Role of water in the enzymatic catalysis: study of ATP + AMP -> 2ADP conversion by adenylate kinase

Details Role of water in the enzymatic catalysis: study of ATP + AMP -> 2ADP conversion by adenylate kinase Role of water in the enzymatic catalysis: study of ATP + AMP -> 2ADP conversion by adenylate kinase

2010-12-21

arxiv.org/abs/1012.4628v1

J. Phys. Chem. A (2010)

Physics

Condensed Matter

Statistical Mechanics

28 pages, 10 figures

Scientific paper

10.1021/jp104787s

The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followed by a phosphate transfer, and then the release of two ADP molecules. We have computed a novel two dimensional configurational free energy surface (2DCFES), with one reaction coordinate each for the LID and the NMP domain motions, with explicit interactions with water. Our computed 2DCFES clearly reveals the existence of a stable half-open-half-closed (HOHC) intermediate state of the enzyme. Cycling of the enzyme through the HOHC state reduces the conformational free energy barrier for the reaction by about 20 kJ/mol. We find that the stability of the half-open-half-closed state (missed in all earlier studies with implicit solvent model) is largely because of the increase of specific interactions of the polar amino acid side chains with water, particularly with the arginine and the histidine residues. Free energy surface of the LID domain is rather rugged, which can conveniently slow down LID's conformational motion, thus facilitating a new substrate capture after the product release in the catalytic cycle.

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