Polarizability of the Active Site in Enzymatic Catalysis: Cytochrome c
Polarizability of the Active Site in Enzymatic Catalysis: Cytochrome c
复制标题
酶催化活性位点的极化率：细胞色素 c
DOI：
10.1021/acs.jpcb.9b09236
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Matyushov, Dmitry V.
中科院分区：
文献类型：
--
作者：
Martin, Daniel R.;Dinpajooh, Mohammadhasan;Matyushov, Dmitry V.
细胞色素中血红素的各向异性极化率被认为是抑制蛋白质电子转移激活势垒（催化效应）的主要因素。极化率耦合到蛋白质和水的电场中，增强了电子转移能隙和相应的方差重组能λvar的波动。由动力学测量得到的重组能λr=（λSt）2/λ var由λ var和Stokes位移重组能λSt组成。与通常报道的λ St相比，由于活性位点的极化率导致λvar> λSt，因此其降低。静电蛋白质-水波动的耦合到可极化的活性位点是占在这里的活性位点哈密顿沿着模拟轨迹的经验价键对角化。我们表明，最近的模拟采用这种技术，未能找到极化率对电子转移动力学的影响，是错误的，忽略了对角偶极矩的哈密顿矩阵和未能旋转的电场产生的蛋白质-水介质的活性位点的分子框架。我们发现，在两个氧化态的血红素的极化率差的张量的各向异性相匹配的第二阶张量的各向异性构造从电场在活性位点。血红素从一侧暴露于水具有显著的催化功能，直接导致场各向异性和相应的激活势垒的降低。
Anisotropic polarizability of the heme in cytochromecis found to be a major factor in suppressing the activation barrier of protein electron transfer (catalytic effect). Polarizability couples to the electric field of protein and water to enhance fluctuations of the electron-transfer energy gap and the corresponding variance reorganization energy λvar. The reorganization energy observable by kinetic measurements λr= (λSt)2/λvaris composed of λvarand the Stokes-shift reorganization energy λSt. It is lowered compared to the usually reported λStdue to polarizability of the active site leading to λvar> λSt. The coupling of electrostatic protein-water fluctuations to the polarizable active site is accounted for here by empirical valence-bond diagonalization of the active-site Hamiltonian along the simulation trajectory. We show that recent simulations employing this technique, which failed to find the effect of polarizability on electron-transfer kinetics, were erroneous in neglecting the diagonal dipole moments in the Hamiltonian matrix and failing to rotate the electric field produced by the protein-water medium into the molecular frame of the active site. We find that anisotropy of the tensor of polarizability difference in the two oxidation states of the heme matches anisotropy of the second-rank tensor constructed from the electric field at the active site. Exposure of the heme to water from only one side carries significant catalytic function, directly leading to the field anisotropy and the corresponding depression of the activation barrier.