Difference between revisions of "Part:BBa K5366019"

 
 
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<partinfo>BBa_K5366019 short</partinfo>
 
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Sequences from the source of Candidatus Aerophobetes bacterium with tagatose-4-epimerase activity
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<i>Candidatus Aerophobetes bacterium</i>-derived sequences with tagatose-4-epimerase activity
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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.
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Using this approach, we calculated the binding free energy between the TET sequences and fructose(Fig. 1).
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  <img class="bild" src="https://static.igem.wiki/teams/5366/part/binding-free-energy.png"><br>
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  <i><b>Fig. 1 Binding free energy between the TET sequence and fructose (using the final selected sequence as an example)<br><br></b></I>
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  <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 TET and fructose is -8.57871kcal/mol.
  
 
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K5366019 SequenceAndFeatures</partinfo>
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<partinfo>BBa_K5366017 SequenceAndFeatures</partinfo>
  
  
 
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===Functional Parameters===
 
===Functional Parameters===
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<partinfo>BBa_K5366019 parameters</partinfo>
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<partinfo>BBa_K5366017 parameters</partinfo>
 
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Latest revision as of 16:29, 30 September 2024


TET

Candidatus Aerophobetes bacterium-derived sequences 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 TET sequences and fructose(Fig. 1).


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

From Figure 1, the free energy of docking between TET and fructose is -8.57871kcal/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 501
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 1003
  • 1000
    COMPATIBLE WITH RFC[1000]