Taraphder Srabani, Maupin C Mark, Swanson Jessica M J, Voth Gregory A
Department of Chemistry, Indian Institute of Technology , Kharagpur 721302, India.
Department of Chemical and Biological Engineering, Colorado School of Mines , 1500 Illinois Street, Golden, Colorado 80401, United States.
J Phys Chem B. 2016 Aug 25;120(33):8389-404. doi: 10.1021/acs.jpcb.6b02166. Epub 2016 Apr 20.
The role of protein dynamics in enzyme catalysis is one of the most highly debated topics in enzymology. The main controversy centers around what may be defined as functionally significant conformational fluctuations and how, if at all, these fluctuations couple to enzyme catalyzed events. To shed light on this debate, the conformational dynamics along the transition path surmounting the highest free energy barrier have been herein investigated for the rate limiting proton transport event in human carbonic anhydrase (HCA) II. Special attention has been placed on whether the motion of an excess proton is correlated with fluctuations in the surrounding protein and solvent matrix, which may be rare on the picosecond and subpicosecond time scales of molecular motions. It is found that several active site residues, which do not directly participate in the proton transport event, have a significant impact on the dynamics of the excess proton. These secondary participants are shown to strongly influence the active site environment, resulting in the creation of water clusters that are conducive to fast, moderately slow, or slow proton transport events. The identification and characterization of these secondary participants illuminates the role of protein dynamics in the catalytic efficiency of HCA II.
蛋白质动力学在酶催化中的作用是酶学领域中争议最大的话题之一。主要争议集中在哪些构象波动可被定义为具有功能意义，以及这些波动（如果有的话）如何与酶催化事件相耦合。为了阐明这一争议，本文研究了人类碳酸酐酶（HCA）II中限速质子传输事件沿跨越最高自由能垒的过渡路径的构象动力学。特别关注了过量质子的运动是否与周围蛋白质和溶剂基质的波动相关，而这种相关性在皮秒和亚皮秒分子运动时间尺度上可能很少见。研究发现，几个不直接参与质子传输事件的活性位点残基对过量质子的动力学有显著影响。这些次要参与者被证明会强烈影响活性位点环境，导致形成有利于快速、适度缓慢或缓慢质子传输事件的水簇。对这些次要参与者的识别和表征揭示了蛋白质动力学在HCA II催化效率中的作用。
