Difference between revisions of "Team:UST Beijing/Modeling"

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  <div class="scroll-link">Project</div></a>
 
  <div class="scroll-link">Project</div></a>
 
  <ul id="csy2">
 
  <ul id="csy2">
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                             <li><a href="https://2017.igem.org/Team:UST_Beijing/Cyclase">Cyclase</a></li>
+
                             <li><a href="https://2017.igem.org/Team:UST_Beijing/Pangu">Pangu</a></li>
 
                             <li><a href="https://2017.igem.org/Team:UST_Beijing/Experiments">Glucosidase</a></li>
 
                             <li><a href="https://2017.igem.org/Team:UST_Beijing/Experiments">Glucosidase</a></li>
 +
                  <li><a href="https://2017.igem.org/Team:UST_Beijing/InterLab">InterLab</a></li>
 
                         </ul>
 
                         </ul>
 
  </li>
 
  </li>
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  <div class="scroll-link" >Parts</div></a></li>
 
  <div class="scroll-link" >Parts</div></a></li>
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  <li><a href="https://2017.igem.org/Team:UST_Beijing/Team">
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  <li><a id="cs4">
 
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  <div class="scroll-link">Team</div></a></li>
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  <div class="scroll-link">Team</div></a>
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  <ul id="csy4">
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            <li><a href="https://2017.igem.org/Team:UST_Beijing/Attributions">Attributions</a></li>
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                            <li><a href="https://2017.igem.org/Team:UST_Beijing/Team">Members</a></li></ul>
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  </li>
 
  <li><a id="cs5">
 
  <li><a id="cs5">
 
  <span id="ca-icon6"></span>
 
  <span id="ca-icon6"></span>
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                   <li><a href="https://2017.igem.org/Team:UST_Beijing/InterLab">InterLab</a></li>
 
                   <li><a href="https://2017.igem.org/Team:UST_Beijing/InterLab">InterLab</a></li>
 
                         </ul>
 
                         </ul>
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Due to the fact that the real structure of Lanosterol Synthase is known, so we begin from protein data bank in Europe.
 
Due to the fact that the real structure of Lanosterol Synthase is known, so we begin from protein data bank in Europe.
 
We firstly obtained Canonical number: P48449(pdb|1w6k|), and then the amino acid sequence of Lanosterol was found in Uniprot, shown as following:
 
We firstly obtained Canonical number: P48449(pdb|1w6k|), and then the amino acid sequence of Lanosterol was found in Uniprot, shown as following:
−
 
+
<p class="text-justify" style="width:700px;text-align: left; font-size:12px;line-height:22px;font-family:Arial">
−
 
+
  >pdb|1w6k|A<br />
 +
MTEGTCLRRRGGPYKTEPATDLGRWRLNCERGRQTWTYLQDERAGREQTGLEAYALGLDTKNYFKDLPKAHTAFEGALNGMTFY<br />
 +
VGLQAEDGHWTGDYGGPLFLLPGLLITCHVARIPLPAGYREEIVRYLRSVQLPDGGWGLHIEDKSTVFGTALNYVSLRILGVGP<br />
 +
DDPDLVRARNILHKKGGAVAIPSWGKFWLAVLNVYSWEGLNTLFPEMWLFPDWAPAHPSTLWCHCRVDGPASTAFQEHVSRIPD<br />
 +
YLWMGLDGMKMQGTNGSQIWDTAFAIQALLEAGGHHRPEFSSCLQKAHEFLRLSQVPDNPPDYQKYYRQMRKGGFSFSTLDCGW<br />
 +
IVSDCTAEALKAVLLLQEKCPHVTEHIPRERLCDAVAVLLNMRNPDGGFATYETKRGGHLLELLNPSEVFGDIMIDYTYVECTS<br />
 +
AVMQALKYFHKRFPEHRAAEIRETLTQGLEFCRRQQRADGSWEGSWGVCFTYGTWFGLEAFACMGQTYRDGTACAEVSRACDFL<br />
 +
LSRQMADGGWGEDFESCEERRYVQSAQSQIHNTCWAMMGLMAVRHPDIEAQERGVRCLLEKQLPNGDWPQENIAGVFNKSCAIS<br />
 +
YTSYRNIFPIWALGRFSQLYPERALAGHP<br />
 
       </p>
 
       </p>
−
<p class="text-justify" style="width:700px;text-align: left; font-size:18px;line-height:28px;font-family:Arial">
 
−
>pdb|1w6k|A
 
−
 
−
      </p><p class="text-justify" style="width:700px;text-align: left; font-size:18px;line-height:28px;font-family:Arial">
 
−
MTEGTCLRRRGGPYKTEPATDLGRWRLNCERGRQTWTYLQDERAGREQTGLEAY<br />
 
−
ALGLDTKNYFKDLPKAHTAFEGALNGMTFYVGLQAEDGHWTGDYGGPLFLLPGL<br />
 
−
LITCHVARIPLPAGYREEIVRYLRSVQLPDGGWGLHIEDKSTVFGTALNYVSLRI<br />
 
−
LGVGPDDPDLVRARNILHKKGGAVAIPSWGKFWLAVLNVYSWEGLNTLFPEMWLF<br />
 
−
PDWAPAHPSTLWCHCRVDGPASTAFQEHVSRIPDYLWMGLDGMKMQGTNGSQIWD<br />
 
−
TAFAIQALLEAGGHHRPEFSSCLQKAHEFLRLSQVPDNPPDYQKYYRQMRKGGFS<br />
 
−
FSTLDCGWIVSDCTAEALKAVLLLQEKCPHVTEHIPRERLCDAVAVLLNMRNPDG<br />
 
−
GFATYETKRGGHLLELLNPSEVFGDIMIDYTYVECTSAVMQALKYFHKRFPEHRA<br />
 
−
AEIRETLTQGLEFCRRQQRADGSWEGSWGVCFTYGTWFGLEAFACMGQTYRDGTA<br />
 
−
CAEVSRACDFLLSRQMADGGWGEDFESCEERRYVQSAQSQIHNTCWAMMGLMAVR<br />
 
−
HPDIEAQERGVRCLLEKQLPNGDWPQENIAGVFNKSCAISYTSYRNIFPIWALGR<br />
 
−
FSQLYPERALAGHP
 
−
      </p>
 
−
<>
 
 
           <br /><br /><br /><br /><br />
 
           <br /><br /><br /><br /><br />
−
 
+
<p class="text-justify" style="width:700px;text-align: left; font-size:18px;line-height:28px;font-family:Arial">
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          <p class="text-justify" style="width:700px;text-indent:1em;text-align: left; font-size:18px;line-height:28px;font-family:Arial" >
+
  And the starting about 90 amino acids are membrane bound sequences. We make a chimera sequence using the Lanosterol Synthase homologue, Dammarenediol Synthase. It’s Pangu sequence. Then, we use the online servers, Swiss-Model, to generate high quality predictions of 3D structure of protein molecules from amino sequences. shown as following:
−
And the starting about 90 amino acids are membrane bound sequences. We make a chimera sequence using the Lanosterol Synthase homologue, Dammarenediol Synthase. It’s Pangu sequence. Then, we use the online servers, Swiss-Model, to generate high quality predictions of 3D structure of protein molecules from amino sequences. shown as following:
+
  
 
      </p>
 
      </p>
 
           <br /><br /><br />
 
           <br /><br /><br />
−
<p class="text-justify" style="width:700px;text-align: left; font-size:18px;line-height:28px;font-family:Arial">
+
<p class="text-justify" style="width:700px;text-align: left; font-size:12px;line-height:22px;font-family:Arial">
−
>pdb||A
+
  >pdb|Pangu|A<br />
−
 
+
    MTEGTCLRRRGGPYKTEPATDLGRWRLNCERGRQTWTYLQDERAGREQTGLEAYALGLDTKNYFKDLPKAHTAFEGALNGMTFYV<br />
−
      </p><p class="text-justify" style="width:700px;text-align: left; font-size:18px;line-height:28px;font-family:Arial">
+
    GLQAEDGHYDAVTTAVKKALRLNRAIQAHDGHWPAENAGSLLYTPPLIIALYISGTIDTILTKQHKKELIRFVYNHQNEDGGWGS<br />
−
MTEGTCLRRRGGPYKTEPATDLGRWRLNCERGRQTWTYLQDERAGREQTGLEAYALG<br />
+
    YIEGHSTMIGSVLSYVMLRLLGEGLAESDDGNGAVERGRKWILDHGGAAGIPSWGKTYLAVLGVYEWEGCNPLPPEFWLFPSSFP<br />
−
LDTKNYFKDLPKAHTAFEGALNGMTFYVGLQAEDGHYDAVTTAVKKALRLNRAIQAHDG<br />
+
    FHPAKMWIYCRCTYMPMSYLYGKRYHGPITDLVLSLRQEIYNIPYEQIKWNQQRHNCCKEDLYYPHTLVQDLVWDGLHYFSEPFL<br />
−
HWPAENAGSLLYTPPLIIALYISGTIDTILTKQHKKELIRFVYNHQNEDGGWGSYIEGHS<br />
+
    KRWPFNKLRKRGLKRVVELMRYGATETRFITTGNGEKALQIMSWWAEDPNGDEFKHHLARIPDFLWIAEDGMTVQSFGSQLWDCI<br />
−
TMIGSVLSYVMLRLLGEGLAESDDGNGAVERGRKWILDHGGAAGIPSWGKTYLAVLGVYE<br />
+
    LATQAIIATNMVEEYGDSLKKAHFFIKESQIKENPRGDFLKMCRQFTKGAWTFSDQDHGCVVSDCTAEALKCLLLLSQMPQDIVG<br />
−
WEGCNPLPPEFWLFPSSFPFHPAKMWIYCRCTYMPMSYLYGKRYHGPITDLVLSLRQEIY<br />
+
    EKPEVERLYEAVNVLLYLQSRVSGGFAVWEPPVPKPYLEMLNPSEIFADIVVEREHIECTASVIKGLMAFKCLHPGHRQKEIEDS<br />
−
NIPYEQIKWNQQRHNCCKEDLYYPHTLVQDLVWDGLHYFSEPFLKRWPFNKLRKRG<br />
+
    VAKAIRYLERNQMPDGSWYGFWGICFLYGTFFTLSGFASAGRTYDNSEAVRKGVKFFLSTQNEEGGWGESLESCPSEKFTPLKGN<br />
−
LKRVVELMRYGATETRFITTGNGEKALQIMSWWAEDPNGDEFKHHLARIPDFLWIAEDGM<br />
+
    RTNLVQTSWAMLGLMFGGQAERDPTPLHRAAKLLINAQMDNGDFPQQEITGVYCKNSMLHYAEYRNIFPLWALGEYRKRVW</p>
−
TVQSFGSQLWDCILATQAIIATNMVEEYGDSLKKAHFFIKESQIKENPRGDFLKMC<br />
+
−
RQFTKGAWTFSDQDHGCVVSDCTAEALKCLLLLSQMPQDIVGEKPEVERLYEAVNVLLYL<br />
+
−
QSRVSGGFAVWEPPVPKPYLEMLNPSEIFADIVVEREHIECTASVIKGLMAFKCLH<br />
+
−
PGHRQKEIEDSVAKAIRYLERNQMPDGSWYGFWGICFLYGTFFTLSGFASAGRTYDNSEA<br />
+
−
VRKGVKFFLSTQNEEGGWGESLESCPSEKFTPLKGNRTNLVQTSWAMLGLMFGGQA<br />
+
−
ERDPTPLHRAAKLLINAQMDNGDFPQQEITGVYCKNSMLHYAEYRNIFPLWALGEYRKRVW   </p>
+
 
<br /><br /><br />
 
<br /><br /><br />
 
<img src="https://static.igem.org/mediawiki/2017/6/6d/USTB-SwissMO01.png">
 
<img src="https://static.igem.org/mediawiki/2017/6/6d/USTB-SwissMO01.png">
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Swiss Model is an automated system for modelling the 3D structure of a protein from its amino acid sequence using homology modelling techniques. We use OSC as the template to predict 3D model of Pangu. The model is named Pangu-Swiss Model.
 
Swiss Model is an automated system for modelling the 3D structure of a protein from its amino acid sequence using homology modelling techniques. We use OSC as the template to predict 3D model of Pangu. The model is named Pangu-Swiss Model.
 
      </p>
 
      </p>
−
 
+
<br /><br />
−
<video autoplay="" loop="" style="width:100%; height:50%;">
+
<video autoplay="" loop="" style="width:70%; height:50%;">
 
         <source src="https://static.igem.org/mediawiki/2017/d/d8/USTB-Protein_Docking.mp4">
 
         <source src="https://static.igem.org/mediawiki/2017/d/d8/USTB-Protein_Docking.mp4">
 
         </video>
 
         </video>
 
     <p class="text-justify" style="width:700px;text-indent:1em;text-align: left; font-size:18px;line-height:28px;font-family:Arial" >
 
     <p class="text-justify" style="width:700px;text-indent:1em;text-align: left; font-size:18px;line-height:28px;font-family:Arial" >
 +
    <br />
 
After docking simulation, make the qualitative analysis of the results of the docking and evaluate model quality on Pangu.    </p>
 
After docking simulation, make the qualitative analysis of the results of the docking and evaluate model quality on Pangu.    </p>
−
          <br /><br/><h2 style="font-family:Arial">Reference</h2><br />
+
      <br /><br />
 +
<h2 style="font-family:Arial">Logistic Function and Enzymatic Activity Simulation</h2><br />
 +
<p class="text-justify" style="width:700px;text-indent:1em;text-align: left; font-size:18px;line-height:28px;font-family:Arial" >
 +
    Integration of Logistic functions to simulate enzymatic measurement during bacterium fermentation.
 +
In our beta-glucosidase expression assay, we incubated the growing bacterium E.coli BL21(DE3) harboring pSB1C3/BBa_K2072000 plasmid with PNPG, a colorless substrate for beta-glucosidase hydrolyzing into yellow PNP. We measured OD620nm to reflect cell number and OD405 nm-1.5*OD620 nm to reflect PNP concentration. During the fermentation, both cell number and PNP are increasing. In order to simulate these factors, we integrate the logistic functions (1): <br />
 +
<img src="https://static.igem.org/mediawiki/2017/2/20/USTB-UBC2017-11-02_015623.jpg"><br />
 +
<img src="https://static.igem.org/mediawiki/2017/6/64/USTB-BCU2017-11-02_020021.jpg"><br />
 +
</p>
 +
<p class="text-justify" style="width:700px;text-indent:1em;text-align: left; font-size:18px;line-height:28px;font-family:Arial" >
 +
So, we get the formula, <br />
 +
    <img src="https://static.igem.org/mediawiki/2017/1/10/USTB-BCU2017-11-02_020325.jpg"><br /></p>
 +
<p class="text-justify" style="width:700px;text-indent:1em;text-align: left; font-size:18px;line-height:28px;font-family:Arial" >
 +
    We used Excel to graph functions (1) and (3) resulting following curves:<br />
 +
<img src="https://static.igem.org/mediawiki/2017/e/e1/USTB-BCU-Figure_formula1.jpg"><br /></p>
 +
 +
<br /><br/><h2 style="font-family:Arial">Reference</h2><br />
 
<p class="text-justify" style="width:700px;text-indent:1em;text-align: left; font-size:18px;line-height:28px;font-family:Arial" >
 
<p class="text-justify" style="width:700px;text-indent:1em;text-align: left; font-size:18px;line-height:28px;font-family:Arial" >
 
Marco Biasini; Stefan Bienert; Andrew Waterhouse; Konstantin Arnold; Gabriel Studer; Tobias Schmidt; Florian Kiefer; Tiziano Gallo Cassarino; Martino Bertoni; Lorenza Bordoli; Torsten Schwede. (2014). SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research (1 July 2014) 42 (W1): W252-W258; doi: 10.1093/nar/gku340. </p>
 
Marco Biasini; Stefan Bienert; Andrew Waterhouse; Konstantin Arnold; Gabriel Studer; Tobias Schmidt; Florian Kiefer; Tiziano Gallo Cassarino; Martino Bertoni; Lorenza Bordoli; Torsten Schwede. (2014). SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research (1 July 2014) 42 (W1): W252-W258; doi: 10.1093/nar/gku340. </p>
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Benkert, P., Biasini, M. and Schwede, T. (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27, 343-350
 
Benkert, P., Biasini, M. and Schwede, T. (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27, 343-350
 
       </p>
 
       </p>
−
<h2 style="font-family:Arial">Logistic Function and Enzymatic Activity Simulation</h2><br />
+
     
−
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Revision as of 18:15, 1 November 2017

<!doctype html> USTB-Beijing | Welcome




Functions are determined by structures. It is helpful for us to grasp the protein structure, and we could know the function of proteins better. So, we use supercomputer to predict the protein structure, since it is much less expensive, faster, and able to a large scale generate protein structures than classical methods.



Protein Structure Models


Due to the fact that the real structure of Lanosterol Synthase is known, so we begin from protein data bank in Europe. We firstly obtained Canonical number: P48449(pdb|1w6k|), and then the amino acid sequence of Lanosterol was found in Uniprot, shown as following:

>pdb|1w6k|A
MTEGTCLRRRGGPYKTEPATDLGRWRLNCERGRQTWTYLQDERAGREQTGLEAYALGLDTKNYFKDLPKAHTAFEGALNGMTFY
VGLQAEDGHWTGDYGGPLFLLPGLLITCHVARIPLPAGYREEIVRYLRSVQLPDGGWGLHIEDKSTVFGTALNYVSLRILGVGP
DDPDLVRARNILHKKGGAVAIPSWGKFWLAVLNVYSWEGLNTLFPEMWLFPDWAPAHPSTLWCHCRVDGPASTAFQEHVSRIPD
YLWMGLDGMKMQGTNGSQIWDTAFAIQALLEAGGHHRPEFSSCLQKAHEFLRLSQVPDNPPDYQKYYRQMRKGGFSFSTLDCGW
IVSDCTAEALKAVLLLQEKCPHVTEHIPRERLCDAVAVLLNMRNPDGGFATYETKRGGHLLELLNPSEVFGDIMIDYTYVECTS
AVMQALKYFHKRFPEHRAAEIRETLTQGLEFCRRQQRADGSWEGSWGVCFTYGTWFGLEAFACMGQTYRDGTACAEVSRACDFL
LSRQMADGGWGEDFESCEERRYVQSAQSQIHNTCWAMMGLMAVRHPDIEAQERGVRCLLEKQLPNGDWPQENIAGVFNKSCAIS
YTSYRNIFPIWALGRFSQLYPERALAGHP






And the starting about 90 amino acids are membrane bound sequences. We make a chimera sequence using the Lanosterol Synthase homologue, Dammarenediol Synthase. It’s Pangu sequence. Then, we use the online servers, Swiss-Model, to generate high quality predictions of 3D structure of protein molecules from amino sequences. shown as following:




>pdb|Pangu|A
MTEGTCLRRRGGPYKTEPATDLGRWRLNCERGRQTWTYLQDERAGREQTGLEAYALGLDTKNYFKDLPKAHTAFEGALNGMTFYV
GLQAEDGHYDAVTTAVKKALRLNRAIQAHDGHWPAENAGSLLYTPPLIIALYISGTIDTILTKQHKKELIRFVYNHQNEDGGWGS
YIEGHSTMIGSVLSYVMLRLLGEGLAESDDGNGAVERGRKWILDHGGAAGIPSWGKTYLAVLGVYEWEGCNPLPPEFWLFPSSFP
FHPAKMWIYCRCTYMPMSYLYGKRYHGPITDLVLSLRQEIYNIPYEQIKWNQQRHNCCKEDLYYPHTLVQDLVWDGLHYFSEPFL
KRWPFNKLRKRGLKRVVELMRYGATETRFITTGNGEKALQIMSWWAEDPNGDEFKHHLARIPDFLWIAEDGMTVQSFGSQLWDCI
LATQAIIATNMVEEYGDSLKKAHFFIKESQIKENPRGDFLKMCRQFTKGAWTFSDQDHGCVVSDCTAEALKCLLLLSQMPQDIVG
EKPEVERLYEAVNVLLYLQSRVSGGFAVWEPPVPKPYLEMLNPSEIFADIVVEREHIECTASVIKGLMAFKCLHPGHRQKEIEDS
VAKAIRYLERNQMPDGSWYGFWGICFLYGTFFTLSGFASAGRTYDNSEAVRKGVKFFLSTQNEEGGWGESLESCPSEKFTPLKGN
RTNLVQTSWAMLGLMFGGQAERDPTPLHRAAKLLINAQMDNGDFPQQEITGVYCKNSMLHYAEYRNIFPLWALGEYRKRVW




Swiss Model is an automated system for modelling the 3D structure of a protein from its amino acid sequence using homology modelling techniques. We use OSC as the template to predict 3D model of Pangu. The model is named Pangu-Swiss Model.




After docking simulation, make the qualitative analysis of the results of the docking and evaluate model quality on Pangu.



Logistic Function and Enzymatic Activity Simulation


Integration of Logistic functions to simulate enzymatic measurement during bacterium fermentation. In our beta-glucosidase expression assay, we incubated the growing bacterium E.coli BL21(DE3) harboring pSB1C3/BBa_K2072000 plasmid with PNPG, a colorless substrate for beta-glucosidase hydrolyzing into yellow PNP. We measured OD620nm to reflect cell number and OD405 nm-1.5*OD620 nm to reflect PNP concentration. During the fermentation, both cell number and PNP are increasing. In order to simulate these factors, we integrate the logistic functions (1):


So, we get the formula,

We used Excel to graph functions (1) and (3) resulting following curves:



Reference


Marco Biasini; Stefan Bienert; Andrew Waterhouse; Konstantin Arnold; Gabriel Studer; Tobias Schmidt; Florian Kiefer; Tiziano Gallo Cassarino; Martino Bertoni; Lorenza Bordoli; Torsten Schwede. (2014). SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research (1 July 2014) 42 (W1): W252-W258; doi: 10.1093/nar/gku340.


Arnold, K., Bordoli, L., Kopp, J. and Schwede, T. (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics, 22, 195-201. Benkert, P., Biasini, M. and Schwede, T. (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27, 343-350








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