O₂ migration pathways are not conserved across proteins of a similar fold

¹ Beckman Institute, University of Illinois

^* To whom correspondence should be addressed. E-mail: kschulte{at}ks.uiuc.edu.

Submitted on March 15, 2007
Revised on March 31, 2007
Accepted on 18 July 2007

	Abstract

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 O₂ 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 O₂ 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 O₂ pathway networks exhibit a large variability between different globins, except when two globins are nearly identical. The locations of the O₂ 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.

Key Words: gas migration pathways, heme proteins, implicit ligand sampling, myoglobin hemoglobin leghemoglobin, oxygen binding sites

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