Paper Citing NAMD - Abstract
Cohen, Jordi; Schulten, Klaus
O-2 migration pathways are not conserved across proteins of a similar fold
BIOPHYSICAL JOURNAL, 93:3591-3600, NOV 2007
Recent advances in computational biology have made it possible to map the complete network and energy profile of gas migration pathways inside proteins. Although 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 12 monomeric globins were 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 modi. cations of these pathways.
DOI:10.1529/biophysj.107.108712
