Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent
Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent
复制标题
DOI：
10.1021/jp060365r
复制
发表时间：
2006-09-28
影响因子：
3.3
通讯作者：
Berne, B. J.
中科院分区：
文献类型：
--
作者：
Liu, Pu;Huang, Xuhui;Berne, B. J.
介绍了一种疏水辅助的复制交换方法（HAREM），用于加速全原子蛋白质在显式溶剂中折叠的模拟。这种方法是基于通过减弱蛋白质-水吸引相互作用（模仿伴侣效应）来夸大水中各种蛋白质氨基酸的疏水作用，同时保持蛋白质原子和水分子之间的其他相互作用不变。将该方法应用于小的代表性蛋白质，α-螺旋3 K（I），并且发现HAREM方法在4 ns内成功地折叠蛋白质，而常规的复制交换方法在5 ns内不能折叠相同的蛋白质，即使具有更多的复制品。
A hydrophobic aided replica exchange method (HAREM) is introduced to accelerate the simulation of all-atom protein folding in explicit solvent. This method is based on exaggerating the hydrophobic effect of various protein amino acids in water by attenuating the protein-water attractive interactions (mimicking the Chaperon effect) while leaving other interactions among protein atoms and water molecules unchanged. The method is applied to a small representative protein, the alpha-helix 3K(I), and it is found that the HAREM method successfully folds the protein within 4 ns, while the regular replica exchange method does not fold the same protein within 5 ns, even with many more replicas.