Finding gas migration pathways in proteins using implicit ligand sampling

Methods in Enzymology
Jordi CohenKlaus Schulten

Abstract

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.

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Citations

Jan 5, 2011·The Journal of Biological Chemistry·Ivan BirukouJohn S Olson
Jan 9, 2013·The Journal of Biological Chemistry·Leonardo BoechiDarío A Estrin
May 9, 2012·The Journal of Chemical Physics·Takayuki TsudukiTakahisa Yamato
Mar 5, 2016·Journal of Chemical Theory and Computation·Maria S ShadrinaGilles H Peslherbe
May 7, 2016·Bioinformatics·Juan P BustamanteLeonardo Boechi
Sep 30, 2016·Biochemistry·Federico M IssoglioSilvina Bartesaghi
Oct 29, 2015·Chemical Science·Natali V Di RussoAdrian E Roitberg
Jun 5, 2013·Physical Chemistry Chemical Physics : PCCP·Stefania AbbruzzettiCristiano Viappiani
Jan 21, 2016·PLoS Computational Biology·Juan P BustamanteMarcelo A Martí
Aug 7, 2020·Journal of Computational Chemistry·Erix W Hernández-RodríguezJulio Caballero
Jan 15, 2014·The Journal of Physical Chemistry. B·Juan P BustamanteCristiano Viappiani

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