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首页> 外文期刊>The journal of physical chemistry, B. Condensed matter, materials, surfaces, interfaces & biophysical >Quantum Mechanics/Molecular Mechanics Restrained Electrostatic Potential Fitting
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Quantum Mechanics/Molecular Mechanics Restrained Electrostatic Potential Fitting

机译：量子力学/分子力学约束静电势拟合

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摘要

We present a quantum mechanics/molecular mechanics (QM/MM) method to evaluate the partial charges of amino acid residues for use in MM potentials based on their protein environment. For each residue of interest, the nearby residues are included in the QM system while the rest of the protein is treated at the MM level of theory. After a short structural optimization, the partial charges of the central residue are fit to the electrostatic potential using the restrained electrostatic potential (RESP) method. The resulting charges and electrostatic potential account for the individual environment of the residue, although they lack the transferable nature of library partial charges. To evaluate the quality of the QM/MM RESP charges, thermodynamic integration is used to measure the pK_a shift of the aspartic acid residues in three different proteins, turkey egg lysozyme, beta-cryptogein, and Thioredoxin. Compared to the AMBER fr99SB library values, the QM/MM RESP charges show better agreement between the calculated and experimental pK, values for almost all of the residues considered.
机译：我们提出一种量子力学/分子力学（QM / MM）方法，以基于其蛋白质环境评估用于MM电势的氨基酸残基的部分电荷。对于每个感兴趣的残基，附近的残基都包含在QM系统中，而其余的蛋白质则在MM的理论水平上进行处理。经过短暂的结构优化后，使用抑制静电势（RESP）方法将中心残基的部分电荷拟合为静电势。生成的电荷和静电势会说明残留物的单个环境，尽管它们缺乏库部分电荷的可转移性。为了评估QM / MM RESP装料的质量，使用热力学积分来测量三种不同蛋白质（火鸡卵溶菌酶，β-cryptogein和硫氧还蛋白）中天冬氨酸残基的pK_a位移。与AMBER fr99SB库值相比，QM / MM RESP电荷在计算的pK和实验的pK值之间具有更好的一致性，几乎所有考虑的残基值。

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