腺苷酸激酶催化产物释放过程中的水化动力学研究

Hydration process in the product releasing of the enzymatic cycle of Adenylate Kinase

腺苷酸激酶(Adenylate Kinase,AdK)是一种多底物反应酶,催化ATP?Mg2++AMP?ADP?Mg2++ADP反应,维持机体能量平衡;其催化循环限速步骤为底物ADP(Adenosine Diphosphate)释放,并伴随蛋白质的构象变化和关键位点水化(hydration)过程.以往的研究表明,底物ATP(Adenosine Triphosphate)和产物ADP共存的复合物共存态(ATP-ADP共存态)有助于作为限速步骤的产物释放.基于分子动力学模拟和哈密顿量副本交换方法研究AdK产物释放过程中,Mg2+、产物磷酸根、底物磷酸根以及催化位点关键氨基酸的水化过程.分子模拟数据表明,在产物ADP释放过程中,与Mg2+结合的磷酸根氧原子逐步被水分子取代,表现出配位交换过程,其中ATP-ADP共存态相较于ADP-ADP共存态表现出更为显著的配位交换. Mg2+周围水分子径向分布函数的差别也表明ATP-ADP共存态下,Mg2+的水化过程需要更多的水分子进入Mg2+的第一配位壳,表现出与双产物共存状态(ADPADP共存态)所不同的行为.另外,还详细研究了产物ADP以及结合位点关键氨基酸的水化过程.由于AdK核心区域的水化过程会影响其产物释放,关于水化过程的研究有助于理解AdK催化循环中的产物释放等物理过程的分子机制.

Adenylate kinase(AdK) is a multisubstrate enzyme catalyzing the reversible phosphoryl transfer reaction ATP?Mg2++AMP?ADP?Mg2++ ADP 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 Mg2+,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 Mg2+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 Mg2+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.