Polarizable embedding for simulating redox potentials of biomolecules
Polarizable embedding for simulating redox potentials of biomolecules
复制标题
用于模拟生物分子氧化还原电位的极化嵌入
DOI：
10.1039/c9cp01533g
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发表时间：
2019
影响因子：
3.3
通讯作者：
Bravaya, Ksenia B.
中科院分区：
文献类型：
--
作者：
Tazhigulov, Ruslan N.;Gurunathan, Pradeep Kumar;Kim, Yongbin;Slipchenko, Lyudmila V.;Bravaya, Ksenia B.
氧化还原反应在包括光合作用和呼吸作用在内的各种生物过程中起着关键作用。因此，氧化还原事件的定量和预测计算表征对于丰富我们对生物氧化还原活性大分子的机制特征的认识是非常可取的。在这里，我们提出了一种利用极化嵌入混合量子经典方法的计算协议，从而准确估计生物大分子的氧化还原电位。特别注意理论描述的基本方面，如环境极化和远程静电相互作用对计算的能量参数的影响。环境（蛋白质和溶剂）极化被证明是准确估计氧化还原电位的关键：考虑和不考虑环境极化的杂化量子经典结果相差1.4 V。远距离静电相互作用对计算的氧化还原电位值有显著贡献，即使在远远超出蛋白质外表面的距离上也是如此。对拟南芥隐色素1蛋白的还原电位进行了模拟实验。理论估计的中点还原电位（0.07 V）与现有的实验数据（- 0.15 V）吻合良好。
Redox reactions play a key role in various biological processes, including photosynthesis and respiration. Quantitative and predictive computational characterization of redox events is therefore highly desirable for enriching our knowledge on mechanistic features of biological redox-active macromolecules. Here, we present a computational protocol exploiting polarizable embedding hybrid quantum-classical approach and resulting in accurate estimates of redox potentials of biological macromolecules. A special attention is paid to fundamental aspects of the theoretical description such as the effects of environment polarization and of the long-range electrostatic interactions on the computed energetic parameters. Environment (protein and the solvent) polarization is shown to be crucial for accurate estimates of the redox potential: hybrid quantum-classical results with and without account for environment polarization differ by 1.4 V. Long-range electrostatic interactions are shown to contribute significantly to the computed redox potential value even at the distances far beyond the protein outer surface. The approach is tested on simulating reduction potential of cryptochrome 1 protein from Arabidopsis thaliana. The theoretical estimate (0.07 V) of the midpoint reduction potential is in good agreement with available experimental data (−0.15 V).