Jordi Cohen, Kenneth W. Olsen, and Klaus Schulten.
Finding gas migration pathways in proteins using implicit ligand
sampling.
In Robert K. Poole, editor, Globins and other NO-reactive
Proteins in Microbes, Plants and Invertebrates, volume 437 of Methods
in Enzymology, pp. 437-455. Elsevier, 2008.
COHE2008
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 which 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.
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