Jordi Cohen and Klaus Schulten. O2 migration pathways are not conserved across proteins of a similar fold. Biophysical Journal, 93:3591-3600, 2007. (PMC: 2072066)

COHE2007 Recent advances in computational biology have made it possible to map the complete network and energy profile of gas migration pathways inside proteins. While networks of O$_2$ pathways have already been characterized for a small number of proteins, the general properties and locations of these pathways have not been previously compared between proteins. In this study, maps of the O$_2$ pathways inside twelve monomeric globins have been computed. It is found that, despite the conserved tertiary structure fold of the studied globins, the shape and topology of O$_2$ pathway networks exhibit a large variability between different globins, except when two globins are nearly identical. The locations of the O$_2$ pathways are, however, found to be correlated with the location of large hydrophobic residues, and a similar correlation is observed in two unrelated protein families: monomeric globins and copper-containing amine oxidases. The results have implications for the evolution of gas pathways in proteins, and for protein-engineering applications involving modifications of these pathways.


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