Prediction of polyelectrolyte polypeptide structures using Monte Carlo conformational search methods with implicit solvation modeling.
Prediction of polyelectrolyte polypeptide structures using Monte Carlo conformational search methods with implicit solvation modeling.
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使用蒙特卡罗构象搜索方法和隐式溶剂化模型预测聚电解质多肽结构。
DOI：
10.1002/pro.5560041007
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发表时间：
1995
期刊：
影响因子：
--
通讯作者：
Goddard3rd,WA
中科院分区：
文献类型：
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作者：
Evans,JS;Chan,SI;Goddard3rd,WA
许多有趣的蛋白质具有含有带负电荷的氨基酸的确定的序列段。目前，实验方法（X射线晶体学，NMR）未能提供这些序列域的结构数据。我们应用二面角概率网格-蒙特卡罗（DPG-MC）构象搜索算法对一系列N-和C-封端的二肽（Glu）20，（Asp）20进行了构象搜索。（PSer）20和（PSer-Asp）10，它们代表许多重要蛋白质中的聚阴离子区域，如甲状旁腺素、钙螯合蛋白、钠通道蛋白和酸性生物矿化蛋白。原子电荷由电荷平衡估算，价态和货车德瓦尔斯参数由Dreiding计算。羧酸盐和磷酸盐基团的溶剂化处理使用钠抗衡离子为每个带电侧链（一个Na+为COO−;两个Na为CO（PO 3）− 2）加上距离依赖性（屏蔽）介电常数ε= ε 0 R，以模拟溶剂水。通过DPG-MC构象搜索（其中，DPG-MC构象搜索的值为10），然后使用Warshel的蛋白质偶极-Langevin偶极方法计算最低能量构象异构体的溶剂化能，获得这些多肽的结构。
Many interesting proteins possess defined sequence stretches containing negatively charged amino acids. At present, experimental methods (X-ray crystallography, NMR) have failed to provide structural data for many of these sequence domains. We have applied the dihedral probability grid-Monte Carlo (DPG-MC) conformational search algorithm to a series of N-and C-capped polyelectrolyte peptides,(Glu) 20,(Asp) 20.(PSer) 20, and (PSer-Asp) 10, that represent polyanionic regions in a number of important proteins, such as parathymosin, calsequestrin, the sodium channel protein, and the acidic biomineralization proteins. The atomic charges were estimated from charge equilibration and the valence and van der Waals parameters are from DREIDING. Solvation of the carboxylate and phosphate groups was treated using sodium counterions for each charged side chain (one Na+ for COO−; two Na for CO (PO 3)− 2) plus a distance-dependent (shielded) dielectric constant, ϵ= ϵ 0 R, to simulate solvent water. The structures of these polyelectrolyte polypeptides were obtained by the DPG-MC conformational search with ϵ 0= 10, followed by calculation of solvation energies for the lowest energy conformers using the protein dipole-Langevin dipole method of Warshel.