Week 4: June 8 2016

Wednesday, 6/8
Members Present: Kat, Hamed, Alex, Cathy, Dk, Tam
- Prepared LB broth to be autoclaved.
- Autoclaved LB.
- Prepared SOC to be autoclaved.
For the next day:
- Autoclave SOC
- Obtain DH10b from Kevin
- Redesign parts to make them IDT-compatible
Purchase label maker
Label everything in the lab
Purchase stationery - sharpies, pens, whiteboard markers, baskets to organise these in drawers
Label MSDS files alphabetically
Ask Susie for ethanol burner for WB403
Gmail correspondence:
- Contact GE Health Life Sciences with regards to legitimacy of Heparin columns and syringe.
I-Tasser Updates:
Job ID: S277386 - GolS flag tag
wt GolS binding pocket.PNG
Highlighted region (yellow) is predicted to be the metal chelation site.
Flag-tag GolS binding pocket.PNG
There is a change in terms of the shape however, the size of the pocket maintains to approximately the same size however, it is quite uncertain whether this similar size pocket would perform with similar affinity compared to the wt GolS. One reason why the pocket could maintain its size compared to His-tag could be due to HIstadine presence in the His-tag that causes the helix formation.
Flag-tag appears to show no change in the metal ion binding pocket size. However it is uncertain as to whether it still retains a high level of affinity for Au ions or other ions. Given the residues are retained, GolS Flag-tag may not change its metal ion binding affinity.
Possibilities with 3D Printing of Proteins:
GolS and its variants can be 3D-printed for better visualization and depiction. Using PyMol, MeshLab and Makerbot Desktop to allow for 3D printing of our proteins. This allows for a better visualization of the protein.
Currently, attempts to convert proteins .pdb file to .x3g (3D printer friendly file).
Concerns for HiTrap Heparin Column:
GE Health Life Sciences provides general protocols for HiTrap Heparin Column usage with syringe. The HiTrap Heparin provider also includes instruction for other procedures.
HiTrap Heparin Column Usage Instruction.pdf
Notes from meeting with Professor Vladimiros Papangelakis:
Rare earth metals exist in very dilute amounts - 50 to 300 ppm
High demand in industries (cellphones, etc) and high intensity magnets for electronic devices, space exploration, hybrid cars, basically high intensity magnetic field for a small compact instrument
Biosensor not useful for commodity metals
Useful application for rare earth metals
Toxic - cyanide high selectivity to bind with gold and form ionic entities that are highly soluble; mix gold with NaCN and blow air + agitate to solubilise gold
To avoid unwanted toxicity - alkaline pH (~9) to prevent formation of gaseous HCN which is volatile, use NaOH or limestone, then contain CN in liquid phase and alkaline for maximum safety
Once gold is extracted, remaining cyanide decomposes under UV (solar) radiation and naturally occuring bacteria chew on cyanide to form CO2 and ammonia
Chemical destruction by strong oxidants or mixture of sulphur dioxide and oxygen (industrial)
Less efficient than cyanide method - chloride ion + air (always need an oxidant) and a ligand (CN- the best, Cl- 2nd best), more effective at high temperature but no guarantee that it will take out ALL the gold
Gold chloride + HCl and stays soluble as long as there are no organics otherwise it will decompose because gold likes to exist in metallic form, not ionic form
Slow leaching makes bigger gold NPs
Keep ionic metal solutions at slightly acidic conditions or highly alkaline conditions - U shaped solubility curve vs pH
Working with synthetic solutions is fine, but real world applications?
Gold prospector needs to leach out the metal from the soil in order for the sensor to work as intended (Part 2, Part 1 is proof of concept of paper working) Cd, Hg, Arsenic, Selenium are toxic
Heavy rare earths are the useful ones >18 atomic number; they all have extremely similar chemical properties, important if we can discover proteins that are sensitive and selective to rare earth metals
Check concept: test on standard rare earth element (lanthanum) which is cheap too
If it works on lanthanum, it would work in general. then we can test against other rare earth chlorides (better because soluble in mildly acidic conditions)
He can give us some lanthanum
Gold exists in 1 and 3 valence, in nature they exist in 3, other rare earths only exist in 3
Maybe achieve selectivity at a different valence state?
He's very encouraging :)
Is okay with contacting him for further info, help with solution preparation