The field of enzymology has long held as its primary scientific objective the explanation of enzyme catalysis at a chemical/structural level. The detail protonation state of ligand during a series of reaction is critical for understanding enzyme mechanism and function. The increasing power of computational tools to the analysis of enzyme catalytic chemistry provides a new level of quantification that is reshaping bioorganic mechanistic concepts. In this work, we selected tryptophan synthase (TRPS) as a model system. The TRPS is a bifunctional, tetrameric enzyme composed of two a- and two �-subunits. The studies of X-ray and NMR crystallography have provided a good structural framework of multiple intermediate of biosynthesis reaction of L-Trp in TRPS such as the TRPS in complex with E(Ain), E(AA), E(Q)indoline and E(Q)2AP. However, it is still lack of a signal in protonation state of each intermediate and how protons transfer. The atomistic molecular dynamic simulations were applied to study different ligand protonation states. Our work reveals a tiny change of single proton results in conformational flexibility of the TRPS and further affects enzyme catalysis. We expect this study can provide insights into enzyme mechanism and biosynthesis process of a protein.

Determining protonation states in the active site of tryptophan synthase by combining molecular dynamics simulations and solid state NMR

248th National Meeting (2014)

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