Difference between revisions of "Part:BBa K5366017"

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	<img class="bild" src="https://static.igem.wiki/teams/5366/part/.png"><br>		<img class="bild" src="https://static.igem.wiki/teams/5366/part/.png"><br>
	<i><b>Fig. 1 Free energy of binding between AJC7 and fructose<br><br></b></I>		<i><b>Fig. 1 Free energy of binding between AJC7 and fructose<br><br></b></I>
−	<div class="unterschrift"><bFig.1 Binding self-energy between selected sequences and fructose</b>	+	<div class="unterschrift"><bFig.1 Binding free energy between the AJC7 sequence and fructose (using the final selected sequence as an example)</b>
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Revision as of 15:48, 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 (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 AJC7 sequences and fructose(Fig. 1).

Fig. 1 Free energy of binding between AJC7 and fructose

From Figure 1, the free energy of docking between AJC7 and fructose is -9.9971kcal/mol.

Sequence and Features