Finding gas migration pathways in proteins using implicit ligand sampling

被引：47

作者：

Cohen, Jordi ^{[1
]}

Olsen, Kenneth W. ^{[2
]}

Schulten, Klaus ^{[1
]}

机构：

[1] Univ Illinois, Beckman Inst, Urbana, IL 61801 USA

[2] Loyola Univ, Dept Chem, Chicago, IL 60626 USA

来源：

GLOBINS AND OTHER NITRIC OXIDE-REACTIVE PROTEINS, PART B | 2008年 / 437卷

关键词：

D O I：

10.1016/S0076-6879(07)37022-5

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：439 / 457

页数：19

共 23 条

[1] Ligand diffusion in the catalase from Proteus mirabilis:: A molecular dynamics study [J].