Cohen Jordi, Olsen Kenneth W, Schulten Klaus
Beckman Institute, University of Illinois, Urbana, Illinois, USA.
Methods Enzymol. 2008;437:439-57. doi: 10.1016/S0076-6879(07)37022-5.
Implicit ligand sampling is a practical, efficient, and accurate method for finding the gas migration pathways for small hydrophobic gas molecules, such as oxygen, inside proteins. The method infers the gas migration pathways by calculating the potential of mean force for the gas molecule everywhere inside the protein by means of a molecular dynamics simulation of the protein in the absence of the gas molecule. Pathways can be constructed by connecting the areas of the protein that are favorable to the presence of gas. This method has the advantage of providing a comprehensive overview of all possible gas migration pathways and barriers in a given protein from a single simulation run. Implicit ligand sampling has been applied to a large number of hemoproteins. The example of the truncated hemoglobin from Paramecium caudatum is given to illustrate the method.
隐式配体采样是一种实用、高效且准确的方法，用于寻找蛋白质内部诸如氧气等小疏水气体分子的气体迁移途径。该方法通过在不存在气体分子的情况下对蛋白质进行分子动力学模拟，计算蛋白质内部各处气体分子的平均力势来推断气体迁移途径。可以通过连接蛋白质中有利于气体存在的区域来构建途径。此方法的优点是从单次模拟运行中就能全面概述给定蛋白质中所有可能的气体迁移途径和障碍。隐式配体采样已应用于大量血红蛋白。以尾草履虫截短血红蛋白为例来说明该方法。
