Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface
Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface
复制标题
DOI：
10.1002/jcc.20716
复制
发表时间：
2007-08-01
影响因子：
3
通讯作者：
Latour, Robert A.
中科院分区：
文献类型：
--
作者：
Sun, Yu;Dominy, Brian N.;Latour, Robert A.
在这项研究中，我们研究了十三种不同的小肽和疏水表面之间的相互作用行为，使用三种越来越复杂的方法来表示溶剂化效应：联合原子隐式溶剂化方法[CHARMM 19力场（C19）与分析连续静电学（ACE）]，全原子隐式溶剂化方法（C22与GBMV）和全原子显式溶剂化方法（C22与TIP 3 P）。每种肽的吸附行为的特征在于通过计算作为肽-表面分离距离的函数的平均力的势。从C22/TIP 3 P模型的结果表明，疏水性肽表现出相对较强的吸附行为，极性和带正电荷的肽表现出可忽略不计的相对较弱的有利的相互作用与表面，和带负电荷的肽强烈抵抗吸附。与TIP 3 P模型相比，ACE和GBMV隐式溶剂模型预测了CH 3-SAM表面上疏水肽的更强吸引力以及带负电荷肽的更强排斥力。这些比较提供了一个基础，从这些隐式溶剂化方法中的每一个可以重新参数化，以提供更密切的协议，明确表示的溶剂化肽和蛋白质吸附功能化表面的模拟。(C)2007 Wiley Periodicals，Inc.
In this study we investigated the interaction behavior between thirteen different small peptides and a hydrophobic surface using three progressively more complex methods of representing solvation effects: a united-atom implicit solvation method [CHARMM 19 force field (C19) with Analytical Continuum Electrostatics (ACE)], an all-atom implicit solvation method (C22 with GBMV), and an all-atom explicit solvation method (C22 with TIP3P). The adsorption behavior of each peptide was characterized by the calculation of the potential of mean force as a function of peptide-surface separation distance. The results from the C22/TIP3P model suggest that hydrophobic peptides exhibit relatively strong adsorption behavior, polar and positively-charged peptides exhibit negligible to relatively weak favorable interactions with the surface, and negatively-charged peptides strongly resist adsorption. Compared to the TIP3P model, the ACE and GBMV implicit solvent models predict much stronger attractions for the hydrophobic peptides as well as stronger repulsions for the negatively-charged peptides on the CH3-SAM surface. These comparisons provide a basis from which each of these implicit solvation methods may be reparameterized to provide closer agreement with explicitly represented solvation in simulations of peptide and protein adsorption to functionalized surfaces. (C) 2007 Wiley Periodicals, Inc.