Difference between revisions of "Part:BBa K5366018"
 
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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.
 
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.
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Using this approach, we calculated the binding free energy between the AJC7 sequences and fructose(Fig. 1).
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Using this approach, we calculated the binding free energy between the MBC sequences and fructose(Fig. 1).
 
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   <img class="bild" src="https://static.igem.wiki/teams/5366/part/.png"><br>
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   <img class="bild" src="https://static.igem.wiki/teams/5366/part/binding-free-energy.png"><br>
 
   <i><b>Fig. 1 Binding free energy between the MBC sequence and fructose (using the final selected sequence as an example)<br><br></b></I>
 
   <i><b>Fig. 1 Binding free energy between the MBC 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>
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From Figure 1, the free energy of docking between MBCand fructose is -7.2569kcal/mol.<!-- Add more about the biology of this part here
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From Figure 1, the free energy of docking between MBC and fructose is -7.2569kcal/mol.<!-- Add more about the biology of this part here
 
===Usage and Biology===
 
===Usage and Biology===
  

Latest revision as of 16:29, 30 September 2024


MBC

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

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 MBC sequences and fructose(Fig. 1).


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

From Figure 1, the free energy of docking between MBC and fructose is -7.2569kcal/mol. Sequence and Features


Assembly Compatibility:
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    INCOMPATIBLE WITH RFC[10]
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    INCOMPATIBLE WITH RFC[12]
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    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
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  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 223
    Illegal PstI site found at 244
    Illegal PstI site found at 619
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    Illegal PstI site found at 871
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    Illegal NgoMIV site found at 1078
    Illegal AgeI site found at 367
  • 1000
    COMPATIBLE WITH RFC[1000]