Difference between revisions of "Part:BBa K5366019"

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	<i>Candidatus Aerophobetes bacterium</i>-derived sequences with tagatose-4-epimerase activity		<i>Candidatus Aerophobetes bacterium</i>-derived sequences with tagatose-4-epimerase activity

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Revision as of 15:53, 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 (ΔE_Binding) is defined as E_Complex = E_Ligand - E_Receptor. 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