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首页> 美国卫生研究院文献>other >Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged–Hydrophobic/Polar and Polar–Hydrophobic/Polar Side Chains
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Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged–Hydrophobic/Polar and Polar–Hydrophobic/Polar Side Chains

机译：基于简单的基于物理的解析公式用于计算氨基酸侧链在水中相互作用的平均力。七。带电–疏水/极性和极性–疏水/极性侧链

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摘要

The physics-based potentials of side-chain–side-chain interactions corresponding to pairs composed of charged and polar, polar and polar, charged and hydrophobic, and hydrophobic and hydrophobic side chains have been determined. A total of 144 four-dimensional potentials of mean force (PMFs) of all possible pairs of molecules modeling these pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expressions were then fitted to the PMFs. Depending on the type of interacting sites, the analytical approximation to the PMF is a sum of terms corresponding to van der Waals interactions and cavity-creation involving the nonpolar sections of the side chains and van der Waals, cavity-creation, and electrostatic (charge–dipole or dipole–dipole) interaction energies and polarization energies involving the charged or polar sections of the side chains. The model used in this work reproduces all features of the interacting pairs. The UNited RESidue force field with the new side-chain–side-chain interaction potentials was preliminarily tested with the N-terminal part of the B-domain of staphylococcal protein A (PDBL 1BDD; a three-α-helix bundle) and UPF0291 protein YnzC from Bacillus subtilis (PDB: 2HEP; an α-helical hairpin).
机译：已确定了与基于荷电和极性，极性和极性，荷电和疏水性以及疏水和疏水性侧链的配对相对应的侧链-侧链相互作用的基于物理的潜力。通过在显性水中作为距离和方向的函数的伞式采样分子动力学模拟，确定了建模这些对的所有可能分子对的144个平均平均力（PMF）的势能，然后将解析表达式拟合为PMF。根据相互作用部位的类型，对PMF的解析近似值是与范德华相互作用和涉及侧链和范德华的非极性部分的范德华相互作用，模腔创建和静电（电荷）的模腔创建相对应的项的总和-偶极或偶极-偶极）相互作用能和涉及侧链带电或极性部分的极化能。本作品中使用的模型再现了相互作用对的所有特征。用葡萄球菌蛋白A（PDBL 1BDD；三α-螺旋束）和UPF0291蛋白的B结构域的N端部分初步测试了具有新的侧链-侧链相互作用潜能的未知残基力场来自枯草芽孢杆菌的YnzC（PDB：2HEP；α螺旋发夹）。

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