Difference between revisions of "Team:SVCE CHENNAI/Description"

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</div>
 
</div>
 
</div>
 
</div>
 +
 
<div class="row">
 
<div class="row">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
−
<h2>Part Enhancement 1 : tsPurple chromoprotein</h2>
+
<h2>Part Enhancement 2 : cjBlue,green chromoprotein</h2>
 
</div>
 
</div>
 
</div>
 
</div>
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<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
 
<p>
 
<p>
−
Insilico analysis was done to construct a 3D model for this part. The sequence for this part was obtained from the iGEM registry and submitted to SWISS MODEL . The protein with the highest sequence similarity was found to be FAR-RED FLUORESCENT PROTEIN AQ143. The secondary structure of this protein was used to construct a 3D model for tsPurple. The predicted 3D structure was a homotetramer. Each monomer subunit had a β barrel with a central α helix.
+
Similar insilico analysis to tsPurple was done for this part. The sequence for this part was obtained from the iGEM registry and submitted to SWISS MODEL . The protein with the highest sequence similarity was found to be template 2ib5.1.A, which is also a chromoprotein. The secondary structure of this protein was used to construct a 3D model for cjBlue. The predicted 3D structure was a homooctamer. Each monomer subunit had a ? barrel with a central ? helix.
−
</p>
+
To determine if the predicted model was authentic, we generated the Ramachandran Plot for this model by using the SWISS MODEL Workspace. A score of 94% in the most favoured regions as was seen in the Ramachandran plot showed that the  predicted model of cjBlue chromoprotein is a very good prediction.
−
</div>
+
−
</div>
+
−
<div class="row">
+
−
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
+
−
<p>
+
−
To determine if the predicted model was authentic, we generated the Ramachandran Plot for this model by using the SWISS MODEL Workspace. A score of 93.3% in the most favoured regions as was seen in the Ramachandran plot showed that the  predicted model of Tinsel Purple chromoprotein is a very good prediction.
+
−
</p>
+
−
</div>
+
−
</div>
+
−
<div class="row">
+
−
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
+
−
<p>
+
−
To find further information on this protein we used ExPASy - ProtParam tool to compute the various physical and chemical parameters for tsPurple. The computed parameters included the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY).
+
−
</p>
+
−
</div>
+
−
</div>
+
−
<div class="row">
+
−
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
+
−
<p>
+
−
And finally, it would be a shame if you created a wonderful construct with this part, but then this protein was cleaved by an enzyme produced by your chassis organism, now wouldn't it?
+
−
To tackle this problem we created a database of all the enzymes that would cleave this chromoprotein, the number and position of the cleavage sites using ExPASy Peptide Cutter.
+
 
</p>
 
</p>
 
</div>
 
</div>
Line 61: Line 41:
 
<div class="row">
 
<div class="row">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12 imagecenter">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12 imagecenter">
−
<img src="https://static.igem.org/mediawiki/2016/6/62/T--SVCE_CHENNAI--Ts2.gif" width="40%">
+
<img src="https://static.igem.org/mediawiki/2016/3/3a/T--SVCE_CHENNAI--Cjblueswiss.gif ">
 
</div>
 
</div>
 
</div>
 
</div>
  
 
<!-- -->
 
<!-- -->
−
<strong>Cartoon representation of tsPurple.</strong>
+
<strong>Cartoon representation of cjBlue.</strong>
 
<div class="row">
 
<div class="row">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12 imagecenter">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12 imagecenter">
−
<img src="https://static.igem.org/mediawiki/2016/7/7f/T--SVCE_CHENNAI--Ts_purple_swiss.png" width="60%">
+
<img src="https://static.igem.org/mediawiki/2016/4/4d/T--SVCE_CHENNAI--Cj_blue_swiss.png ">
 
</div>
 
</div>
 
</div>
 
</div>
−
 
 
<div class="row">
 
<div class="row">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
Line 79: Line 58:
 
<div>
 
<div>
 
<!-- -->
 
<!-- -->
−
<br>Number of amino acids: 228
+
<br>Number of amino acids: 232
−
<br>Molecular weight: 25546.26
+
<br>Molecular weight: 26173.80
−
<br>Theoretical pI: 6.65
+
<br>Theoretical pI: 7.53
−
<br>Total number of negatively charged residues (Asp + Glu): 27
+
<br>Total number of negatively charged residues (Asp + Glu): 24
−
<br>Total number of positively charged residues (Arg + Lys): 26
+
<br>Total number of positively charged residues (Arg + Lys): 25
  
  
Line 89: Line 68:
 
<br><strong>Atomic composition:</strong>
 
<br><strong>Atomic composition:</strong>
  
−
<br>Carbon          (C)       - 1134
+
<br>Carbon          (C)       - 1151
−
<br>Hydrogen        (H)       - 1747
+
<br>Hydrogen        (H)       - 1776
−
<br>Nitrogen        (N)         - 303
+
<br>Nitrogen        (N)       - 314
−
<br>Oxygen          (O)         - 334
+
<br>Oxygen          (O)       - 347
−
<br>Sulfur          (S)         - 18
+
<br>Sulfur          (S)       - 19
  
  
 
<!-- -->
 
<!-- -->
−
<br>Formula: C<sub>1134</sub>H<sub>1747</sub>N<sub>303</sub>O<sub>334</sub>S<sub>18</sub>
+
<br>Formula: C<sub>1151</sub>H<sub>1776</sub>N<sub>314</sub>O<sub>347</sub>S<sub>19</sub>
−
<br>Total number of atoms: 3536
+
<br>Total number of atoms: 3607
  
  
Line 106: Line 85:
 
<br>Extinction coefficients are in units of  M<sup>-1</sup> cm<sup>-1</sup>, at 280 nm measured in water.
 
<br>Extinction coefficients are in units of  M<sup>-1</sup> cm<sup>-1</sup>, at 280 nm measured in water.
  
−
<br>Ext. coefficient :  24910
+
<br>Ext. coefficient :  28015
−
<br>Abs 0.1% (=1 g/l):  0.975, assuming all pairs of Cys residues form cystines
+
<br>Abs 0.1% (=1 g/l):  1.070, assuming all pairs of Cys residues form cystines
  
−
<br>Ext. coefficient :  24410
+
<br>Ext. coefficient :  27390
−
<br>Abs 0.1% (=1 g/l):  0.956, assuming all Cys residues are reduced
+
<br>Abs 0.1% (=1 g/l):  1.046, assuming all Cys residues are reduced
  
  
Line 126: Line 105:
 
<!-- -->
 
<!-- -->
 
<br><strong>Instability index:</strong>
 
<br><strong>Instability index:</strong>
−
 
+
<br>The instability index (II) is computed to be 29.86.
−
<br>The instability index (II) is computed to be 31.19
+
 
<br>This classifies the protein as stable.
 
<br>This classifies the protein as stable.
  
  
  
−
<br>Aliphatic index: 61.97
+
<br>Aliphatic index: 58.84
  
−
<br>Grand average of hydropathicity (GRAVY): -0.395
+
<br>Grand average of hydropathicity (GRAVY): -0.558
 
</div>
 
</div>
−
           
+
 
  
  
 
<div class="col-xs-12 col-sm-12 col-md-6 col-lg-6">
 
<div class="col-xs-12 col-sm-12 col-md-6 col-lg-6">
 
<p class="parajustify">
 
<p class="parajustify">
−
Interested in knowing about this protein? <a href="http://parts.igem.org/Part:BBa_K1033906"> click here.</a>  
+
<br>Interested in knowing about this protein? <a href="http://parts.igem.org/Part:BBa_K592011 "> click here.</a>  
 
</p>
 
</p>
 +
</div>
 
</div>
 
</div>
 
<div class="row">
 
<div class="row">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
−
<h2>Part Enhancement 2 : cjBlue,green chromoprotein</h2>
+
<h2>Part Enhancement 3 : RNA thermometer (ROSE)</h2>
 
</div>
 
</div>
 
</div>
 
</div>
Line 153: Line 132:
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
 
<p>
 
<p>
−
Similar insilico analysis to tsPurple was done for this part. The sequence for this part was obtained from the iGEM registry and submitted to SWISS MODEL . The protein with the highest sequence similarity was found to be template 2ib5.1.A, which is also a chromoprotein. The secondary structure of this protein was used to construct a 3D model for cjBlue. The predicted 3D structure was a homooctamer. Each monomer subunit had a ? barrel with a central ? helix.
+
We used SimRNAweb which is a web server for RNA 3D structure modeling to create a model for the RNA thermometer.
−
To determine if the predicted model was authentic, we generated the Ramachandran Plot for this model by using the SWISS MODEL Workspace. A score of 94% in the most favoured regions as was seen in the Ramachandran plot showed that the  predicted model of cjBlue chromoprotein is a very good prediction.
+
 
</p>
 
</p>
 
</div>
 
</div>
Line 164: Line 142:
 
<div class="row">
 
<div class="row">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12 imagecenter">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12 imagecenter">
−
<img src="https://static.igem.org/mediawiki/2016/3/3a/T--SVCE_CHENNAI--Cjblueswiss.gif ">
+
<img src="https://static.igem.org/mediawiki/2016/6/64/T--SVCE_CHENNAI--RNAtfinal6.gif">
 +
</div>
 +
</div>
 +
<div class="col-xs-12 col-sm-12 col-md-6 col-lg-6">
 +
<p class="parajustify">
 +
<br>Interested in seeing the secondary structure of this model? <a href="http://parts.igem.org/Part:BBa_K115001"> Click here.</a>
 +
</p>
 +
</div>
 +
<div class="row">
 +
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
 +
<h2>Part Enhancement 1 : tsPurple chromoprotein</h2>
 +
</div>
 +
</div>
 +
<hr class="mainline">
 +
<div class="row">
 +
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
 +
<p>
 +
Insilico analysis was done to construct a 3D model for this part. The sequence for this part was obtained from the iGEM registry and submitted to SWISS MODEL . The protein with the highest sequence similarity was found to be FAR-RED FLUORESCENT PROTEIN AQ143. The secondary structure of this protein was used to construct a 3D model for tsPurple. The predicted 3D structure was a homotetramer. Each monomer subunit had a β barrel with a central α helix.
 +
</p>
 +
</div>
 +
</div>
 +
<div class="row">
 +
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
 +
<p>
 +
To determine if the predicted model was authentic, we generated the Ramachandran Plot for this model by using the SWISS MODEL Workspace. A score of 93.3% in the most favoured regions as was seen in the Ramachandran plot showed that the  predicted model of Tinsel Purple chromoprotein is a very good prediction.
 +
</p>
 +
</div>
 +
</div>
 +
<div class="row">
 +
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
 +
<p>
 +
To find further information on this protein we used ExPASy - ProtParam tool to compute the various physical and chemical parameters for tsPurple. The computed parameters included the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY).
 +
</p>
 +
</div>
 +
</div>
 +
<div class="row">
 +
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
 +
<p>
 +
And finally, it would be a shame if you created a wonderful construct with this part, but then this protein was cleaved by an enzyme produced by your chassis organism, now wouldn't it?
 +
To tackle this problem we created a database of all the enzymes that would cleave this chromoprotein, the number and position of the cleavage sites using ExPASy Peptide Cutter.
 +
</p>
 
</div>
 
</div>
 
</div>
 
</div>
 +
  
 
<!-- -->
 
<!-- -->
−
<strong>Cartoon representation of cjBlue.</strong>
+
<strong>The 3D structure</strong>
 
<div class="row">
 
<div class="row">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12 imagecenter">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12 imagecenter">
−
<img src="https://static.igem.org/mediawiki/2016/4/4d/T--SVCE_CHENNAI--Cj_blue_swiss.png ">
+
<img src="https://static.igem.org/mediawiki/2016/6/62/T--SVCE_CHENNAI--Ts2.gif" width="40%">
 
</div>
 
</div>
 
</div>
 
</div>
 +
 +
<!-- -->
 +
<strong>Cartoon representation of tsPurple.</strong>
 +
<div class="row">
 +
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12 imagecenter">
 +
<img src="https://static.igem.org/mediawiki/2016/7/7f/T--SVCE_CHENNAI--Ts_purple_swiss.png" width="60%">
 +
</div>
 +
</div>
 +
 
<div class="row">
 
<div class="row">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
 
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
Line 181: Line 209:
 
<div>
 
<div>
 
<!-- -->
 
<!-- -->
−
<br>Number of amino acids: 232
+
<br>Number of amino acids: 228
−
<br>Molecular weight: 26173.80
+
<br>Molecular weight: 25546.26
−
<br>Theoretical pI: 7.53
+
<br>Theoretical pI: 6.65
−
<br>Total number of negatively charged residues (Asp + Glu): 24
+
<br>Total number of negatively charged residues (Asp + Glu): 27
−
<br>Total number of positively charged residues (Arg + Lys): 25
+
<br>Total number of positively charged residues (Arg + Lys): 26
  
  
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<br><strong>Atomic composition:</strong>
 
<br><strong>Atomic composition:</strong>
  
−
<br>Carbon          (C)       - 1151
+
<br>Carbon          (C)       - 1134
−
<br>Hydrogen        (H)       - 1776
+
<br>Hydrogen        (H)       - 1747
−
<br>Nitrogen        (N)       - 314
+
<br>Nitrogen        (N)         - 303
−
<br>Oxygen          (O)       - 347
+
<br>Oxygen          (O)         - 334
−
<br>Sulfur          (S)       - 19
+
<br>Sulfur          (S)         - 18
  
  
 
<!-- -->
 
<!-- -->
−
<br>Formula: C<sub>1151</sub>H<sub>1776</sub>N<sub>314</sub>O<sub>347</sub>S<sub>19</sub>
+
<br>Formula: C<sub>1134</sub>H<sub>1747</sub>N<sub>303</sub>O<sub>334</sub>S<sub>18</sub>
−
<br>Total number of atoms: 3607
+
<br>Total number of atoms: 3536
  
  
Line 208: Line 236:
 
<br>Extinction coefficients are in units of  M<sup>-1</sup> cm<sup>-1</sup>, at 280 nm measured in water.
 
<br>Extinction coefficients are in units of  M<sup>-1</sup> cm<sup>-1</sup>, at 280 nm measured in water.
  
−
<br>Ext. coefficient :  28015
+
<br>Ext. coefficient :  24910
−
<br>Abs 0.1% (=1 g/l):  1.070, assuming all pairs of Cys residues form cystines
+
<br>Abs 0.1% (=1 g/l):  0.975, assuming all pairs of Cys residues form cystines
  
−
<br>Ext. coefficient :  27390
+
<br>Ext. coefficient :  24410
−
<br>Abs 0.1% (=1 g/l):  1.046, assuming all Cys residues are reduced
+
<br>Abs 0.1% (=1 g/l):  0.956, assuming all Cys residues are reduced
  
  
Line 228: Line 256:
 
<!-- -->
 
<!-- -->
 
<br><strong>Instability index:</strong>
 
<br><strong>Instability index:</strong>
−
<br>The instability index (II) is computed to be 29.86.
+
 
 +
<br>The instability index (II) is computed to be 31.19
 
<br>This classifies the protein as stable.
 
<br>This classifies the protein as stable.
  
  
  
−
<br>Aliphatic index: 58.84
+
<br>Aliphatic index: 61.97
  
−
<br>Grand average of hydropathicity (GRAVY): -0.558
+
<br>Grand average of hydropathicity (GRAVY): -0.395
 
</div>
 
</div>
−
 
−
 
−
 
 
<div class="col-xs-12 col-sm-12 col-md-6 col-lg-6">
 
<div class="col-xs-12 col-sm-12 col-md-6 col-lg-6">
 
<p class="parajustify">
 
<p class="parajustify">
−
<br>Interested in knowing about this protein? <a href="http://parts.igem.org/Part:BBa_K592011 "> click here.</a>
+
Interested in knowing about this protein? <a href="http://parts.igem.org/Part:BBa_K1033906"> click here.</a>  
−
</p>
+
−
</div>
+
−
</div>
+
−
<div class="row">
+
−
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
+
−
<h2>Part Enhancement 3 : RNA thermometer (ROSE)</h2>
+
−
</div>
+
−
</div>
+
−
<hr class="mainline">
+
−
<div class="row">
+
−
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12">
+
−
<p>
+
−
We used SimRNAweb which is a web server for RNA 3D structure modeling to create a model for the RNA thermometer.
+
−
</p>
+
−
</div>
+
−
</div>
+
−
 
+
−
 
+
−
<!-- -->
+
−
<strong>The 3D structure</strong>
+
−
<div class="row">
+
−
<div class="col-xs-12 col-sm-12 col-md-12 col-lg-12 imagecenter">
+
−
<img src="https://static.igem.org/mediawiki/2016/6/64/T--SVCE_CHENNAI--RNAtfinal6.gif">
+
−
</div>
+
−
</div>
+
−
<div class="col-xs-12 col-sm-12 col-md-6 col-lg-6">
+
−
<p class="parajustify">
+
−
<br>Interested in seeing the secondary structure of this model? <a href="http://parts.igem.org/Part:BBa_K115001"> Click here.</a>  
+
 
</p>
 
</p>
 
</div>
 
</div>

Revision as of 07:06, 19 October 2016

Lactoshield - SVCE_CHENNAI Lactoshield - SVCE_CHENNAI

Lactoshield - SVCE_CHENNAI

In-silico Results

In-silico studies play a major part of any biotechnological project.

Part Enhancement 2 : cjBlue,green chromoprotein

Similar insilico analysis to tsPurple was done for this part. The sequence for this part was obtained from the iGEM registry and submitted to SWISS MODEL . The protein with the highest sequence similarity was found to be template 2ib5.1.A, which is also a chromoprotein. The secondary structure of this protein was used to construct a 3D model for cjBlue. The predicted 3D structure was a homooctamer. Each monomer subunit had a ? barrel with a central ? helix. To determine if the predicted model was authentic, we generated the Ramachandran Plot for this model by using the SWISS MODEL Workspace. A score of 94% in the most favoured regions as was seen in the Ramachandran plot showed that the predicted model of cjBlue chromoprotein is a very good prediction.

The 3D structure
Cartoon representation of cjBlue.

Physical and chemical properties


Number of amino acids: 232
Molecular weight: 26173.80
Theoretical pI: 7.53
Total number of negatively charged residues (Asp + Glu): 24
Total number of positively charged residues (Arg + Lys): 25
Atomic composition:
Carbon (C) - 1151
Hydrogen (H) - 1776
Nitrogen (N) - 314
Oxygen (O) - 347
Sulfur (S) - 19
Formula: C1151H1776N314O347S19
Total number of atoms: 3607
Extinction coefficients:
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.
Ext. coefficient : 28015
Abs 0.1% (=1 g/l): 1.070, assuming all pairs of Cys residues form cystines
Ext. coefficient : 27390
Abs 0.1% (=1 g/l): 1.046, assuming all Cys residues are reduced
Estimated half-life:
The N-terminal of the sequence considered is M (Met).
The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro).
>20 hours (yeast, in vivo).
>10 hours (Escherichia coli, in vivo).
Instability index:
The instability index (II) is computed to be 29.86.
This classifies the protein as stable.
Aliphatic index: 58.84
Grand average of hydropathicity (GRAVY): -0.558


Interested in knowing about this protein? click here.

Part Enhancement 3 : RNA thermometer (ROSE)

We used SimRNAweb which is a web server for RNA 3D structure modeling to create a model for the RNA thermometer.

The 3D structure


Interested in seeing the secondary structure of this model? Click here.

Part Enhancement 1 : tsPurple chromoprotein

Insilico analysis was done to construct a 3D model for this part. The sequence for this part was obtained from the iGEM registry and submitted to SWISS MODEL . The protein with the highest sequence similarity was found to be FAR-RED FLUORESCENT PROTEIN AQ143. The secondary structure of this protein was used to construct a 3D model for tsPurple. The predicted 3D structure was a homotetramer. Each monomer subunit had a β barrel with a central α helix.

To determine if the predicted model was authentic, we generated the Ramachandran Plot for this model by using the SWISS MODEL Workspace. A score of 93.3% in the most favoured regions as was seen in the Ramachandran plot showed that the predicted model of Tinsel Purple chromoprotein is a very good prediction.

To find further information on this protein we used ExPASy - ProtParam tool to compute the various physical and chemical parameters for tsPurple. The computed parameters included the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY).

And finally, it would be a shame if you created a wonderful construct with this part, but then this protein was cleaved by an enzyme produced by your chassis organism, now wouldn't it? To tackle this problem we created a database of all the enzymes that would cleave this chromoprotein, the number and position of the cleavage sites using ExPASy Peptide Cutter.

The 3D structure
Cartoon representation of tsPurple.

Physical and chemical properties


Number of amino acids: 228
Molecular weight: 25546.26
Theoretical pI: 6.65
Total number of negatively charged residues (Asp + Glu): 27
Total number of positively charged residues (Arg + Lys): 26
Atomic composition:
Carbon (C) - 1134
Hydrogen (H) - 1747
Nitrogen (N) - 303
Oxygen (O) - 334
Sulfur (S) - 18
Formula: C1134H1747N303O334S18
Total number of atoms: 3536
Extinction coefficients:
Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.
Ext. coefficient : 24910
Abs 0.1% (=1 g/l): 0.975, assuming all pairs of Cys residues form cystines
Ext. coefficient : 24410
Abs 0.1% (=1 g/l): 0.956, assuming all Cys residues are reduced
Estimated half-life:
The N-terminal of the sequence considered is M (Met).
The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro).
>20 hours (yeast, in vivo).
>10 hours (Escherichia coli, in vivo).
Instability index:
The instability index (II) is computed to be 31.19
This classifies the protein as stable.
Aliphatic index: 61.97
Grand average of hydropathicity (GRAVY): -0.395

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