Ab initio based calculations of electron-transfer rates in metalloproteins.
Ab initio based calculations of electron-transfer rates in metalloproteins.
复制标题
金属蛋白中电子转移速率的从头计算。
DOI：
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发表时间：
2005
影响因子：
3.3
通讯作者：
D. Beratan
中科院分区：
文献类型：
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作者：
T. Prytkova;I. Kurnikov;D. Beratan
电子转移理论中一个长期存在的挑战是计算蛋白质中长距离反应的准确速率。我们描述了一个从头算Hartree-Fock方法来计算电子耦合相互作用和电子转移速率的蛋白质，允许有利的比较与实验。该方法包括以下关键特征;每个特征对于可靠的速率计算都是必不可少的：（1）对多个隧穿路径上的贡献求和，（2）对热可接近的蛋白质构象上的耦合求平均，（3）明确地描述供体和受体电子结构，包括溶剂化效应，以及对几乎简并的供体-受体配体-场态的多个能级交叉上的耦合求平均，以及（4）消除与扩散基函数相关联的基组伪像。供体-受体距离和途径干扰耦合的强烈依赖性导致计算的电子耦合值与蛋白质几何形状的大的变化，和最强的耦合构象占主导地位的电子转移速率。因此，对蛋白质和氧化还原辅因子的热可及构象进行平均是必要的。这种方法进行了测试，使用高温非绝热速率表达式和比较简单的途径，平均障碍，和半经验INDO模型上的六个修饰的天青衍生物。用分裂价基组进行的从头算Hartree-Fock计算结果与实验结果符合得很好。较长距离衍生物的预测利率被低估了3-8倍。这一分析表明，定量可靠的蛋白质电子转移速率计算所需的关键成分是可访问的。
A long-standing challenge in electron-transfer theory is to compute accurate rates of long-distance reactions in proteins. We describe an ab initio Hartree-Fock approach to compute electronic-coupling interactions and electron-transfer rates in proteins that allows the favorable comparison with experiment. The method includes the following key features; each is essential for reliable rate computations: (1) summing contributions over multiple tunneling pathways, (2) averaging couplings over thermally accessible protein conformations, (3) describing donor and acceptor electronic structure explicitly, including solvation effects, and averaging coupling over multiple energy-level crossings of the nearly degenerate donor-acceptor ligand-field states, and (4) eliminating basis set artifacts associated with diffuse basis functions. The strong dependence of coupling on donor-acceptor distance and on pathway interferences causes large variations of the computed electron-coupling values with protein geometry, and the strongest coupled conformers dominate the electron-transfer rate. As such, averaging over thermally accessible conformers of the protein and of the redox cofactors is essential. This approach was tested on six ruthenium-modified azurin derivatives using the high temperature nonadiabatic rate expression and compared with simpler pathways, average barrier, and semiempirical INDO models. Results of ab initio Hartree-Fock calculations with a split-valence basis set are in good agreement with the experimental rates. Predicted rates in the longer-distance derivatives are underestimated by 3-8-fold. This analysis indicates that the key ingredients needed for quantitatively reliable protein electron-transfer rate calculations are accessible.