Hydride transfer in liver alcohol dehydrogenase: Quantum dynamics, kinetic isotope effects, and role of enzyme motion
Hydride transfer in liver alcohol dehydrogenase: Quantum dynamics, kinetic isotope effects, and role of enzyme motion
复制标题
DOI：
10.1021/ja011384b
复制
发表时间：
2001-11-14
影响因子：
15
通讯作者：
Hammes-Schiffer, S
中科院分区：
文献类型：
--
作者：
Billeter, SR;Webb, SP;Hammes-Schiffer, S
通过包括整个溶剂化酶运动的实时动态模拟，研究了肝醇脱氢酶（LADH）催化的氢化物转移反应的量子动力学。电子量子效应通过经验价键势纳入，转移氢的核量子效应通过混合量子/经典分子动力学方法纳入，其中转移氢核由三维振动波函数表示。平衡过渡态理论速率常数由绝热量子自由能剖面确定，该剖面包括转移核的零点运动自由能。非平衡动力学效应通过基于具有量子跃迁的实时分子动力学（MDQT）表面跳跃轨迹的反应通量方案计算传递系数来确定。这些传递系数接近1的值意味着诸如势垒重交叉等非平衡动力学效应对于该反应不是主导的。计算得到的总速率的氘和氚动力学同位素效应与实验结果一致。这些模拟阐明了核量子效应的基本性质，并提供了沿供体 - 受体轴方向氢隧穿的证据。对平衡和非平衡模拟过程中的几何参数的分析提供了对特定酶运动和酶活性之间关系的深入了解。发现供体 - 受体距离、催化锌 - 底物氧距离以及辅酶（NAD⁺/NADH）环角强烈影响活化自由能垒，而供体 - 受体距离和辅酶环角之一被发现与势垒重交叉程度相关。发现VAL - 203与反应中心之间的距离显著影响活化自由能，但不影响势垒重交叉程度。这一结果表明，实验观察到的VAL - 203突变对酶活性的影响是由于过渡态和反应物之间平衡自由能差的改变，而不是非平衡动力学因素。VAL - 203的促进运动通过涉及THR - 178和辅酶的空间相互作用来表征。
The quantum dynamics of the hydride transfer reaction catalyzed by liver alcohol dehydrogenase (LADH) are studied with real-time dynamical simulations including the motion of the entire solvated enzyme. The electronic quantum effects are incorporated with an empirical valence bond potential, and the nuclear quantum effects of the transferring hydrogen are incorporated with a mixed quantum/classical molecular dynamics method in which the transferring hydrogen nucleus is represented by a three-dimensional vibrational wave function. The equilibrium transition state theory rate constants are determined from the adiabatic quantum free energy profiles, which include the free energy of the zero point motion for the transferring nucleus. The nonequilibrium dynamical effects are determined by calculating the transmission coefficients with a reactive flux scheme based on real-time molecular dynamics with quantum transitions (MDQT) surface hopping trajectories. The values of nearly unity for these transmission coefficients imply that nonequilibrium dynamical effects such as barrier recrossings are not dominant for this reaction. The calculated deuterium and tritium kinetic isotope effects for the overall rate agree with experimental results. These simulations elucidate the fundamental nature of the nuclear quantum effects and provide evidence of hydrogen tunneling in the direction along the donor-acceptor axis. An analysis of the geometrical parameters during the equilibrium and nonequilibrium simulations provides insight into the relation between specific enzyme motions and enzyme activity. The donor-acceptor distance, the catalytic zinc-substrate oxygen distance, and the coenzyme (NAD(+)/ NADH) ring angles are found to strongly impact the activation free energy barrier, while the donor-acceptor distance and one of the coenzyme ring angles are found to be correlated to the degree of barrier recrossing. The distance between VAL-203 and the reactive center is found to significantly impact the activation free energy but not the degree of barrier recrossing. This result indicates that the experimentally observed effect of mutating VAL-203 on the enzyme activity is due to the alteration of the equilibrium free energy difference between the transition state and the reactant rather than nonequilibrium dynamical factors. The promoting motion of VAL-203 is characterized in terms of steric interactions involving THR-178 and the coenzyme.