Difference between revisions of "Part:BBa K5366019"
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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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In the present study, an unknown functional protein from <i>Candidatus Aerophobetes bacterium</i>, exhibiting Tagatose-4-epimerase activity, was identified through gene mining and designated as TET.
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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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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 TET 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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   <i><b> Fig. 1 Free energy of binding between TET and fructose<br><br></b></I>
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   <i><b>Fig. 1 Free energy of binding between TET and fructose<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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   <div class="unterschrift"><bFig.1 Binding free energy between the TET sequence and fructose (using the final selected sequence as an example)</b>
 
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From Figure 1, the free energy of docking between TET and fructose is -6.5787.<!-- Add more about the biology of this part here
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From Figure 1, the free energy of docking between TET and fructose is -8.57871kcal/mol.
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<!-- Add more about the biology of this part here
 
===Usage and Biology===
 
===Usage and Biology===
  
 
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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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Revision as of 15:52, 30 September 2024


AJC7

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 Free energy of binding between TET and fructose

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]