Difference between revisions of "Part:BBa K5366020"

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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.

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 HDM and fructose (Fig. 1).

Fig. 1 Free energy of binding between HDM and fructose