Constant pH molecular dynamics in generalized born implicit solvent
Constant pH molecular dynamics in generalized born implicit solvent
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DOI：
10.1002/jcc.20139
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发表时间：
2004-12-01
影响因子：
3
通讯作者：
McCammon, JA
中科院分区：
文献类型：
--
作者：
Mongan, J;Case, DA;McCammon, JA
提出了一种新的恒pH分子动力学方法，该方法采用广义玻恩（GB）静电理论.质子化状态建模与不同的电荷集，滴定残留物样品的玻尔兹曼分布的质子化状态的模拟过程中，使用Monte Carlo采样的基础上GB衍生的能量。该方法适用于四种不同的晶体结构的鸡蛋清溶菌酶（HEWL）。从模拟中得出的pK（a）预测值相对于实验值的均方根（RMS）误差为0.82。四种晶体结构之间的结果的相似性表明，该方法是独立的起始晶体结构，这是在大多数静电的唯一模型。构象和质子化状态之间的强相关性，并指出和定量分析，强调采样质子化状态的重要性，结合动力学。(C)2004 Wiley Periodicals，Inc.
A new method is proposed for constant pH molecular dynamics (MD), employing generalized Born (GB) electrostatics. Protonation states are modeled with different charge sets, and titrating residues sample a Boltzmann distribution of protonation states as the simulation progresses, using Monte Carlo sampling based on GB-derived energies. The method is applied to four different crystal structures of hen egg-white lysozyme (HEWL). pK(a) predictions derived from the simulations have root-mean-square (RMS) error of 0.82 relative to experimental values. Similarity of results between the four crystal structures shows the method to be independent of starting crystal structure; this is in contrast to most electrostatics-only models. A strong correlation between conformation and protonation state is noted and quantitatively analyzed, emphasizing the importance of sampling protonation states in conjunction with dynamics. (C) 2004 Wiley Periodicals, Inc.