Difference between revisions of "Part:BBa K5366020"
Line 7: Line 7:
 
In the present study, an unknown functional protein from <i>Thermotogales bacterium</i>, exhibiting Tagatose-4-epimerase activity, was identified through gene mining and designated as HDM.
 
In the present study, an unknown functional protein from <i>Thermotogales bacterium</i>, exhibiting Tagatose-4-epimerase activity, was identified through gene mining and designated as HDM.
 
   
 
   
−
The binding free energy of the receptor-ligand complex was calculated using a CHARMm-based energy functional along with implicit solvent methods. These free energies were estimated by minimizing the ligand energy in the presence of the receptor, employing both the steepest descent and conjugate gradient methods. Instead of utilizing the more costly molecular surface approximation, the effective Born radius was calculated using the Generalized Born Simple Switching (GBSW) implicit solvent model. This model features smooth dielectric boundaries that incorporate van der Waals surfaces. Using this approach, we calculated the free energy of binding between HDM and fructose (Fig. 1).
+
We calculated the binding free energy of the receptor-ligand complexes using the CHARMm-based energy function and an implicit solvent model. The binding energy between the receptor and ligand (ΔE<sub>Binding</sub>) is defined as E<sub>Complex</sub> = E<sub>Ligand</sub> - E<sub>Receptor</sub>. To estimate these free energies, we minimized the ligand energy in the presence of the receptor using the steepest descent and conjugate gradient methods. The effective Born radii were computed using the Generalized Born Simple Switching (GBSW) implicit solvent model, replacing the costly molecular surface approximation with a smooth dielectric boundary combined with a van der Waals surface.
 +
Using this approach, we calculated the binding free energy between the HDM sequences and fructose(Fig. 1).
 
<html>
 
<html>
 
<style>
 
<style>
Line 14: Line 15:
 
<p>
 
<p>
 
   <img class="bild" src="https://static.igem.wiki/teams/5366/part/.png"><br>
 
   <img class="bild" src="https://static.igem.wiki/teams/5366/part/.png"><br>
−
   <i><b>Fig. 1 Free energy of binding between HDM and fructose<br><br></b></I>
+
   <i><b>Fig. 1 Binding free energy between the HDM sequence and fructose (using the final selected sequence as an example)<br><br></b></I>
 
   <div class="unterschrift"><bFig. 1 Construction of pMTL-Pfba-Bs2 recombinant plasmid</b>
 
   <div class="unterschrift"><bFig. 1 Construction of pMTL-Pfba-Bs2 recombinant plasmid</b>
 
   </div>
 
   </div>
 
</p>
 
</p>
 
</html>
 
</html>
−
From Figure 1, the free energy of docking between HDM and fructose is -18.902.<!-- Add more about the biology of this part here
+
From Figure 1, the free energy of docking between HDM and fructose is -15.05281kcal/mol.
 +
<!-- Add more about the biology of this part here
 
===Usage and Biology===
 
===Usage and Biology===
  

Revision as of 15:57, 30 September 2024


HDM

Sequences of Thermotogales bacterium origin with tagatose-4- epimerase activity

In the present study, an unknown functional protein from Thermotogales bacterium, exhibiting Tagatose-4-epimerase activity, was identified through gene mining and designated as HDM.

We calculated the binding free energy of the receptor-ligand complexes using the CHARMm-based energy function and an implicit solvent model. The binding energy between the receptor and ligand (ΔEBinding) is defined as EComplex = ELigand - EReceptor. To estimate these free energies, we minimized the ligand energy in the presence of the receptor using the steepest descent and conjugate gradient methods. The effective Born radii were computed using the Generalized Born Simple Switching (GBSW) implicit solvent model, replacing the costly molecular surface approximation with a smooth dielectric boundary combined with a van der Waals surface. Using this approach, we calculated the binding free energy between the HDM sequences and fructose(Fig. 1).


Fig. 1 Binding free energy between the HDM sequence and fructose (using the final selected sequence as an example)

From Figure 1, the free energy of docking between HDM and fructose is -15.05281kcal/mol. Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 363
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]