor function. These and other luminescent biosensors will be useful for the sensitive detection of cellular physiology in research and drug discovery.}, author = {Fan, Frank and Binkowski, Brock F and Butler, Braeden L and Stecha, Peter F and Lewis, Martin K and Wood, Keith V}, doi = {10.1021/cb8000414}, isbn = {1554-8929}, issn = {15548929}, journal = {ACS Chemical Biology}, number = {6}, pages = {346--351}, pmid = {18570354}, title = {{Novel genetically encoded biosensors using firefly luciferase}}, volume = {3}, year = {2008} } @article{Conti, abstract = {Background: Firefly luciferase is a 62 kDa protein that catalyzes the production of light. In the presence of MgATP and molecular oxygen, the enzyme oxidizes its substrate, firefly luciferin, emitting yellow-green light. The reaction proceeds through activation of the substrate to form an adenylate intermediate. Firefly luciferase shows extensive sequence homology with a number of enzymes that utilize ATP in adenylation reactions. Results: We have determined the crystal structure of firefly luciferase at 2.0 {\AA} resolution. The protein is folded into two compact domains. The large N-terminal domain consists of a ␤-barrel and two ␤-sheets. The sheets are flanked by ␣-helices to form an ␣␤␣␤␣ five-layered structure. The C-terminal portion of the molecule forms a distinct domain, which is separated from the N-terminal domain by a wide cleft. Conclusions: Firefly luciferase is the first member of a superfamily of homologous enzymes, which includes acyl-coenzyme A ligases and peptide synthetases, to have its structure characterized. The residues conserved within the superfamily are located on the surfaces of the two domains on either side of the cleft, but are too far apart to interact simultaneously with the substrates. This suggests that the two domains will close in the course of the reaction. Firefly luciferase has a novel structural framework for catalyzing adenylate-forming reactions.}, author = {Conti, Elena and Franks, Nick P and Brick, Peter}, title = {{Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes}} } @article{Shekhawat2009, author = {Shekhawat, Sujan S and Porter, Jason R and Sriprasad, Akshay and Ghosh, Indraneel}, journal = {Jacs}, number = {42}, pages = {15284--15290}, title = {{An Autoinhibited Coiled-Coil Design Strategy for Split-Protein Protease Sensors}}, volume = {131}, year = {2009} } @article{Wehr2006, abstract = {Signaling cascades integrate extracellular stimuli primarily through regulated protein-protein interactions (PPIs). Intracellular signal transduction strictly depends on PPIs occurring at the membrane and in the cytosol. To monitor constitutive and regulated protein interactions within living mammalian cells, we have developed a biological assay termed split TEV. We engineered inactive fragments of the NIa protease from the tobacco etch virus (TEV protease) that regain activity only when coexpressed as fusion constructs with interacting proteins. Functional reconstitution of TEV protease fragments can be monitored with 'proteolysis-only' reporters, which can be previously silent fluorescent and luminescent reporter proteins. Additionally, proteolytically cleavable inactive transcription factors can be combined with any downstream reporter gene of choice to yield 'transcription-coupled' reporter systems. Thus, split TEV combines the advantages of split enzyme- and reporter gene-mediated assays, and provides full flexibility with regard to the final readout. In a first biological application, we monitored neuregulin-induced ErbB2/ErbB4 receptor tyrosine kinase heterodimerization.}, author = {Wehr, Michael C and Laage, Rico and Bolz, Ulrike and Fischer, Tobias M and Grünewald, Sylvia and Scheek, Sigrid and Bach, Alfred and Nave, Klaus-Armin and Rossner, Moritz J}, doi = {10.1038/nmeth967}, issn = {1548-7091}, journal = {Nature methods}, month = {dec}, number = {12}, pages = {985--93}, pmid = {17072307}, title = {{Monitoring regulated protein-protein interactions using split TEV}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17072307}, volume = {3}, year = {2006} } @article{Inobe2016, abstract = {Most proteins form larger protein complexes and perform multiple functions in the cell. Thus, artificial regulation of protein complex formation controls the cellular functions that involve protein complexes. Although several artificial dimerization systems have already been used for numerous applications in biomedical research, cellular protein complexes form not only simple dimers but also larger oligomers. In this study, we showed that fusion proteins comprising the induced heterodimer formation proteins FRB and FKBP formed various oligomers upon addition of rapamycin. By adjusting the configuration of fusion proteins, we succeeded in generating an inducible tetramer formation system. Proteins of interest also formed tetramers by fusing to the inducible tetramer formation system, which exhibits its utility in a broad range of biological applications.}, author = {Inobe, Tomonao and Nukina, Nobuyuki}, doi = {10.1016/j.jbiosc.2015.12.004}, issn = {1347-4421}, journal = {Journal of bioscience and bioengineering}, keywords = {Chemically-induced oligomerization,FKBP,FRB,Oligomer,Protein engineering,Rapamycin}, month = {jul}, number = {1}, pages = {40--6}, pmid = {26777239}, title = {{Rapamycin-induced oligomer formation system of FRB-FKBP fusion proteins}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26777239}, volume = {122}, year = {2016} } @article{Murase, author = {Murase, Kohji and Hirano, Yoshinori and Sun, Tai-Ping and Hakoshima, Toshio}, doi = {10.1038/nature07519}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Murase et al. - Unknown - Gibberellin-induced DELLA recognition by the gibberellin receptor GID1.pdf:pdf}, title = {{Gibberellin-induced DELLA recognition by the gibberellin receptor GID1}}, journal = {Nature} } @unpublished{Farrar2000, abstract = {The coumermycin-GyrB system is a useful strategy for regulating protein homodimerization and activation both in cell extracts and in intact cell culture systems. Coumermycin-based dimerization strategies are currently being used to identify biological responses (such as changes in gene transcription) induced by the Raf and Jak/signal transducers and activators of transcription (STAT) signal transduction pathways. As the utility of dimerization-based strategies becomes evident, they are applied to an increasing number of signal transduction pathways. An important development in this process is the generation of heterodimeric reagents incorporating GyrB-binding groups. The relative ease by which novobiocin can be synthetically modified to incorporate novel chemical entities should permit facile development of such reagents. It is interesting to investigate how specific pathways interact by using chemically distinct dimerization methods to regulate the activity of each independently. Such approaches provide important insights into the overall regulation of cell signaling.}, author = {Farrar, Michael A. and Olson, Steven H. and Perlmutter, Roger M.}, booktitle = {Methods in Enzymology}, doi = {10.1016/S0076-6879(00)27293-5}, isbn = {9780121822286}, issn = {00766879}, pages = {421--IN5}, title = {{[31] Coumermycin-induced dimerization of GyrB-containing fusion proteins}}, volume = {327}, year = {2000} } @article{Moran1999, abstract = {We have investigated the folding behavior of dimeric and covalently crosslinked versions of the 33-residue alpha-helical GCN4-p1 coiled coil derived from the leucine zipper region of the transcriptional activator GCN4. The effects of multisite substitutions indicate that folding occurs along multiple routes with nucleation sites located throughout the protein. The similarity in activation energies of the different routes together with an analysis of intrinsic helical propensities indicate that minimal helix is present before a productive collision of the two chains. However, approximately one-third to one-half of the total helical structure is formed in the postcollision transition state ensemble. For the crosslinked, monomeric version, folding occurs along a single robust pathway. Here, the region nearest the crosslink, with the least helical propensity, is structured in the transition state whereas the region farthest from the tether, with the most propensity, is completely unstructured. Hence, the existence of transition state heterogeneity and the selection of folding routes critically depend on chain topology.}, author = {Moran, L B and Schneider, J P and Kentsis, A and Reddy, G A and Sosnick, T R}, doi = {10.1073/PNAS.96.19.10699}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, month = {sep}, number = {19}, pages = {10699--704}, pmid = {10485889}, publisher = {National Academy of Sciences}, title = {{Transition state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking}}, volume = {96}, year = {1999} } @article{Zhou2004, abstract = {A protein molecule exists in either a compact folded state or a variable and open unfolded state. Since the unfolded state is favored by chain entropy, restricting its entropy is an attractive mechanism for shifting the equilibrium toward the folded state. A number of entropy-based strategies have been engineered or used by natural proteins to increase the folding stability:  (a) shortening of loop lengths, (b) covalent linkage of dimeric proteins, (c) backbone cyclization, (d) catenation, (e) spatial confinement, and (f) macromolecular crowding. Theoretical analyses demonstrate the importance of accounting for consequences on the folded as well as the unfolded state and provide guidance for further exploitation of these stabilization strategies.}, author = {Zhou, Huan-Xiang}, doi = {10.1021/AR0302282}, publisher = { American Chemical Society }, title = {{Loops, Linkages, Rings, Catenanes, Cages, and Crowders:  Entropy-Based Strategies for Stabilizing Proteins}}, year = {2004} } @article{Negron2014, abstract = {Molecular engineering of protein assemblies, including the fabrication of nanostructures and synthetic signaling pathways, relies on the availability of modular parts that can be combined to give different structures and functions. Currently, a limited number of well-characterized protein interaction components are available. Coiled-coil interaction modules have been demonstrated to be useful for biomolecular design, and many parallel homodimers and heterodimers are available in the coiled-coil toolkit. In this work, we sought to design a set of orthogonal antiparallel homodimeric coiled coils using a computational approach. There are very few antiparallel homodimers described in the literature, and none have been measured for cross-reactivity. We tested the ability of the distance-dependent statistical potential DFIRE to predict orientation preferences for coiled-coil dimers of known structure. The DFIRE model was then combined with the CLASSY multistate protein design framework to engineer sets of three orthogonal antiparallel homodimeric coiled coils. Experimental measurements confirmed the successful design of three peptides that preferentially formed antiparallel homodimers that, furthermore, did not interact with one additional previously reported antiparallel homodimer. Two designed peptides that formed higher-order structures suggest how future design protocols could be improved. The successful designs represent a significant expansion of the existing protein-interaction toolbox for molecular engineers.}, author = {Negron, Christopher and Keating, Amy E.}, doi = {10.1021/ja507847t}, issn = {15205126}, journal = {Journal of the American Chemical Society}, number = {47}, pages = {16544--16556}, pmid = {25337788}, title = {{A set of computationally designed orthogonal antiparallel homodimers that expands the synthetic coiled-coil toolkit}}, volume = {136}, year = {2014} } @article{Singh2014, abstract = {Recently, a number of synthetic biologic gates including AND, OR, NOR, NOT, XOR and NAND have been engineered and characterized in a wide range of hosts. The hope in the emerging synthetic biology community is to construct an inventory of well-characterized parts and install distinct gene and circuit behaviours that are externally controllable. Though the field is still growing and major successes are yet to emerge, the payoffs are predicted to be significant. In this review, we highlight specific examples of logic gates engineering with applications towards fundamental understanding of network complexity and generating a novel socially useful applications.}, author = {Singh, Vijai}, doi = {10.1007/s11693-014-9154-6}, issn = {1872-5325}, journal = {Systems and synthetic biology}, month = {dec}, number = {4}, pages = {271--82}, pmid = {26396651}, publisher = {Springer}, title = {{Recent advances and opportunities in synthetic logic gates engineering in living cells}}, volume = {8}, year = {2014} } @article{Woolfson2005, abstract = {Protein design allows sequence-to-structure relationships in proteins to be examined and, potentially, new protein structures and functions to be made to order. To succeed, however, the protein-design process requires reliable rules that link protein sequence to structure⧸function. Although our present understanding of coiled-coil folding and assembly is not complete, through numerous bioinformatics and experimental studies there are now sufficient rules to allow confident design attempts of naturally observed and even novel coiled-coil motifs. This review summarizes the current design rules for coiled coils, and describes some of the key successful coiled-coil designs that have been created to date. The designs range from those for relatively straightforward, naturally observed structures—including parallel and antiparallel dimers, trimers and tetramers, all of which have been made as homomers and heteromers—to more exotic structures that expand the repertoire of Nature's coiled-coil structures. Examples in the second bracket include a probe that binds a cancer-associated coiled-coil protein; a tetramer with a right-handed supercoil; sticky-ended coiled coils that self-assemble to form fibers; coiled coils that switch conformational state; a three-component two-stranded coiled coil; and an antiparallel dimer that directs fragment complementation of larger proteins. Some of the more recent examples show an important development in the field; namely, new designs are being created with function as well as structure in mind. This will remain one of the key challenges in coiled-coil design in the next few years. Other challenges that lie ahead include the need to discover more rules for coiled-coil prediction and design, and to implement these in prediction and design algorithms. The considerable success of coiled-coil design so far bodes well for this, however. It is likely that these challenges will be met and surpassed.}, author = {Woolfson, Derek N.}, doi = {S0065323305700048 [pii] 10.1016/S0065-3233(05)70004-8}, edition = {2005/04/20}, editor = {{David A. D. Parry}, and John M. Squire}, isbn = {0065-3233 (Print) 0065-3233 (Linking)}, journal = {Adv Protein Chem}, pages = {79--112}, pmid = {15837514}, publisher = {Academic Press}, series = {Fibrous Proteins: Coiled-Coils, Collagen and Elastomers}, title = {{The Design of Coiled-Coil Structures and Assemblies}}, volume = {70}, year = {2005} } @article{Gradisar2011, abstract = {We used the principles governing the selectivity and stability of coiled-coil segments to design and experimentally test a set of four pairs of parallel coiled-coil-forming peptides composed of four heptad repeats. The design was based on maximizing the difference in stability between desired pairs and the most stable unwanted combinations using N-terminal helix initiator residues, favorable combinations of the electrostatic and hydrophobic interaction motifs and negative design motif based on burial of asparagine residues. Experimental analysis of all 36 pair combinations among the eight peptides was performed by circular dichroism (CD). On the basis of CD spectra, each peptide formed a high level of $\alpha$-helical structure exclusively in combination with its designed peptide partner which demonstrates the orthogonality of the designed peptide pair set.}, author = {Gradišar, Helena and Jerala, Roman}, doi = {10.1002/psc.1331}, issn = {1099-1387}, journal = {Journal of peptide science : an official publication of the European Peptide Society}, month = {feb}, number = {2}, pages = {100--6}, pmid = {21234981}, title = {{De novo design of orthogonal peptide pairs forming parallel coiled-coil heterodimers}}, volume = {17}, year = {2011} } @article{Ranade2014, abstract = {Mechanosensation is perhaps the last sensory modality not understood at the molecular level. Ion channels that sense mechanical force are postulated to play critical roles in a variety of biological processes including sensing touch/pain (somatosensation), sound (hearing), and shear stress (cardiovascular physiology); however, the identity of these ion channels has remained elusive. We previously identified Piezo1 and Piezo2 as mechanically activated cation channels that are expressed in many mechanosensitive cell types. Here, we show that Piezo1 is expressed in endothelial cells of developing blood vessels in mice. Piezo1-deficient embryos die at midgestation with defects in vascular remodeling, a process critically influenced by blood flow. We demonstrate that Piezo1 is activated by shear stress, the major type of mechanical force experienced by endothelial cells in response to blood flow. Furthermore, loss of Piezo1 in endothelial cells leads to deficits in stress fiber and cellular orientation in response to shear stress, linking Piezo1 mechanotransduction to regulation of cell morphology. These findings highlight an essential role of mammalian Piezo1 in vascular development during embryonic development.}, author = {Ranade, Sanjeev S and Qiu, Zhaozhu and Woo, Seung-Hyun and Hur, Sung Sik and Murthy, Swetha E and Cahalan, Stuart M and Xu, Jie and Mathur, Jayanti and Bandell, Michael and Coste, Bertrand and Li, Yi-Shuan J and Chien, Shu and Patapoutian, Ardem}, doi = {10.1073/pnas.1409233111}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, month = {jul}, number = {28}, pages = {10347--52}, pmid = {24958852}, publisher = {National Academy of Sciences}, title = {{Piezo1, a mechanically activated ion channel, is required for vascular development in mice}}, volume = {111}, year = {2014} } @article{Seriani2016, abstract = {Mechanical stimulation appears to be a critical modulator for many aspects of biology, both of living tissue and cells. The cell-stretcher, a novel device for the mechanical uniaxial stimulation of populations of cells, is described. The system is based on a variable stroke cam-lever-tappet mechanism which allows the delivery of cyclic stimuli with frequencies of up to 10 Hz and deformation between 1{\%} and 20{\%}. The kinematics is presented and a simulation of the dynamics of the system is shown, in order to compute the contact forces in the mechanism. The cells, following cultivation and preparation, are plated on an ad hoc polydimethylsiloxane membrane which is then loaded on the clamps of the cell-stretcher via force-adjustable magnetic couplings. In order to show the viability of the experimentation and biocompatibility of the cell-stretcher, a set of two in vitro tests were performed. Human epithelial carcinoma cell line A431 and Adult Mouse Ventricular Fibroblasts (AMVFs) from a dual reporter mouse were subject to 0.5 Hz, 24 h cyclic stretching at 15{\%} strain, and to 48 h stimulation at 0.5 Hz and 15{\%} strain, respectively. Visual analysis was performed on A431, showing definite morphological changes in the form of cellular extroflections in the direction of stimulation compared to an unstimulated control. A cytometric analysis was performed on the AMVF population. Results show a post-stimulation live-dead ratio deviance of less than 6{\%} compared to control, which proves that the environment created by the cell-stretcher is suitable for in vitro experimentation.}, author = {Seriani, S and {Del Favero}, G and Mahaffey, J and Marko, D and Gallina, P and Long, C S and Mestroni, L and Sbaizero, O}, doi = {10.1063/1.4959884}, issn = {1089-7623}, journal = {The Review of scientific instruments}, month = {aug}, number = {8}, pages = {084301}, pmid = {27587132}, title = {{The cell-stretcher: A novel device for the mechanical stimulation of cell populations}}, volume = {87}, year = {2016} } @article{Shah2014, abstract = {Mechanical stimuli are important in directing the fate of stem cells; the effects of mechanical stimuli reported in recent research are reviewed here. Stem cells normally undergo two fundamental processes: proliferation, in which their numbers multiply, and differentiation, in which they transform into the specialized cells needed by the adult organism. Mechanical stimuli are well known to affect both processes of proliferation and differentiation, although the complete pathways relating specific mechanical stimuli to stem cell fate remain to be elucidated. We identified two broad classes of research findings and organized them according to the type of mechanical stress (compressive, tensile or shear) of the stimulus. Firstly, mechanical stress of any type activates stretch-activated channels (SACs) on the cell membrane. Activation of SACs leads to cytoskeletal remodelling and to the expression of genes that regulate the basic growth, survival or apoptosis of the cells and thus regulates proliferation. Secondly, mechanical stress on cells that are physically attached to an extracellular matrix (ECM) initiates remodelling of cell membrane structures called integrins. This second process is highly dependent on the type of mechanical stress applied and result into various biological responses. A further process, the Wnt pathway, is also implicated: crosstalk between the integrin and Wnt pathways regulates the switch from proliferation to differentiation and finally regulates the type of differentiation. Therefore, the stem cell differentiation process involves different signalling molecules and their pathways and most likely depends upon the applied mechanical stimulation.}, author = {Shah, Nirali and Morsi, Yosry and Manasseh, Richard}, doi = {10.1002/cbf.3027}, issn = {1099-0844}, journal = {Cell biochemistry and function}, month = {jun}, number = {4}, pages = {309--25}, pmid = {24574137}, title = {{From mechanical stimulation to biological pathways in the regulation of stem cell fate}}, volume = {32}, year = {2014} } @article{Veltmann, abstract = {Background}, author = {Veltmann, Moritz and Hollborn, Margrit and Reichenbach, Andreas and Wiedemann, Peter and Kohen, Leon and Bringmann, Andreas}, doi = {10.1371/journal.pone.0147312}, title = {{Osmotic Induction of Angiogenic Growth Factor Expression in Human Retinal Pigment Epithelial Cells}}, year = {2016}, journal = {PLoS One} } @article{Meister2016, abstract = {This is an analysis of how magnetic fields affect biological molecules and cells. It was prompted by a series of prominent reports regarding magnetism in biological systems. The first claims to have identified a protein complex that acts like a compass needle to guide magnetic orientation in animals (Qin et al., 2016). Two other articles report magnetic control of membrane conductance by attaching ferritin to an ion channel protein and then tugging the ferritin or heating it with a magnetic field (Stanley et al., 2015; Wheeler et al., 2016). Here I argue that these claims conflict with basic laws of physics. The discrepancies are large: from 5 to 10 log units. If the reported phenomena do in fact occur, they must have causes entirely different from the ones proposed by the authors. The paramagnetic nature of protein complexes is found to seriously limit their utility for engineering magnetically sensitive cells.}, author = {Meister, Markus and Arosio, P. and Ingrassia, R. and Cavadini, P. and Babincová, M. and Leszczynska, D. and Sourivong, P. and Babinec, P. and Bazylinski, DA. and Frankel, RB. and Cao, E. and Cordero-Morales, JF. and Liu, B. and Qin, F. and Julius, D. and Chen, G. and Davila, AF. and Fleissner, G. and Winklhofer, M. and Petersen, N. and Demir, S. and Jeon, I-R. and Long, JR. and Harris, TD. and Dunlop, DJ. and Dutz, S. and Hergt, R. and Dutz, S. and Hergt, R. and Fantechi, E. and Innocenti, C. and Zanardelli, M. and Fittipaldi, M. and Falvo, E. and Carbo, M. and Shullani, V. and Mannelli, L. Di Cesare and Ghelardini, C. and Ferretti, AM. and Ponti, A. and Sangregorio, C. and Ceci, P. and Fantechi, E. and Innocenti, C. and Albino, M. and Lottini, E. and Sangregorio, C. and Feynman, RP. and Leighton, RB. and Sands, ML. and Fortin, JP. and Wilhelm, C. and Servais, J. and Ménager, C. and Bacri, JC. and Gazeau, F. and Ge, Z. and Cahill, DG. and Braun, PV. and Gupta, A. and Kane, RS. and Borca-Tasciuc, D-A. and Hergt, R. and Hiergeist, R. and Zeisberger, M. and Glöckl, G. and Weitschies, W. and Ramirez, LP. and Hilger, I. and Kaiser, WA. and Hergt, R. and Dutz, S. and Müller, R. and Zeisberger, M. and Mueller, R. and Howard, J. and Hudspeth, AJ. and Huang, H. and Delikanli, S. and Zeng, H. and Ferkey, DM. and Pralle, A. and Jackson, JD. and Jandacka, P. and Burda, H. and Pistora, J. and Johnsen, S. and Lohmann, KJ. and Keblinski, P. and Cahill, DG. and Bodapati, A. and Sullivan, CR. and Taton, TA. and Kirschvink, JL. and Walker, MM. and Diebel, CE. and Kirschvink, JL. and Winklhofer, M. and Walker, MM. and Leibiger, IB. and Berggren, PO. and Lewis, S. and Lohmann, KJ. and Maddox, J. and Randi, J. and Stewart, WW. and Maier-Hauff, K. and Ulrich, F. and Nestler, D. and Niehoff, H. and Wust, P. and Thiesen, B. and Orawa, H. and Budach, V. and Jordan, A. and Michaelis, L. and Coryell, CD. and Granick, S. and Owen, CS. and Lindsay, JG. and Pankhurst, QA. and Connolly, J. and Jones, SK. and Dobson, J. and Papaefthymiou, GC. and Piñol, R. and Brites, CD. and Bustamante, R. and Martínez, A. and Silva, NJ. and Murillo, JL. and Cases, R. and Carrey, J. and Estepa, C. and Sosa, C. and Palacio, F. and Carlos, LD. and Millán, A. and Purushotham, S. and Ramanujan, RV. and Qin, S. and Yin, H. and Yang, C. and Dou, Y. and Liu, Z. and Zhang, P. and Yu, H. and Huang, Y. and Feng, J. and Hao, J. and Hao, J. and Deng, L. and Yan, X. and Dong, X. and Zhao, Z. and Jiang, T. and Wang, HW. and Luo, SJ. and Xie, C. and Rabin, Y. and Ranade, SS. and Qiu, Z. and Woo, SH. and Hur, SS. and Murthy, SE. and Cahalan, SM. and Xu, J. and Mathur, J. and Bandell, M. and Coste, B. and Li, YS. and Chien, S. and Patapoutian, A. and Riedinger, A. and Guardia, P. and Curcio, A. and Garcia, MA. and Cingolani, R. and Manna, L. and Pellegrino, T. and Ritz, T. and Ahmad, M. and Mouritsen, H. and Wiltschko, R. and Wiltschko, W. and Schenck, JF. and Dumoulin, CL. and Redington, RW. and Kressel, HY. and Elliott, RT. and McDougall, IL. and Schoffa, G. and Soffe, R. and Baratchi, S. and Tang, SY. and Nasabi, M. and McIntyre, P. and Mitchell, A. and Khoshmanesh, K. and Stanley, SA. and Sauer, J. and Kane, RS. and Dordick, JS. and Friedman, JM. and Wheeler, MA. and Smith, CJ. and Ottolini, M. and Barker, BS. and Purohit, AM. and Grippo, RM. and Gaykema, RP. and Spano, AJ. and Beenhakker, MP. and Kucenas, S. and Patel, MK. and Deppmann, CD. and Güler, AD. and Zborowski, M. and Fuh, CB. and Green, R. and Baldwin, NJ. and Reddy, S. and Douglas, T. and Mann, S. and Chalmers, JJ.}, doi = {10.7554/eLife.17210}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Meister et al. - 2016 - Physical limits to magnetogenetics.pdf:pdf}, issn = {2050-084X}, journal = {eLife}, keywords = {biophysics,magnetic control,magnetoreception,neuroscience,none,physical plausibility,structural biology}, pages = {589--599}, pmid = {27529126}, publisher = {eLife Sciences Publications Limited}, title = {{Physical limits to magnetogenetics.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/27529126 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5016093}, volume = {5}, year = {2016} } @article{Qin2015, author = {Qin, Siying and Yin, Hang and Yang, Celi and Dou, Yunfeng and Liu, Zhongmin and Zhang, Peng and Yu, He and Huang, Yulong and Feng, Jing and Hao, Junfeng and Hao, Jia and Deng, Lizong and Yan, Xiyun and Dong, Xiaoli and Zhao, Zhongxian and Jiang, Taijiao and Wang, Hong-Wei and Luo, Shu-Jin and Xie, Can}, doi = {10.1038/nmat4484}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Qin et al. - 2015 - A magnetic protein biocompass.pdf:pdf}, issn = {1476-1122}, journal = {Nature Materials}, month = {nov}, number = {2}, pages = {217--226}, publisher = {Nature Research}, title = {{A magnetic protein biocompass}}, url = {http://www.nature.com/doifinder/10.1038/nmat4484}, volume = {15}, year = {2015} } @article{Stanley2015, abstract = {Means for temporally regulating gene expression and cellular activity are invaluable for elucidating underlying physiological processes and would have therapeutic implications. Here we report the development of a genetically encoded system for remote regulation of gene expression by low-frequency radio waves (RFs) or a magnetic field. Iron oxide nanoparticles are synthesized intracellularly as a GFP-tagged ferritin heavy and light chain fusion. The ferritin nanoparticles associate with a camelid anti-GFP-transient receptor potential vanilloid 1 fusion protein, $\alpha$GFP-TRPV1, and can transduce noninvasive RF or magnetic fields into channel activation, also showing that TRPV1 can transduce a mechanical stimulus. This, in turn, initiates calcium-dependent transgene expression. In mice with stem cell or viral expression of these genetically encoded components, remote stimulation of insulin transgene expression with RF or a magnet lowers blood glucose. This robust, repeatable method for remote regulation in vivo may ultimately have applications in basic science, technology and therapeutics.}, author = {Stanley, Sarah A and Sauer, Jeremy and Kane, Ravi S and Dordick, Jonathan S and Friedman, Jeffrey M}, doi = {10.1038/nm.3730}, issn = {1546-170X}, journal = {Nature medicine}, month = {jan}, number = {1}, pages = {92--8}, pmid = {25501906}, title = {{Remote regulation of glucose homeostasis in mice using genetically encoded nanoparticles.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25501906 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4894538}, volume = {21}, year = {2015} } @article{Acharya2002, abstract = {We use a heterodimerizing leucine zipper system to examine the contribution of the interhelical a-a' interaction to dimer stability for six amino acids (A, V, L, I, K, and N). Circular dichroism (CD) spectroscopy monitored the thermal denaturation of 36 heterodimers that generate six homotypic and 30 heterotypic a-a' interactions. Isoleucine (I-I) is the most stable homotypic a-a' interaction, being 9.2 kcal/mol per dimer more stable than the A-A interaction and 4.0 kcal/mol per dimer more stable than either the L-L or V-V interaction, and 7.0 kcal/mol per dimer more stable than the N-N interaction. Only lysine was less stable than alanine. An alanine-based double-mutant thermodynamic cycle calculated coupling energies between the a and a' positions in the heterodimer. The aliphatic amino acids L, V, and I prefer to form homotypic interactions with coupling energies of -0.6 to -0.9 kcal/mol per dimer, but the heterotypic aliphatic interactions have positive coupling energies of <1.0 kcal/mol per dimer. The asparagine homotypic interaction has a coupling energy of -0.5 kcal/mol per dimer, while heterotypic interactions with the aliphatic amino acids produce coupling energies ranging from 2.6 to 4.9 kcal/mol per dimer. The homotypic K-K interaction is 2.9 kcal/mol per dimer less stable than the A-A interaction, but the coupling energy is only 0.3 kcal/mol per dimer. Heterotypic interactions with lysine and either asparagine or aliphatic amino acids produce similar coupling energies ranging from -0.2 to -0.7 kcal/mol per dimer. Thus, of the amino acids that were examined, asparagine contributes the most to dimerization specificity because of the large positive coupling energies in heterotypic interactions with the aliphatic amino acids which results in the N-N homotypic interaction.}, author = {Acharya, Asha and Ruvinov, Sergei B and Gal, Jozsef and Moll, Jonathan R and Vinson, Charles}, issn = {0006-2960}, journal = {Biochemistry}, month = {dec}, number = {48}, pages = {14122--31}, pmid = {12450375}, title = {{A heterodimerizing leucine zipper coiled coil system for examining the specificity of a position interactions: amino acids I, V, L, N, A, and K}}, volume = {41}, year = {2002} } @article{Hadley2006, abstract = {Interactions between R-helical segments constitute a very com-mon theme in protein tertiary and quaternary structure. 1 Thus, elucidation of the factors that control interhelical affinity is essential to understanding protein folding and protein-protein recognition at a fundamental level. The minimum interaction increment, a dimeric coiled-coil, involves just two R-helices. 2 Both parallel and antiparallel R-helical coiled-coil dimers are common; however, biophysical scrutiny has focused almost entirely on parallel dimers. 3 Here we describe the first systematic study of the effect of side-chain variation on the recognition of an R-helical surface by an antiparallel partner. Our findings reveal differences in packing preferences between parallel and antiparallel coiled-coils, and our experimental strategy should be of general utility. Coiled-coil dimerization is driven largely by burial of hydro-phobic surfaces. 4 Sequences that engage in coiled-coil interactions display a characteristic seven-residue repeat pattern in which the first and fourth positions bear hydrophobic side chains. The positions in this " heptad repeat " are conventionally designated a-g. Hydrophobic side chains, at a and d, form a continuous stripe along one side of the R-helix; these stripes lie at the core of the dimer interface. We sought an experimental approach that would support rapid evaluation of the effects on antiparallel coiled-coil stability exerted by mutations at a and/or d positions. Toward this end, we designed a pair of short R-helix-prone segments that could associate to form an antiparallel coiled-coil. These segments were connected with a flexible linker 5 containing a central thioester bond to generate R-helical hairpin molecule N T -C (Figure 1a). Thiol-thioester exchange occurs rapidly in aqueous solution at neutral pH; therefore, the equilibrium constant for thiol-thioester exchange (K TE) involv-ing a molecule such as N T -C can provide insight on noncovalent attraction between the two R-helical peptide segments (Figure 1b). 6 Mutations at a or d positions that lead to more or less favorable intramolecular association between the N-and C-helix segments in the full-length thioester (i.e., larger or smaller K CC) should be manifested as a larger or smaller K TE , which can be measured directly by HPLC. Related studies have been carried out via thiol-disulfide exchange, using peptides bearing Cys residues; 7 however, thiol-thioester exchange offers technical ad{\ldots}}, author = {Hadley, Erik B and Gellman, Samuel H}, doi = {10.1021/ja067178r}, journal = {J. AM. CHEM. SOC}, pages = {16444--16445}, title = {{An Antiparallel r-Helical Coiled-Coil Model System for Rapid Assessment of Side-Chain Recognition at the Hydrophobic Interface}}, volume = {128}, year = {2006} } @article{Acharya2002a, abstract = {We use a heterodimerizing leucine zipper system to examine the contribution of the interhelical a-a' interaction to dimer stability for six amino acids (A, V, L, I, K, and N). Circular dichroism (CD) spectroscopy monitored the thermal denaturation of 36 heterodimers that generate six homotypic and 30 heterotypic a-a' interactions. Isoleucine (I-I) is the most stable homotypic a-a' interaction, being 9.2 kcal/mol per dimer more stable than the A-A interaction and 4.0 kcal/mol per dimer more stable than either the L-L or V-V interaction, and 7.0 kcal/mol per dimer more stable than the N-N interaction. Only lysine was less stable than alanine. An alanine-based double-mutant thermodynamic cycle calculated coupling energies between the a and a' positions in the heterodimer. The aliphatic amino acids L, V, and I prefer to form homotypic interactions with coupling energies of -0.6 to -0.9 kcal/mol per dimer, but the heterotypic aliphatic interactions have positive coupling energies of <1.0 kcal/mol per dimer. The asparagine homotypic interaction has a coupling energy of -0.5 kcal/mol per dimer, while heterotypic interactions with the aliphatic amino acids produce coupling energies ranging from 2.6 to 4.9 kcal/mol per dimer. The homotypic K-K interaction is 2.9 kcal/mol per dimer less stable than the A-A interaction, but the coupling energy is only 0.3 kcal/mol per dimer. Heterotypic interactions with lysine and either asparagine or aliphatic amino acids produce similar coupling energies ranging from -0.2 to -0.7 kcal/mol per dimer. Thus, of the amino acids that were examined, asparagine contributes the most to dimerization specificity because of the large positive coupling energies in heterotypic interactions with the aliphatic amino acids which results in the N-N homotypic interaction.}, author = {Acharya, Asha and Ruvinov, Sergei B and Gal, Jozsef and Moll, Jonathan R and Vinson, Charles}, issn = {0006-2960}, journal = {Biochemistry}, month = {dec}, number = {48}, pages = {14122--31}, pmid = {12450375}, title = {{A heterodimerizing leucine zipper coiled coil system for examining the specificity of a position interactions: amino acids I, V, L, N, A, and K}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12450375}, volume = {41}, year = {2002} } @article{Litowski2001, abstract = {The E/K coil, a heterodimeric coiled-coil, has been designed as a universal peptide capture and delivery system for use in applications such as biosensors and affinity chromatography. In this design, heterodimer formation is specified through the placement of charged residues at the e and g positions of the heptad repeat. The affinity and stability of the E/K coil has been modified in order to allow a greater range of conditions for association and dissociation by varying the chain length to obtain three, four and five heptad coiled-coils (21, 28 and 35 residues per polypeptide chain). The effect of chain length on stability and folding was examined by circular dichroism spectroscopy, guanidine hydrochloride denaturation, and redox equilibrium experiments. It was found that increases in chain length produced increases in the stability of heterodimeric coiled-coils, but in a nonlinear fashion. The resulting disulfide-bridged heterostranded molecules and reduced heterodimers span a wide range of stabilities (deltaG=3.3-11.9 kcal/mol), greatly expanding their scope for use in protein engineering and biomedical applications.}, author = {Litowski, J R and Hodges, R S}, issn = {1397-002X}, journal = {The journal of peptide research : official journal of the American Peptide Society}, month = {dec}, number = {6}, pages = {477--92}, pmid = {12005418}, title = {{Designing heterodimeric two-stranded alpha-helical coiled-coils: the effect of chain length on protein folding, stability and specificity.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12005418}, volume = {58}, year = {2001} } @article{Oakley1998, abstract = {Coiled coils consist of bundles of two or more alpha-helices that are aligned in a parallel or an antiparallel relative orientation. The designed peptides, Acid-p1 and Base-p1, associate in solution to form a parallel, heterodimeric two-stranded coiled coil [O'Shea, E. K., Lumb, K. J., and Kim, P. S. (1993) Curr. Biol. 3, 658]. The buried interface of this complex is formed by hydrophobic Leu residues, with the exception of an Asn residue from each strand that is positioned to engage in a buried polar interaction. Substitution of these buried Asn residues by Leu residues results in a loss of structural uniqueness, as evidenced by a lack of a particular helix orientation in the Acid-Base coiled-coil complex [Lumb, K. J., and Kim, P. S. (1995) Biochemistry 34, 8642]. Here, we alter the positions of the Asn residues in the Acid and Base peptides such that a buried polar interaction is only expected to occur when the helices are in an antiparallel orientation. The resulting peptides, Acid-a1 and Base-a1, associate to form a helical heterodimer, as shown by circular dichroism (CD) and equilibrium sedimentation centrifugation. The helix orientation preference has been measured using covalently linked, disulfide-containing heterodimers in which the constituent peptides are constrained to interact in either a parallel or an antiparallel orientation. Although both the parallel and antiparallel heterodimers form stable, helical structures, the antiparallel heterodimer is the predominant species at equilibrium when the heterodimers are allowed to undergo thiol-disulfide exchange. In addition, the antiparallel heterodimer is more stable to chemical denaturation than the parallel counterpart by approximately 2.3 kcal/mol. These results demonstrate that a single buried polar interaction in the interface between the helices of a coiled coil is sufficient to determine the relative orientation of its constituent helices.}, author = {Oakley, M G and Kim, P S}, doi = {10.1021/bi981269m}, issn = {0006-2960}, journal = {Biochemistry}, month = {sep}, number = {36}, pages = {12603--10}, pmid = {9730833}, title = {{A buried polar interaction can direct the relative orientation of helices in a coiled coil.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/9730833}, volume = {37}, year = {1998} } @article{Woolfson2005, abstract = {Protein design allows sequence-to-structure relationships in proteins to be examined and, potentially, new protein structures and functions to be made to order. To succeed, however, the protein-design process requires reliable rules that link protein sequence to structure?function. Although our present understanding of coiled-coil folding and assembly is not complete, through numerous bioinformatics and experimental studies there are now sufficient rules to allow confident design attempts of naturally observed and even novel coiled-coil motifs. This review summarizes the current design rules for coiled coils, and describes some of the key successful coiled-coil designs that have been created to date. The designs range from those for relatively straightforward, naturally observed structures-including parallel and antiparallel dimers, trimers and tetramers, all of which have been made as homomers and heteromers-to more exotic structures that expand the repertoire of Nature's coiled-coil structures. Examples in the second bracket include a probe that binds a cancer-associated coiled-coil protein; a tetramer with a right-handed supercoil; sticky-ended coiled coils that self-assemble to form fibers; coiled coils that switch conformational state; a three-component two-stranded coiled coil; and an antiparallel dimer that directs fragment complementation of larger proteins. Some of the more recent examples show an important development in the field; namely, new designs are being created with function as well as structure in mind. This will remain one of the key challenges in coiled-coil design in the next few years. Other challenges that lie ahead include the need to discover more rules for coiled-coil prediction and design, and to implement these in prediction and design algorithms. The considerable success of coiled-coil design so far bodes well for this, however. It is likely that these challenges will be met and surpassed.}, author = {Woolfson, Derek N}, doi = {10.1016/S0065-3233(05)70004-8}, issn = {0065-3233}, journal = {Advances in protein chemistry}, pages = {79--112}, pmid = {15837514}, title = {{The design of coiled-coil structures and assemblies.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15837514}, volume = {70}, year = {2005} } @article{Hadley2006a, author = {Hadley, Erik B. and Gellman, Samuel H.}, doi = {10.1021/ja067178r}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, month = {dec}, number = {51}, pages = {16444--16445}, title = {{An Antiparallel $\alpha$-Helical Coiled-Coil Model System for Rapid Assessment of Side-Chain Recognition at the Hydrophobic Interface}}, url = {http://pubs.acs.org/doi/abs/10.1021/ja067178r}, volume = {128}, year = {2006} } @article{Gradisar2011a, abstract = {We used the principles governing the selectivity and stability of coiled-coil segments to design and experimentally test a set of four pairs of parallel coiled-coil-forming peptides composed of four heptad repeats. The design was based on maximizing the difference in stability between desired pairs and the most stable unwanted combinations using N-terminal helix initiator residues, favorable combinations of the electrostatic and hydrophobic interaction motifs and negative design motif based on burial of asparagine residues. Experimental analysis of all 36 pair combinations among the eight peptides was performed by circular dichroism (CD). On the basis of CD spectra, each peptide formed a high level of $\alpha$-helical structure exclusively in combination with its designed peptide partner which demonstrates the orthogonality of the designed peptide pair set.}, author = {Gradišar, Helena and Jerala, Roman}, doi = {10.1002/psc.1331}, issn = {1099-1387}, journal = {Journal of peptide science : an official publication of the European Peptide Society}, month = {feb}, number = {2}, pages = {100--6}, pmid = {21234981}, title = {{De novo design of orthogonal peptide pairs forming parallel coiled-coil heterodimers}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21234981}, volume = {17}, year = {2011} } @article{Shekhawat2009, abstract = {Proteases are widely studied as they are integral players in cell-cycle control and apoptosis. We report a new approach for the design of a family of genetically encoded turn-on protease biosensors. In our design, an autoinhibited coiled-coil switch is turned on upon proteolytic cleavage, which results in the complementation of split-protein reporters. Utilizing this new autoinhibition design paradigm, we present the rational construction and optimization of three generations of protease biosensors, with the final design providing a 1000-fold increase in bioluminescent signal upon addition of the TEV protease. We demonstrate the generality of the approach utilizing two different split-protein reporters, firefly luciferase and $\beta$-lactamase, while also testing our design in the context of a therapeutically relevant protease, caspase-3. Finally, we present a dual protease sensor geometry that allows for the use of these turn-on sensors as potential AND logic gates. Thus, these studies potentially provide a ne...}, author = {Shekhawat, Sujan S. and Porter, Jason R. and Sriprasad, Akshay and Ghosh, Indraneel}, doi = {10.1021/ja9050857}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Shekhawat et al. - 2009 - An Autoinhibited Coiled-Coil Design Strategy for Split-Protein Protease Sensors.pdf:pdf}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, month = {oct}, number = {42}, pages = {15284--15290}, publisher = { American Chemical Society}, title = {{An Autoinhibited Coiled-Coil Design Strategy for Split-Protein Protease Sensors}}, url = {http://pubs.acs.org/doi/abs/10.1021/ja9050857}, volume = {131}, year = {2009} } @article{Kiani2014, author = {Kiani, Samira and Beal, Jacob and Ebrahimkhani, Mohammad R and Huh, Jin and Hall, Richard N and Xie, Zhen and Li, Yinqing and Weiss, Ron}, doi = {10.1038/nmeth.2969}, issn = {1548-7091}, journal = {Nature Methods}, month = {may}, number = {7}, pages = {723--726}, publisher = {Nature Research}, title = {{CRISPR transcriptional repression devices and layered circuits in mammalian cells}}, url = {http://www.nature.com/doifinder/10.1038/nmeth.2969}, volume = {11}, year = {2014} } @article{Ye2013, abstract = {Synthetic biology is the science of reassembling cataloged and standardized biological items in a systematic and rational manner to create and engineer functional biological designer devices, systems and organisms with novel and useful, preferably therapeutic functions. Synthetic biology has significantly advanced the design of complex genetic networks that can reprogram metabolic activities in mammalian cells and provide novel therapeutic strategies for future gene-based and cell-based therapies. Synthetic biology-inspired therapeutic strategies provide new opportunities for improving human health in the 21st century. This review covers the most recent synthetic mammalian circuits designed for therapy of diseases such as metabolic disorders, cancer, and immune disorders. We conclude by discussing current challenges and future perspectives for biomedical applications of synthetic mammalian gene networks.}, author = {Ye, Haifeng and Aubel, Dominique and Fussenegger, Martin}, doi = {10.1016/j.cbpa.2013.10.006}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Ye, Aubel, Fussenegger - 2013 - Synthetic mammalian gene circuits for biomedical applications.pdf:pdf}, issn = {13675931}, journal = {Current Opinion in Chemical Biology}, number = {6}, pages = {910--917}, title = {{Synthetic mammalian gene circuits for biomedical applications}}, volume = {17}, year = {2013} } @article{Walker, author = {Walker, John M}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Walker - Unknown - METHODS I N MOLECULAR BIOLOGY TM Series Editor.pdf:pdf}, title = {{METHODS I N MOLECULAR BIOLOGY TM Series Editor}}, url = {www.springer.com/series/7651} } @article{Miyamoto2013, abstract = {One fascinating recent avenue of study in the field of synthetic biology is the creation of biomolecule-based computers. The main components of a computing device consist of an arithmetic logic unit, the control unit, memory, and the input and output devices. Boolean logic gates are at the core of the operational machinery of these parts, and hence to make biocomputers a reality, biomolecular logic gates become a necessity. Indeed, with the advent of more sophisticated biological tools, both nucleic acid- and protein-based logic systems have been generated. These devices function in the context of either test tubes or living cells and yield highly specific outputs given a set of inputs. In this review, we discuss various types of biomolecular logic gates that have been synthesized, with particular emphasis on recent developments that promise increased complexity of logic gate circuitry, improved computational speed, and potential clinical applications.}, author = {Miyamoto, Takafumi and Razavi, Shiva and DeRose, Robert and Inoue, Takanari}, doi = {10.1021/sb3001112}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Miyamoto et al. - 2013 - Synthesizing Biomolecule-Based Boolean Logic Gates.pdf:pdf}, issn = {2161-5063}, journal = {ACS Synthetic Biology}, keywords = {Boolean logic gate,biocomputers,biomolecular devices,chemically inducible dimerization,circuit design,synthetic biology}, month = {feb}, number = {2}, pages = {72--82}, publisher = {American Chemical Society}, title = {{Synthesizing Biomolecule-Based Boolean Logic Gates}}, url = {http://pubs.acs.org/doi/abs/10.1021/sb3001112}, volume = {2}, year = {2013} } @article{Gaber2014, author = {Gaber, Rok and Lebar, Tina and Majerle, Andreja and Šter, Branko and Dobnikar, Andrej and Benčina, Mojca and Jerala, Roman}, doi = {10.1038/nchembio.1433}, issn = {1552-4450}, journal = {Nature Chemical Biology}, month = {jan}, number = {3}, pages = {203--208}, publisher = {Nature Research}, title = {{Designable DNA-binding domains enable construction of logic circuits in mammalian cells}}, url = {http://www.nature.com/doifinder/10.1038/nchembio.1433}, volume = {10}, year = {2014} } @article{Goni-Moreno2012, abstract = {BACKGROUND Engineering genetic Boolean logic circuits is a major research theme of synthetic biology. By altering or introducing connections between genetic components, novel regulatory networks are built in order to mimic the behaviour of electronic devices such as logic gates. While electronics is a highly standardized science, genetic logic is still in its infancy, with few agreed standards. In this paper we focus on the interpretation of logical values in terms of molecular concentrations. RESULTS We describe the results of computational investigations of a novel circuit that is able to trigger specific differential responses depending on the input standard used. The circuit can therefore be dynamically reconfigured (without modification) to serve as both a NAND/NOR logic gate. This multi-functional behaviour is achieved by a) varying the meanings of inputs, and b) using branch predictions (as in computer science) to display a constrained output. A thorough computational study is performed, which provides valuable insights for the future laboratory validation. The simulations focus on both single-cell and population behaviours. The latter give particular insights into the spatial behaviour of our engineered cells on a surface with a non-homogeneous distribution of inputs. CONCLUSIONS We present a dynamically-reconfigurable NAND/NOR genetic logic circuit that can be switched between modes of operation via a simple shift in input signal concentration. The circuit addresses important issues in genetic logic that will have significance for more complex synthetic biology applications.}, author = {Goñi-Moreno, Angel and Amos, Martyn}, doi = {10.1186/1752-0509-6-126}, issn = {1752-0509}, journal = {BMC systems biology}, month = {sep}, pages = {126}, pmid = {22989145}, title = {{A reconfigurable NAND/NOR genetic logic gate.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22989145 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3776446}, volume = {6}, year = {2012} } @article{Ashkenasy2004, abstract = {Living cells can process rapidly and simultaneously multiple extracellular input signals through the complex networks of evolutionary selected biomolecular interactions and chemical transformations. Recent approaches to molecular computation have increasingly sought to mimic or exploit various aspects of biology. A number of studies have adapted nucleic acids and proteins to the design of molecular logic gates and computational systems, while other works have affected computation in living cells via biochemical pathway engineering. Here we report that de novo designed synthetic peptide networks can also mimic some of the basic logic functions of the more complex biological networks. We show that segments of a small network whose graph structure is composed of five nodes and 15 directed edges can express OR, NOR, and NOTIF logic.}, author = {Ashkenasy, Gonen and Ghadiri, M Reza}, doi = {10.1021/ja046745c}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, month = {sep}, number = {36}, pages = {11140--1}, pmid = {15355081}, title = {{Boolean logic functions of a synthetic peptide network.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15355081 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC1829323}, volume = {126}, year = {2004} } @article{King2013, abstract = {Ultrasound-induced neurostimulation has recently gained increasing attention, but little is known about the mechanisms by which it affects neural activity or about the range of acoustic parameters and stimulation protocols that elicit responses. We have established conditions for transcranial stimulation of the nervous system in vivo, using the mouse somatomotor response. We report that (1) continuous-wave stimuli are as effective as or more effective than pulsed stimuli in eliciting responses, and responses are elicited with stimulus onset rather than stimulus offset; (2) stimulation success increases as a function of both acoustic intensity and acoustic duration; (3) interactions of intensity and duration suggest that successful stimulation results from the integration of stimulus amplitude over a time interval of 50 to 150 ms; and (4) the motor response elicited appears to be an all-or-nothing phenomenon, meaning stronger stimulus intensities and durations increase the probability of a motor response without affecting the duration or strength of the response. © 2013 World Federation for Ultrasound in Medicine {\&} Biology.}, author = {King, Randy L. and Brown, Julian R. and Newsome, William T. and Pauly, Kim Butts}, doi = {10.1016/j.ultrasmedbio.2012.09.009}, isbn = {1879-291X (Electronic)$\backslash$r0301-5629 (Linking)}, issn = {03015629}, journal = {Ultrasound in Medicine and Biology}, number = {2}, pages = {312--331}, pmid = {23219040}, title = {{Effective parameters for ultrasound-induced in vivo neurostimulation}}, volume = {39}, year = {2013} } @article{Majerle2015, abstract = {The high mutation rate of the human immunodeficiency virus type 1 (HIV-1) virus is a major problem since it evades the function of antibodies and chemical inhibitors. Here, we demonstrate a viral detection strategy based on synthetic biology principles to detect a specific viral function rather than a particular viral protein. The resistance caused by mutations can be circumvented since the mutations that cause the loss of function also incapacitate the virus. Many pathogens encode proteases that are essential for their replication and that have a defined substrate specificity. A genetically encoded sensor composed of a fused membrane anchor, viral protease target site, and an orthogonal transcriptional activator was engineered into a human cell line. The HIV-1 protease released the transcriptional activator from the membrane, thereby inducing transcription of the selected genes. The device was still strongly activated by clinically relevant protease mutants that are resistant to protease inhibitors. In the future, a similar principle could be applied to detect also other pathogens and functions.}, author = {Majerle, Andreja and Gaber, Rok and Benčina, Mojca and Jerala, Roman}, doi = {10.1021/sb5002483}, issn = {2161-5063}, journal = {ACS Synthetic Biology}, number = {6}, pages = {667--672}, pmid = {25393958}, title = {{Function-based mutation-resistant synthetic signaling device activated by HIV-1 proteolysis}}, volume = {4}, year = {2015} } @article{Hynynen1998, abstract = {Utilization of therapeutic ultrasound in the brain has been seriously limited by the commonly accepted view that these exposures would require that a piece of the skull bone be removed to allow the ultrasound beam to propagate into the brain. In this paper, the feasibility of delivering ultrasound therapy through the intact skull was studied. Sonications were performed through a piece of human skull with focused transducers at 0.248, 0.559, 1.0 and 1.68 MHz. The skull attenuated and distorted the field; however, a sharp focal spot was created at frequencies of 1 MHz or lower. At the higher frequency, the focus was destroyed. To investigate the feasibility of compensating for the ultrasound field distortion caused by the bone, phased array experiments were performed. Two arrays with 64 elements, operating at 0.6 MHz and 1.58 MHz, were used in these experiments. The phase shifts caused by the skull were measured for each element of the arrays and then compensated for by phase-control circuitry. These phase corrections allowed a sharp focus to be generated at both frequencies. Finally, tissue destruction was induced by using pulsed sonication through a piece of human skull in a rabbit brain in vivo at the frequency of 0.559 MHz. In summary, the results showed that transcranial delivery of therapeutic ultrasound into the brain may be feasible.}, author = {Hynynen, Kullervo and Jolesz, Ferenc A.}, doi = {10.1016/S0301-5629(97)00269-X}, isbn = {0301-5629 (Print)$\backslash$r0301-5629 (Linking)}, issn = {03015629}, journal = {Ultrasound in Medicine and Biology}, number = {2}, pages = {275--283}, pmid = {9550186}, title = {{Demonstration of potential noninvasive ultrasound brain therapy through an intact skull}}, volume = {24}, year = {1998} } @article{Warden2014, abstract = {Genetically encoded optical actuators and indicators have changed the land-scape of neuroscience, enabling targetable control and readout of specific components of intact neural circuits in behaving animals. Here, we review the development of optical neural interfaces, focusing on hardware designed for optical control of neural activity, integrated optical control and electrical readout, and optical readout of population and single-cell neural activity in freely moving mammals.}, author = {Warden, Melissa R and Cardin, Jessica A and Deisseroth, Karl}, doi = {10.1146/annurev-bioeng-071813-104733}, isbn = {1523-9829}, issn = {1545-4274}, journal = {Annu. Rev. Biomed. Eng}, pages = {103--29}, pmid = {25014785}, title = {{Optical Neural Interfaces}}, volume = {16}, year = {2014} } @article{Perozo2003, abstract = {Mechanosensitive channels function as electromechanical switches with the capability to sense the physical state of lipid bilayers. The X-ray crystal structures of MscL and MscS offer a unique opportunity to identify the types of protein motions associated with the opening and closing of these structurally unrelated channels, while providing the framework to address a mechanism of tension sensing that is defined by channel-lipid interactions. Recent functional, structural and dynamic data offer fresh insights into the molecular basis of gating for these membrane proteins.}, author = {Perozo, Eduardo and Rees, Douglas C.}, doi = {10.1016/S0959-440X(03)00106-4}, isbn = {0959440X}, issn = {0959440X}, journal = {Current Opinion in Structural Biology}, number = {4}, pages = {432--442}, pmid = {12948773}, title = {{Structure and mechanism in prokaryotic mechanosensitive channels}}, volume = {13}, year = {2003} } @article{Pivetti2003, abstract = {Mechanosensitive (MS) channels that provide protection against hypoosmotic shock are found in the membranes of organisms from the three domains of life: bacteria, archaea, and eucarya. Two families of ubiquitous MS channels are recognized, and these have been designated the MscL and MscS families. A high-resolution X-ray crystallographic structure is available for a member of the MscL family, and extensive molecular genetic, biophysical, and biochemical studies conducted in many laboratories have allowed postulation of a gating mechanism allowing the interconversion of a tightly closed state and an open state that controls transmembrane ion and metabolite fluxes. In contrast to the MscL channel proteins, which are of uniform topology, the much larger MscS family includes protein members with topologies that are predicted to vary from 3 to 11 alpha-helical transmembrane segments (TMSs) per polypeptide chain. Sequence analyses reveal that the three C-terminal TMSs of MscS channel proteins are conserved among family members and that the third of these three TMSs exhibits a 20-residue motif that is shared by the channel-forming TMS (TMS 1) of the MscL proteins. We propose that this C-terminal TMS in MscS family homologues serves as the channel-forming helix in a homooligomeric structure. The presence of a conserved residue pattern for the putative channel-forming TMSs in the MscL and MscS family proteins suggests a common structural organization, gating mechanism, and evolutionary origin.}, author = {Pivetti, Christopher D and Yen, Ming-Ren and Miller, Samantha and Busch, Wolfgang and Tseng, Yi-Hsiung and Booth, Ian R and Saier, Milton H}, doi = {10.1128/MMBR.67.1.66}, isbn = {1092-2172 (Print) 1092-2172 (Linking)}, issn = {1092-2172}, journal = {Microbiology and molecular biology reviews : MMBR}, number = {1}, pages = {66--85}, pmid = {12626684}, title = {{Two families of mechanosensitive channel proteins.}}, volume = {67}, year = {2003} } @article{Bianchi2007, abstract = {The survival of an organism depends on its ability to respond to its environment through its senses. The sense of touch is one of the most vital; still, it is the least understood. In the process of touch sensation, a mechanical stimulus is converted into electrical signals. Groundbreaking electrophysiological experiments in organisms ranging from bacteria to mammals have suggested that this conversion may occur through the activation of ion channels that gate in response to mechanical stimuli. However, the molecular identity of these channels has remained elusive for a very long time. Breakthroughs in our understanding of the cellular and molecular mechanisms of touch sensation have come from the analysis of touch-insensitive mutants in model organisms such as Caenorhabditis elegans and Drosophila melanogaster. This review will focus on the elegant genetic, molecular, imaging, and electrophysiological studies that demonstrate that a channel complex composed of two members of the DEG/ENaC gene family of channel subunits (named for the C. elegans degenerins and the related mammalian epithelial amiloride-sensitive Na channel), MEC-4 and MEC-10, and accessory subunits is gated by mechanical forces in touch-sensing neurons from C. elegans. I also report here electrophysiological and behavioral studies employing knockout mice that have recently shown that mammalian homologues of MEC-4, MEC-10, and accessory subunits are needed for normal mechanosensitivity in mouse, suggesting a conserved function for this channel family across species. The C. elegans genome encodes 28 DEG/ENaC channels: I discuss here the global role of DEG/ENaCs in mechanosensation, reporting findings on the role of other three nematode DEG/ENaCs (UNC-8, DEL-1, and UNC-105) in mechanosensitive and stretch-sensitive behaviors. Finally, this review will discuss findings in which members of another family of ion channels, the Transient Receptor Potential channels family, have been implicated in mechanosensitive behaviors in organisms ranging from C. elegans to mammals.}, author = {Bianchi, Laura}, doi = {10.1007/s12035-007-8009-5}, issn = {1559-1182}, journal = {Molecular Neurobiology}, number = {3}, pages = {254--271}, title = {{Mechanotransduction: Touch and Feel at the Molecular Level as Modeled in Caenorhabditis elegans}}, volume = {36}, year = {2007} } @book{Nilius2007, abstract = {The transient receptor potential (TRP) superfamily consists of a large number of cation channels that are mostly permeable to both monovalent and divalent cations. The 28 mammalian TRP channels can be subdivided into six main subfamilies: the TRPC (canonical), TRPV (vanilloid), TRPM (melastatin), TRPP (polycystin), TRPML (mucolipin), and the TRPA (ankyrin) groups. TRP channels are expressed in almost every tissue and cell type and play an important role in the regulation of various cell functions. Currently, significant scientific effort is being devoted to understanding the physiology of TRP channels and their relationship to human diseases. At this point, only a few channelopathies in which defects in TRP genes are the direct cause of cellular dysfunction have been identified. In addition, mapping of TRP genes to susceptible chromosome regions (e.g., translocations, breakpoint intervals, increased frequency of polymorphisms) has been considered suggestive of the involvement of these channels in hereditary diseases. Moreover, strong indications of the involvement of TRP channels in several diseases come from correlations between levels of channel expression and disease symptoms. Finally, TRP channels are involved in some systemic diseases due to their role as targets for irritants, inflammation products, and xenobiotic toxins. The analysis of transgenic models allows further extrapolations of TRP channel deficiency to human physiology and disease. In this review, we provide an overview of the impact of TRP channels on the pathogenesis of several diseases and identify several TRPs for which a causal pathogenic role might be anticipated.}, author = {Nilius, Bernd and Owsianik, Grzegorz and Voets, Thomas and Peters, John a J.a.}, booktitle = {Physiological {\ldots}}, doi = {10.1152/physrev.00021.2006.}, isbn = {0000016772}, issn = {0031-9333}, number = {1}, pages = {165--217}, pmid = {17237345}, title = {{Transient receptor potential cation channels in disease}}, volume = {87}, year = {2007} } @article{Xu2001, author = {Xu, Shang-zhong and Beech, David J}, journal = {Circulation Research}, pages = {84--87}, title = {{TrpC1 Is a Membrane-Spanning Subunit of Store-Operated Ca2+ Channels in Native Vascular Smooth Muscle Cells}}, volume = {88}, year = {2001} } @article{Ye2013, author = {Ye, Haifeng and Aubel, Dominique and Fussenegger, Martin and Lyon, Claude Bernard}, doi = {10.1016/j.cbpa.2013.10.006}, issn = {1367-5931}, journal = {Current Opinion in Chemical Biology}, number = {6}, pages = {910--917}, publisher = {Elsevier Ltd}, title = {{ScienceDirect Synthetic mammalian gene circuits for biomedical applications}}, volume = {17}, year = {2013} } @article{Haswell2011, author = {Haswell, Elizabeth S. and Phillips, Rob and Rees, Douglas C.}, doi = {10.1016/j.pestbp.2011.02.012.Investigations}, isbn = {8585348585}, issn = {15378276}, journal = {Structure}, number = {10}, pages = {1356--1369}, pmid = {1000000221}, title = {{Mechanosensitive channels: what can they do and how they do it?}}, volume = {19}, year = {2011} } @article{Christensen2007, abstract = {Ion channels of the transient receptor potential (TRP) superfamily are involved in a wide variety of neural signalling processes, most prominently in sensory receptor cells. They are essential for mechanosensation in systems ranging from fruitfly hearing, to nematode touch, to mouse mechanical pain. However, it is unclear in many instances whether a TRP channel directly transduces the mechanical stimulus or is part of a downstream signalling pathway. Here, we propose criteria for establishing direct mechanical activation of ion channels and review these criteria in a number of mechanosensory systems in which TRP channels are involved.}, author = {Christensen, Adam P and Corey, David P}, doi = {10.1038/nrn2149}, issn = {1471-003X}, journal = {Nature reviews. Neuroscience}, month = {jul}, number = {7}, pages = {510--21}, pmid = {17585304}, title = {{TRP channels in mechanosensation: direct or indirect activation?}}, volume = {8}, year = {2007} } @article{Zheng2013, abstract = {Transient receptor potential (TRP) channels are cellular sensors for a wide spectrum of physical and chemical stimuli. They are involved in the formation of sight, hearing, touch, smell, taste, temperature, and pain sensation. TRP channels also play fundamental roles in cell signaling and allow the host cell to respond to benign or harmful environmental changes. As TRP channel activation is controlled by very diverse processes and, in many cases, exhibits complex polymodal properties, understanding how each TRP channel responds to its unique forms of activation energy is both crucial and challenging. The past two decades witnessed significant advances in understanding the molecular mechanisms that underlie TRP channels activation. This review focuses on our current understanding of the molecular determinants for TRP channel activation}, author = {Zheng, Jie}, doi = {10.1002/cphy.c120001.Molecular}, isbn = {2040-4603}, issn = {2040-4603}, journal = {Compr Physiol}, number = {1}, pages = {221--242}, pmid = {23720286}, title = {{Molecular Mechanism of TRP Channels}}, volume = {3}, year = {2013} } @article{Ibsen2015, abstract = {A major challenge in neuroscience is to reliably activate individual neurons, particularly those in deeper brain regions. Current optogenetic approaches require invasive surgical procedures to deliver light of specific wavelengths to target cells to activate or silence them. Here, we demonstrate the use of low-pressure ultrasound as a non-invasive trigger to activate specific ultrasonically sensitized neurons in the nematode, Caenorhabditis elegans. We first show that wild-type animals are insensitive to low-pressure ultrasound and require gas-filled microbubbles to transduce the ultrasound wave. We find that neuron-specific misexpression of TRP-4, the pore-forming subunit of a mechanotransduction channel, sensitizes neurons to ultrasound stimulus, resulting in behavioural outputs. Furthermore, we use this approach to manipulate the function of sensory neurons and interneurons and identify a role for PVD sensory neurons in modifying locomotory behaviours. We suggest that this method can be broadly applied to manipulate cellular functions in vivo.}, author = {Ibsen, Stuart and Tong, Ada and Schutt, Carolyn and Esener, Sadik and Chalasani, Sreekanth H}, doi = {10.1038/ncomms9264}, isbn = {2041-1723}, issn = {2041-1723}, journal = {Nature Communications}, pages = {1--12}, pmid = {26372413}, publisher = {Nature Publishing Group}, title = {{Sonogenetics is a non-invasive approach to activating neurons in Caenorhabditis elegans}}, volume = {6}, year = {2015} } @article{Carrington1988, abstract = {Mature viral-encoded proteins of tobacco etch virus (TEV) arise by proteolytic processing of a large precursor. The proteinase responsible for most of these cleavages is a viral-encoded 49-kDa protein. All known or predicted cleavage sites in the TEV polyprotein are flanked by the conserved sequence motif Glu-Xaa-Xaa-Tyr-Xaa-Gln-Ser or Gly, with the scissile bond located between the Gln-Ser or Gly dipeptide. By using cell-free systems to manipulate and express cloned cDNA sequences, a 25-amino acid segment containing a putative proteolytic cleavage site of the TEV polyprotein has been introduced into the TEV capsid protein sequence. This recombinant protein is cleaved by the 49-kDa proteinase at the introduced cleavage site, thus demonstrating portability of a functional cleavage site. The role of the conserved amino acid sequence in determining substrate activity was tested by construction of engineered proteins that contained part or all of this motif. A protein that harbored an insertion of the conserved 7-amino acid segment was cleaved by the 49-kDa TEV proteinase. Cleavage of the synthetic precursor was shown to occur accurately between the expected Gln-Ser dipeptide by microsequence analysis. Proteins containing insertions that generated only the Gln-Ser, or only the serine moiety of the conserved sequence, were insensitive to the 49-kDa proteinase.}, author = {Carrington, J C and Dougherty, W G}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, month = {may}, number = {10}, pages = {3391--5}, pmid = {3285343}, publisher = {National Academy of Sciences}, title = {{A viral cleavage site cassette: identification of amino acid sequences required for tobacco etch virus polyprotein processing.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/3285343 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC280215}, volume = {85}, year = {1988} } @article{Phan2002, abstract = {Because of its stringent sequence specificity, the 3C-type protease from tobacco etch virus (TEV) is frequently used to remove affinity tags from recombinant proteins. It is unclear, however, exactly how TEV protease recognizes its substrates with such high selectivity. The crystal structures of two TEV protease mutants, inactive C151A and autolysis-resistant S219D, have now been solved at 2.2- and 1.8-A resolution as complexes with a substrate and product peptide, respectively. The enzyme does not appear to have been perturbed by the mutations in either structure, and the modes of binding of the product and substrate are virtually identical. Analysis of the protein-ligand interactions helps to delineate the structural determinants of substrate specificity and provides guidance for reengineering the enzyme to further improve its utility for biotechnological applications.}, author = {Phan, Jason and Zdanov, Alexander and Evdokimov, Artem G and Tropea, Joseph E and Peters, Howard K and Kapust, Rachel B and Li, Mi and Wlodawer, Alexander and Waugh, David S}, doi = {10.1074/jbc.M207224200}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Phan et al. - 2002 - Structural basis for the substrate specificity of tobacco etch virus protease.pdf:pdf}, issn = {0021-9258}, journal = {The Journal of biological chemistry}, month = {dec}, number = {52}, pages = {50564--72}, pmid = {12377789}, publisher = {American Society for Biochemistry and Molecular Biology}, title = {{Structural basis for the substrate specificity of tobacco etch virus protease.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12377789}, volume = {277}, year = {2002} } @article{Merzlyak2007, abstract = {Fluorescent proteins have become extremely popular tools for in vivo imaging and especially for the study of localization, motility and interaction of proteins in living cells. Here we report TagRFP, a monomeric red fluorescent protein, which is characterized by high brightness, complete chromophore maturation, prolonged fluorescence lifetime and high pH-stability. These properties make TagRFP an excellent tag for protein localization studies and fluorescence resonance energy transfer (FRET) applications.}, author = {Merzlyak, Ekaterina M and Goedhart, Joachim and Shcherbo, Dmitry and Bulina, Mariya E and Shcheglov, Aleksandr S and Fradkov, Arkady F and Gaintzeva, Anna and Lukyanov, Konstantin A and Lukyanov, Sergey and Gadella, Theodorus W J and Chudakov, Dmitriy M}, doi = {10.1038/nmeth1062}, issn = {1548-7091}, journal = {Nature methods}, month = {jul}, number = {7}, pages = {555--7}, pmid = {17572680}, title = {{Bright monomeric red fluorescent protein with an extended fluorescence lifetime.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17572680}, volume = {4}, year = {2007} } @unpublished{Farrar2000, abstract = {The coumermycin-GyrB system is a useful strategy for regulating protein homodimerization and activation both in cell extracts and in intact cell culture systems. Coumermycin-based dimerization strategies are currently being used to identify biological responses (such as changes in gene transcription) induced by the Raf and Jak/signal transducers and activators of transcription (STAT) signal transduction pathways. As the utility of dimerization-based strategies becomes evident, they are applied to an increasing number of signal transduction pathways. An important development in this process is the generation of heterodimeric reagents incorporating GyrB-binding groups. The relative ease by which novobiocin can be synthetically modified to incorporate novel chemical entities should permit facile development of such reagents. It is interesting to investigate how specific pathways interact by using chemically distinct dimerization methods to regulate the activity of each independently. Such approaches provide important insights into the overall regulation of cell signaling.}, author = {Farrar, Michael A. and Olson, Steven H. and Perlmutter, Roger M.}, booktitle = {Methods in Enzymology}, doi = {10.1016/S0076-6879(00)27293-5}, isbn = {9780121822286}, issn = {00766879}, pages = {421--IN5}, title = {{[31] Coumermycin-induced dimerization of GyrB-containing fusion proteins}}, volume = {327}, year = {2000} } @article{Gibson2009, author = {Gibson, Daniel G and Young, Lei and Chuang, Ray-Yuan and Venter, J Craig and Hutchison, Clyde A and Smith, Hamilton O}, doi = {10.1038/nmeth.1318}, issn = {1548-7091}, journal = {Nature Methods}, month = {may}, number = {5}, pages = {343--345}, publisher = {Nature Publishing Group}, title = {{Enzymatic assembly of DNA molecules up to several hundred kilobases}}, url = {http://www.nature.com/doifinder/10.1038/nmeth.1318}, volume = {6}, year = {2009} } @article{Henrich2003, abstract = {In eukaryotes, many essential secreted proteins and peptide hormones are excised from larger precursors by members of a class of calcium-dependent endoproteinases, the prohormone-proprotein convertases (PCs). Furin, the best-characterized member of the mammalian PC family, has essential functions in embryogenesis and homeostasis but is also implicated in various pathologies such as tumor metastasis, neurodegeneration and various bacterial and viral diseases caused by such pathogens as anthrax and pathogenic Ebola virus strains. Furin cleaves protein precursors with narrow specificity following basic Arg-Xaa-Lys/Arg-Arg-like motifs. The 2.6 A crystal structure of the decanoyl-Arg-Val-Lys-Arg-chloromethylketone (dec-RVKR-cmk)-inhibited mouse furin ectodomain, the first PC structure, reveals an eight-stranded jelly-roll P domain associated with the catalytic domain. Contoured surface loops shape the active site by cleft, thus explaining furin's stringent requirement for arginine at P1 and P4, and lysine at P2 sites by highly charge-complementary pockets. The structure also explains furin's preference for basic residues at P3, P5 and P6 sites. This structure will aid in the rational design of antiviral and antibacterial drugs.}, author = {Henrich, Stefan and Cameron, Angus and Bourenkov, Gleb P and Kiefersauer, Reiner and Huber, Robert and Lindberg, Iris and Bode, Wolfram and Than, Manuel E}, doi = {10.1038/nsb941}, issn = {1072-8368}, journal = {Nature structural biology}, month = {jul}, number = {7}, pages = {520--6}, pmid = {12794637}, title = {{The crystal structure of the proprotein processing proteinase furin explains its stringent specificity.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12794637}, volume = {10}, year = {2003} } @article{Cesaratto2015, abstract = {Tobacco etch virus protease (TEVp) is a unique endopeptidase with stringent substrate specificity. TEVp has been widely used as a purified protein for in vitro applications, but also as a biological tool directly expressing it in living cells. To adapt the protease to diverse applications, several TEVp mutants with different stability and enzymatic properties have been reported. Herein we describe the development of a novel engineered TEVp mutant designed to be active in the secretory pathway. While wild type TEVp targeted to the secretory pathway of mammalian cells is synthetized as an N-glycosylated and catalytically inactive enzyme, a TEVp mutant with selected mutations at two verified N-glycosylation sites and at an exposed cysteine was highly efficient. This mutant was very active in the endoplasmic reticulum (ER) of living cells and can be used as a biotechnological tool to cleave proteins within the secretory pathway. As an immediate practical application we report the expression of a complete functional monoclonal antibody expressed from a single polypeptide, which was cleaved by our TEVp mutant into the two antibody chains and secreted as an assembled and functional molecule. In addition, we show active TEVp mutants lacking auto-cleavage activity.}, author = {Cesaratto, Francesca and L{\'{o}}pez-Requena, Alejandro and Burrone, Oscar R and Petris, Gianluca}, doi = {10.1016/j.jbiotec.2015.08.026}, issn = {1873-4863}, journal = {Journal of biotechnology}, keywords = {ER,ERAD,Glycosylation,Sec-TEV,Secretory pathway,TEV protease}, month = {oct}, pages = {159--66}, pmid = {26327323}, title = {{Engineered tobacco etch virus (TEV) protease active in the secretory pathway of mammalian cells.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26327323}, volume = {212}, year = {2015} } @article{Munro1987, abstract = {Proteins that permanently reside in the lumen of the endoplasmic reticulum (ER) must somehow be distinguished from newly synthesized secretory proteins, which pass through this compartment on their way out of the cell. Three luminal ER proteins whose sequence is known, grp78 ("BiP"), grp94, and protein disulphide isomerase, share the carboxy-terminal sequence Lys-Asp-Glu-Leu (KDEL). We show that deletion (or extension) of the carboxyl terminus of grp78 results in secretion of this protein when it is expressed in COS cells. Conversely, a derivative of chicken lysozyme containing the last six amino acids of grp78 fails to be secreted and instead accumulates in the ER. We propose that the KDEL sequence marks proteins that are to be retained in the ER and discuss possible retention mechanisms.}, author = {Munro, S and Pelham, H R}, issn = {0092-8674}, journal = {Cell}, month = {mar}, number = {5}, pages = {899--907}, pmid = {3545499}, title = {{A C-terminal signal prevents secretion of luminal ER proteins.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/3545499}, volume = {48}, year = {1987} } @article{Jackson1990, abstract = {Several families of transmembrane endoplasmic reticulum (ER) proteins contain retention motifs in their cytoplasmically exposed tails. Mutational analyses demonstrated that two lysines positioned three and four or five residues from the C-terminus represent the retention motif. The introduction of a lysine preceding the lysine that occurs three residues from the terminus of Lyt2 renders this cell surface protein a resident of the ER. Likewise, the appropriate positioning of two lysine residues in a poly-serine sequence confines marker proteins to the ER. Arginines or histidines cannot replace lysines, suggesting that simple charge interactions are not sufficient to explain the retention. The identified consensus motif may serve as a retrieval signal that brings proteins back from a sorting compartment adjacent to the ER.}, author = {Jackson, M R and Nilsson, T and Peterson, P A}, issn = {0261-4189}, journal = {The EMBO journal}, month = {oct}, number = {10}, pages = {3153--62}, pmid = {2120038}, publisher = {European Molecular Biology Organization}, title = {{Identification of a consensus motif for retention of transmembrane proteins in the endoplasmic reticulum}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/2120038 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC552044}, volume = {9}, year = {1990} } @article{Stornaiuolo2003, abstract = {Many endoplasmic reticulum (ER) proteins maintain their residence by dynamic retrieval from downstream compartments of the secretory pathway. In previous work we compared the retrieval process mediated by the two signals, KKMP and KDEL, by appending them to the same neutral reporter protein, CD8, and found that the two signals determine a different steady-state localization of the reporter. CD8-K (the KDEL-bearing form) was restricted mainly to the ER, whereas CD8-E19 (the KKMP-bearing form) was distributed also to the intermediate compartment and Golgi complex. To investigate whether this different steady-state distribution reflects a difference in exit rates from the ER and/or in retrieval, we have now followed the first steps of export of the two constructs from the ER and their trafficking between ER and Golgi complex. Contrary to expectation, we find that CD8-K is efficiently recruited into transport vesicles, whereas CD8-E19 is not. Thus, the more restricted ER localization of CD8-K must be explained by a more efficient retrieval to the ER. Moreover, because most of ER resident CD8-K is not O-glycosylated but almost all CD8-E19 is, the results suggest that CD8-K is retrieved from the intermediate compartment, before reaching the Golgi, where O-glycosylation begins. These results illustrate how different retrieval signals determine different trafficking patterns and pose novel questions on the underlying molecular mechanisms.}, author = {Stornaiuolo, Mariano and Lotti, Lavinia V and Borgese, Nica and Torrisi, Maria-Rosaria and Mottola, Giovanna and Martire, Gianluca and Bonatti, Stefano}, doi = {10.1091/mbc.E02-08-0468}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Stornaiuolo et al. - 2003 - KDEL and KKXX retrieval signals appended to the same reporter protein determine different trafficking betwee.pdf:pdf}, issn = {1059-1524}, journal = {Molecular biology of the cell}, month = {mar}, number = {3}, pages = {889--902}, pmid = {12631711}, publisher = {American Society for Cell Biology}, title = {{KDEL and KKXX retrieval signals appended to the same reporter protein determine different trafficking between endoplasmic reticulum, intermediate compartment, and Golgi complex}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/12631711 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC151567}, volume = {14}, year = {2003} } @article{Chen2013, abstract = {Optical control of protein interactions has emerged as a powerful experimental paradigm for manipulating and studying various cellular processes. Tools are now available for controlling a number of cellular functions, but some fundamental processes, such as protein secretion, have been difficult to engineer using current optical tools. Here we use UVR8, a plant photoreceptor protein that forms photolabile homodimers, to engineer the first light-triggered protein secretion system. UVR8 fusion proteins were conditionally sequestered in the endoplasmic reticulum, and a brief pulse of light triggered robust forward trafficking through the secretory pathway to the plasma membrane. UVR8 was not responsive to excitation light used to image cyan, green, or red fluorescent protein variants, allowing multicolor visualization of cellular markers and secreted protein cargo as it traverses the cellular secretory pathway. We implemented this novel tool in neurons to demonstrate restricted, local trafficking of secretory cargo near dendritic branch points.}, author = {Chen, Daniel and Gibson, Emily S and Kennedy, Matthew J}, doi = {10.1083/jcb.201210119}, issn = {1540-8140}, journal = {The Journal of cell biology}, month = {may}, number = {4}, pages = {631--40}, pmid = {23671313}, title = {{A light-triggered protein secretion system}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23671313 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3653365}, volume = {201}, year = {2013} } @article{Adams2005, abstract = {SUMMARY The genomes of plant viruses in the family Potyviridae encode large polyproteins that are cut by virus-encoded proteases into ten mature proteins. Three different types of protease have been identified, each of which cuts at sites with a distinctive sequence pattern. The experimental evidence for this specificity is reviewed and the cleavage site patterns are compiled for all sequenced species within the family. Seven of the nine cleavage sites in each species are cut by the viral NIa-Pro and patterns around these sites are related where possible to the active site-substrate interactions recently deduced following the resolution of the crystal structure of Tobacco etch virus (TEV) NIa-Pro (Phan et al., 2002. J. Biol. Chem. 277, 50564-50572). In particular, a revised series of cleavage sites for Sweet potato mild mottle virus (genus Ipomovirus) is proposed with a conserved His at the P1 position. This is supported by homology modelling studies using the TEV structure as a template. The data also provide a standard to correct the annotation of some other published sequences and to help predict these sites in further virus sequences as they become available. Comprehensive data for all sequences of each virus in the family, together with some summaries, have been made available at http://www.rothamsted.bbsrc.ac.uk/ppi/links/pplinks/potycleavage/index.html.}, author = {Adams, Michael J and Antoniw, John F and Beaudoin, Frederic}, doi = {10.1111/j.1364-3703.2005.00296.x}, issn = {1364-3703}, journal = {Molecular plant pathology}, month = {jul}, number = {4}, pages = {471--87}, pmid = {20565672}, title = {{Overview and analysis of the polyprotein cleavage sites in the family Potyviridae.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20565672}, volume = {6}, year = {2005} } @article{Adams2005a, abstract = {SUMMARY The genomes of plant viruses in the family Potyviridae encode large polyproteins that are cut by virus-encoded proteases into ten mature proteins. Three different types of protease have been identified, each of which cuts at sites with a distinctive sequence pattern. The experimental evidence for this specificity is reviewed and the cleavage site patterns are compiled for all sequenced species within the family. Seven of the nine cleavage sites in each species are cut by the viral NIa-Pro and patterns around these sites are related where possible to the active site-substrate interactions recently deduced following the resolution of the crystal structure of Tobacco etch virus (TEV) NIa-Pro (Phan et al., 2002. J. Biol. Chem. 277, 50564-50572). In particular, a revised series of cleavage sites for Sweet potato mild mottle virus (genus Ipomovirus) is proposed with a conserved His at the P1 position. This is supported by homology modelling studies using the TEV structure as a template. The data also provide a standard to correct the annotation of some other published sequences and to help predict these sites in further virus sequences as they become available. Comprehensive data for all sequences of each virus in the family, together with some summaries, have been made available at http://www.rothamsted.bbsrc.ac.uk/ppi/links/pplinks/potycleavage/index.html.}, author = {Adams, Michael J and Antoniw, John F and Beaudoin, Frederic}, doi = {10.1111/j.1364-3703.2005.00296.x}, issn = {1364-3703}, journal = {Molecular plant pathology}, month = {jul}, number = {4}, pages = {471--87}, pmid = {20565672}, title = {{Overview and analysis of the polyprotein cleavage sites in the family Potyviridae.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20565672}, volume = {6}, year = {2005} } @article{Fernandez-Rodriguez2016, abstract = {Genetic engineering projects often require control over when a protein is degraded. To this end, we use a fusion between a degron and an inactivating peptide that can be added to the N-terminus of a protein. When the corresponding protease is expressed, it cleaves the peptide and the protein is degraded. Three protease:cleavage site pairs from Potyvirus are shown to be orthogonal and active in exposing degrons, releasing inhibitory domains and cleaving polyproteins. This toolbox is applied to the design of genetic circuits as a means to control regulator activity and degradation. First, we demonstrate that a gate can be constructed by constitutively expressing an inactivated repressor and having an input promoter drive the expression of the protease. It is also shown that the proteolytic release of an inhibitory domain can improve the dynamic range of a transcriptional gate (200-fold repression). Next, we design polyproteins containing multiple repressors and show that their cleavage can be used to control multiple outputs. Finally, we demonstrate that the dynamic range of an output can be improved (8-fold to 190-fold) with the addition of a protease-cleaved degron. Thus, controllable proteolysis offers a powerful tool for modulating and expanding the function of synthetic gene circuits.}, author = {Fernandez-Rodriguez, Jesus and Voigt, Christopher A}, doi = {10.1093/nar/gkw537}, issn = {1362-4962}, journal = {Nucleic acids research}, month = {jul}, number = {13}, pages = {6493--502}, pmid = {27298256}, title = {{Post-translational control of genetic circuits using Potyvirus proteases.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/27298256}, volume = {44}, year = {2016} } @article{Garcia1991, abstract = {Plasmids encoding chimeric NIa-type proteases made of sequences from the polyviruses plum pox virus (PPV) and tobacco etch virus (TEV) have been constructed. Their proteolytic activity on the large nuclear inclusion protein (NIa)-capsid protein (CP) junction of each virus was assayed in Escherichia coli cells. The amino half of the protease seemed to be involved neither in the enzymatic catalysis nor in substrate recognition. In spite of the large homology among the PPV and TEV NIa-type proteases, the exchange of fragments from the carboxyl halves of the molecules usually caused a drastic decrease in the enzymatic activity. Inactive chimeric proteases did not interfere with cleavage by PPV wild type protease expressed from a second plasmid. The results suggest that the recognition and catalytic sites of the NIa proteases are closely interlinked and, although residues relevant for the correct interaction with the substrate could be present in other parts of the protein, a main determinant for substrate specificity should lie in a region situated, approximately, between positions 30 and 90 from the carboxyl end. This region includes the conserved His at position 360 of PPV or 355 of TEV, which has been postulated to interact with the Gin at position −1 of the cleavage sites.}, author = {Garcia, Juan Antonio and Lain, Sonia}, doi = {10.1016/0014-5793(91)80360-F}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Garcia, Lain - 1991 - Proteolytic activity of plum pox virus—tobacco etch virus chimeric NIa proteases.pdf:pdf}, issn = {00145793}, journal = {FEBS Letters}, number = {1}, pages = {67--72}, publisher = {No longer published by Elsevier}, title = {{Proteolytic activity of plum pox virus—tobacco etch virus chimeric NIa proteases}}, volume = {281}, year = {1991} } @article{Gulya2002, abstract = {ABSTRACT Sunflower mosaic is caused by a putative member of the family Potyviridae. Sunflower mosaic virus (SuMV) was characterized in terms of host range, physical and biological characteristics, and partial nucleotide and amino acid sequence. Cells infected with SuMV had cytoplasmic inclusion bodies typical of potyviruses. Of 74 genera tested, only species in Helianthus, Sanvitalia, and Zinnia, all Asteraceae, were systemic hosts. Commercial sunflower hybrids from the United States, Europe, and South Africa were all equally susceptible. The mean length of purified particles is approximately 723 nm. The virus was transmitted by Myzus persicae and Capitphorus elaegni, and also was seedborne in at least one sunflower cultivar. Indirect enzyme-linked immunosorbent assay tests with a broad-spectrum potyvirus monoclonal antibody were strongly positive. SuMV-specific polyclonal antisera recognized SuMV and, to a lesser extent, Tobacco etch virus (TEV). When tested against a panel of 31 potyvirus-differentiating monoclonal antibodies, SuMV was distinct from any potyvirus previously tested. SuMV shared four epitopes with TEV, but had a reaction profile more similar to Tulip breaking virus (TBV). SuMV did not possess epitopes unique only to TBV. The predicted coat protein had a molecular weight of 30.5 kDa. The 3' end of the virus genome was cloned and sequenced. Phylogenetic analysis of the coat protein amino acid sequence revealed that SuMV is a distinct species within the family Potyviridae, most closely related to TEV.}, author = {Gulya, T J and Shiel, P J and Freeman, T and Jordan, R L and Isakeit, T and Berger, P H}, doi = {10.1094/PHYTO.2002.92.7.694}, issn = {0031-949X}, journal = {Phytopathology}, month = {jul}, number = {7}, pages = {694--702}, pmid = {18943264}, title = {{Host Range and Characterization of Sunflower mosaic virus.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18943264}, volume = {92}, year = {2002} } @article{Seo2016, author = {Seo, Jang-Kyun and Choi, Hong-Soo and Kim, Kook-Hyung}, doi = {10.1038/srep22436}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Seo et al. - 2016 - Engineering of soybean mosaic virus as a versatile tool for studying protein–protein interactions in soybean.pdf:pdf}, issn = {2045-2322}, journal = {Scientific Reports}, month = {feb}, pages = {22436}, publisher = {Nature Publishing Group}, title = {{Engineering of soybean mosaic virus as a versatile tool for studying protein–protein interactions in soybean}}, url = {http://www.nature.com/articles/srep22436}, volume = {6}, year = {2016} } @article{Yoon2000, abstract = {Tobacco vein mottling virus (TVMV) belongs to the potyviridae that consists of about 200 plant viruses. Potyviruses have RNA genomes of approximately 10,000 bases from which a single polyprotein is expressed from each virus upon infection. The NIa proteinase is known to process the polyprotein at seven distinct junctions between proteins. Kinetic constants were determined for the reactions of the recombinant TVMV NIa protease (27 kDa) with synthetic oligopeptides containing the sequences for the cleavage sites. For optimum activity, the substrate needs to have six amino acids (P6-P1) in the amino region and four (P1'-P4') in the carboxy region, including four conserved amino acids (V-R-F-Q) in P4-P1 positions. Mutation of any of four conserved amino acids to Gly made the substrate inert to the enzyme. Among the substrates, the oligopeptides containing the sequences for junctions, P3-6K1, NIa (VPg-Pro), and NIa-NIb were not processed by the NIa protease. Those junctions have Glu at P3, Glu at P1, and Thr at P2. The implications of high substrate specificity and size dependence in polyprotein processing and viral replication are discussed.}, author = {Yoon, H Y and Hwang, D C and Choi, K Y and Song, B D}, issn = {1016-8478}, journal = {Molecules and cells}, month = {apr}, number = {2}, pages = {213--9}, pmid = {10850664}, title = {{Proteolytic processing of oligopeptides containing the target sequences by the recombinant tobacco vein mottling virus NIa proteinase.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10850664}, volume = {10}, year = {2000} } @article{Zheng2008, abstract = {Site-specific proteases are the most popular kind of enzymes for removing the fusion tags from fused target proteins. Nuclear inclusion protein a (NIa) proteases obtained from the family Potyviridae have become promising due to their high activities and stringencies of sequences recognition. NIa proteases from tobacco etch virus (TEV) and tomato vein mottling virus (TVMV) have been shown to process recombinant proteins successfully in vitro. In this report, recombinant PPV (plum pox virus) NIa protease was employed to process fusion proteins with artificial cleavage site in vitro. Characteristics such as catalytic ability and affecting factors (salt, temperature, protease inhibitors, detergents, and denaturing reagents) were investigated. Recombinant PPV NIa protease expressed and purified from Escherichia coli demonstrated efficient and specific processing of recombinant GFP and SARS-CoV nucleocapsid protein, with site F (N V V V H Q black triangle down A) for PPV NIa protease artificially inserted between the fusion tags and the target proteins. Its catalytic capability is similar to those of TVMV and TEV NIa protease. Recombinant PPV NIa protease reached its maximal proteolytic activity at approximately 30 degrees C. Salt concentration and only one of the tested protease inhibitors had minor influences on the proteolytic activity of PPV NIa protease. Recombinant PPV NIa protease was resistant to self-lysis for at least five days.}, author = {Zheng, Nuoyan and P{\'{e}}rez, Jos{\'{e}} de Jes{\'{u}}s and Zhang, Zhonghui and Dom{\'{\i}}nguez, Elvira and Garcia, Juan Antonio and Xie, Qi}, doi = {10.1016/j.pep.2007.10.008}, issn = {1046-5928}, journal = {Protein expression and purification}, month = {feb}, number = {2}, pages = {153--62}, pmid = {18024078}, title = {{Specific and efficient cleavage of fusion proteins by recombinant plum pox virus NIa protease.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18024078}, volume = {57}, year = {2008} } @article{, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Unknown - Unknown - Plum pox potyvirus.pdf:pdf}, title = {{Plum pox potyvirus}} } @article{Oakley1998, author = {Oakley, Martha G and Kim, Peter S}, journal = {Biochemistry}, number = {36}, pages = {12603--12610}, publisher = {ACS Publications}, title = {{A buried polar interaction can direct the relative orientation of helices in a coiled coil}}, volume = {37}, year = {1998} } @article{Woolfson2005, abstract = {Protein design allows sequence-to-structure relationships in proteins to be examined and, potentially, new protein structures and functions to be made to order. To succeed, however, the protein-design process requires reliable rules that link protein sequence to structure⧸function. Although our present understanding of coiled-coil folding and assembly is not complete, through numerous bioinformatics and experimental studies there are now sufficient rules to allow confident design attempts of naturally observed and even novel coiled-coil motifs. This review summarizes the current design rules for coiled coils, and describes some of the key successful coiled-coil designs that have been created to date. The designs range from those for relatively straightforward, naturally observed structures—including parallel and antiparallel dimers, trimers and tetramers, all of which have been made as homomers and heteromers—to more exotic structures that expand the repertoire of Nature's coiled-coil structures. Examples in the second bracket include a probe that binds a cancer-associated coiled-coil protein; a tetramer with a right-handed supercoil; sticky-ended coiled coils that self-assemble to form fibers; coiled coils that switch conformational state; a three-component two-stranded coiled coil; and an antiparallel dimer that directs fragment complementation of larger proteins. Some of the more recent examples show an important development in the field; namely, new designs are being created with function as well as structure in mind. This will remain one of the key challenges in coiled-coil design in the next few years. Other challenges that lie ahead include the need to discover more rules for coiled-coil prediction and design, and to implement these in prediction and design algorithms. The considerable success of coiled-coil design so far bodes well for this, however. It is likely that these challenges will be met and surpassed.}, author = {Woolfson, Derek N.}, doi = {S0065323305700048 [pii] 10.1016/S0065-3233(05)70004-8}, edition = {2005/04/20}, editor = {and John M. Squire {David A. D. Parry}}, isbn = {0065-3233 (Print) 0065-3233 (Linking)}, journal = {Adv Protein Chem}, pages = {79--112}, pmid = {15837514}, publisher = {Academic Press}, series = {Fibrous Proteins: Coiled-Coils, Collagen and Elastomers}, title = {{The Design of Coiled-Coil Structures and Assemblies}}, volume = {70}, year = {2005} } @book{mollerpocket, title={Pocket atlas of cross sectional anatomy: computed tomography and magnetic resonance imaging. Vol. 1., Head, neck, spine and joints}, author={M{\"o}ller, Torsten B and Reif, Emil}, publisher={Thieme} } @article{sprawls1989ultrasound, title={Ultrasound Production and Interactions}, author={Sprawls, Perry}, journal={Ultrasound Production and Interactions Web site}, year={1989} } @article{Stein2014, abstract = {The bottom-up design of protein-based signaling networks is a key goal of synthetic biology; yet, it remains elusive due to our inability to tailor-make signal transducers and receptors that can be readily compiled into defined signaling networks. Here, we report a generic approach for the construction of protein-based molecular switches based on artficially autoinhibited proteases. Using structure-guided design and directed protein evolution, we created signal transducers based on artificially autoinhibited proteases that can be activated following site-specific proteolysis and also demonstrate the modular design of an allosterically regulated protease receptor following recombination with an affinity clamp peptide receptor. Notably, the receptor's mode of action can be varied from >5-fold switch-OFF to >30-fold switch-ON solely by changing the length of the connecting linkers, demonstrating a high functional plasticity not previously observed in naturally occurring receptor systems. We also create an integrated signaling circuit based on two orthogonal autoinhibited protease units that can propagate and amplify molecular queues generated by the protease receptor. Finally, we present a generic two-component receptor architecture based on proximity-based activation of two autoinhibited proteases. Overall, the approach allows the design of protease-based signaling networks that, in principle, can be connected to any biological process.}, author = {Stein, Viktor and Alexandrov, Kirill}, doi = {10.1073/pnas.1405220111}, file = {:C$\backslash$:/Users/Frank/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Stein, Alexandrov - 2014 - Protease-based synthetic sensing and signal amplification.pdf:pdf}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {proteases,protein engineering,protein switches,synthetic biology}, month = {nov}, number = {45}, pages = {15934--9}, pmid = {25355910}, publisher = {National Academy of Sciences}, title = {{Protease-based synthetic sensing and signal amplification}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25355910 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4234609}, volume = {111}, year = {2014} }