TCB Publications - Abstract
Jordi Cohen, Kwiseon Kim, Paul King, Michael Seibert, and Klaus Schulten. Finding gas diffusion pathways in proteins: Application to O2 and H2 transport in CpI [FeFe]-hydrogenase and the role of packing defects. Structure, 13:1321-1329, 2005.
and O between the external solution and the
hydrogen-producing active site of CpI [FeFe]-hydrogenase from
Clostridium pasteurianum. Two distinct methodologies for studying gas
access are discussed and applied: (1) temperature-controlled locally
enhanced sampling, and (2) volumetric solvent accessibility maps,
providing consistent results. Both methodologies confirm the existence
and function of a previously hypothesized pathway and reveal a second
major pathway which had not been detected by previous analyses of
CpI's static crystal structure. Our results suggest that small
hydrophobic molecules, such as H and O, diffusing inside CpI,
take advantage of well-defined pre-existing packing defects which are
not always apparent from the protein's static structure, but which can
be predicted from the protein's dynamical motion. Finally, we describe two contrasting modes of intra-protein transport for H and O, which in our model are differentiated only by their size.
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