Difference between revisions of "Part:BBa K5366017"
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<i><b>Fig. 1 Binding free energy between the AJC7 sequence and fructose (using the final selected sequence as an example)<br><br></b></I> | <i><b>Fig. 1 Binding free energy between the AJC7 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> | ||
Latest revision as of 16:28, 30 September 2024
AJC7
Pseudothermotoga hypogea DSM-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 AJC7 sequences and fructose(Fig. 1).
Fig. 1 Binding free energy between the AJC7 sequence and fructose (using the final selected sequence as an example)
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 501
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal AgeI site found at 1003
- 1000COMPATIBLE WITH RFC[1000]