Theoretical investigation on binding process of allophanate to allophanate hydrolase

Abstract

Several molecular simulation methods were integrated to investigate the detailed binding process of allophanate to allophanate hydrolase and predict their stable complex structure. The optimal enzyme-substrate complex conformation demonstrates that along with Arg307 and Tyr299, Gly124 is also one of the key anchor residues in the stable complex. The energetic calculation suggests the existence of an intermediate state in the enzyme-substrate binding process. The further atomic-level investigation illuminates that Tyr299, Arg307 and Ser172 can stabilize the substrate in the intermediate state. By this token, the residues Arg307 and Tyr299 function in both binding process and getting stable state.

Keywords

Allophanate hydrolase / Molecular dynamics simulation / Substrate binding / Free energy / Intermediate state

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