National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.
Phys Rev E. 2019 Nov;100(5-1):052409. doi: 10.1103/PhysRevE.100.052409.
Natural enzymes often have enormous catalytic power developed by evolution. Revealing the underlying physical strategy used by enzymes to achieve high catalysis efficiency is one of the central focuses in the field of biological physics. Our recent work demonstrated that multisubstrate enzymes can utilize steric frustration encountered in the substrate-product cobound complex to overcome the bottleneck of the enzymatic cycle [W. Li et al., Phys. Rev. Lett. 122, 238102 (2019)10.1103/PhysRevLett.122.238102]. However, the key atomic-level interactions by which the steric frustration contributes to the enzymatic cycle remain elusive. In this work we study the microscopic mechanism for the role of the substrate-product frustration on the key physical steps in the enzymatic cycle of adenylate kinase (AdK), a multisubstrate enzyme catalyzing the reversible phosphoryl transfer reaction ATP+AMP⇋ADP+ADP. By using atomistic molecular dynamics simulations with enhanced sampling, we showed that the competitive interactions from the phosphate groups of the substrate ATP and product ADP in the ATP-ADP cobound complex of the AdK lead to local frustration in the binding pockets. Such local frustration disrupts the hydrogen bond network around the binding pockets, which causes lowered barrier height for the opening of the enzyme conformations and expedited release of the bottleneck product ADP. Our results directly demonstrated from the atomistic level that the local frustration in the active sites of the enzyme can be utilized to facilitate the key physical steps of the enzymatic cycle, providing numerical evidence to the predictions of the previous theoretical work.
天然酶通常具有巨大的催化能力，这是进化的结果。揭示酶实现高催化效率所采用的潜在物理策略是生物物理领域的核心关注点之一。我们最近的工作表明，多底物酶可以利用底物-产物复合结合物中遇到的空间位阻来克服酶循环的瓶颈[W. Li 等人，物理评论快报 122, 238102 (2019)10.1103/PhysRevLett.122.238102]。然而，空间位阻有助于酶循环的关键原子级相互作用仍然难以捉摸。在这项工作中，我们研究了腺嘌呤激酶（AdK）酶循环中关键物理步骤上的底物-产物位阻作用的微观机制，腺嘌呤激酶是一种多底物酶，催化可逆的磷酸转移反应 ATP+AMP ⇋ADP+ADP。通过使用增强采样的原子分子动力学模拟，我们表明底物 ATP 和产物 ADP 的磷酸基团在 AdK 的 ATP-ADP 复合结合物中产生的竞争相互作用导致结合口袋中的局部位阻。这种局部位阻破坏了结合口袋周围的氢键网络，从而降低了酶构象打开的势垒高度，并加速了瓶颈产物 ADP 的释放。我们的结果直接从原子水平证明了酶活性位点的局部位阻可以被用来促进酶循环的关键物理步骤，为之前理论工作的预测提供了数值证据。
