Difference between revisions of "Part:BBa K5366020"

Revision as of 15:58, 30 September 2024

HDM

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

In the present study, an unknown functional protein from Thermotogales bacterium, exhibiting Tagatose-4-epimerase activity, was identified through gene mining and designated as HDM.

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 HDM sequences and fructose(Fig. 1).

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