关键词: 腺苷酸激酶, 水化过程, 分子动力学, 产物释放, 催化循环

Abstract:

Adenylate kinase (AdK) is a multisubstrate enzyme catalyzing the reversible phosphoryl transfer reaction\mathrm{A}\mathrm{T}\mathrm{P}?\mathrm{M}{\mathrm{g}}^{\mathrm{2}+}+\mathrm{A}\mathrm{M}\mathrm{P}?\mathrm{A}\mathrm{D}\mathrm{P}?\mathrm{M}{\mathrm{g}}^{\mathrm{2}+}+\mathrm{A}\mathrm{D}\mathrm{P} and maintaining the energy balance of the body. The rate?limiting step of the whole AdK catalytic cycle is the product ADP releasing which is coupled with conformational change and hydration process. Recent research reveals that the substrate ATP and product ADP cobound state tends to facilitate the rate?limiting product releasing. In this work，by using all?atom molecular dynamics simulations with hamiltonian replica exchange and umbrella sampling，we simulated the hydration process of the\mathrm{M}{\mathrm{g}}^{\mathrm{2}+}，phosphate groups of the products/substrates and the key residues in the binding sites during the disassociation of product ADP. The results show that the oxygen atoms of the phosphate groups coordinated with\mathrm{M}{\mathrm{g}}^{\mathrm{2}+} can be gradually replaced by water molecules during the releaing process of the product ADP，demonstrating a coordination exchange process. Meanwhile，the results show that the coordination exchange is more prominent in the substrate?product cobound state than that in the two?product bound state. In addition，the radial distribution function of water molecules around the\mathrm{M}{\mathrm{g}}^{\mathrm{2}+} reveals that more water molecules enter into the fist cooridnation shell in the substrate?product cobound state. We also analyzed the detailed hydration process of the product ADP and the key residues in the binding sites. As the hydration process can affect the product releasing，our work provides insight into the detailed molecular mechanism of the product release of the enzymatic cycle of AdK.

Key words: Adenylate Kinase, hydration, molecular dynamics, product release, enzymatic cycle