TY - JOUR
T1 - Finding gas diffusion pathways in proteins
T2 - Application to O2 and H2 transport in CpI [FeFe]-hydrogenase and the role of packing defects
AU - Cohen, Jordi
AU - Kim, Kwiseon
AU - King, Paul
AU - Seibert, Michael
AU - Schulten, Klaus
N1 - Funding Information:
We wish to thank Maria Ghirardi and Wesley B. Jones at the National Renewable Energy Laboratory for helpful discussions. This work was supported by the National Institutes of Health Research grant P41-RR05969, the National Science Foundation supercomputer time grant NRAC MCA93S028, the DOE Hydrogen Fuel Cells and Infrastructure Technologies Program (K.K., P.K., and M.S.), the Office of Basic Energy Sciences, DOE (K.K., P.K., and M.S.) and by a DOE Hydrogen Fuel Initiative Award (J.C. and R.S.). Three-dimensional molecular graphics were generated by using the VMD visualization software ( Humphrey et al., 1996 ).
PY - 2005/9
Y1 - 2005/9
N2 - We report on a computational investigation of the passive transport of H2 and O2 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 that had not been detected by previous analyses of CpI's static crystal structure. Our results suggest that small hydrophobic molecules, such as H2 and O2, diffusing inside CpI, take advantage of well-defined preexisting packing defects that are not always apparent from the protein's static structure, but that can be predicted from the protein's dynamical motion. Finally, we describe two contrasting modes of intraprotein transport for H2 and O2, which in our model are differentiated only by their size.
AB - We report on a computational investigation of the passive transport of H2 and O2 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 that had not been detected by previous analyses of CpI's static crystal structure. Our results suggest that small hydrophobic molecules, such as H2 and O2, diffusing inside CpI, take advantage of well-defined preexisting packing defects that are not always apparent from the protein's static structure, but that can be predicted from the protein's dynamical motion. Finally, we describe two contrasting modes of intraprotein transport for H2 and O2, which in our model are differentiated only by their size.
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U2 - 10.1016/j.str.2005.05.013
DO - 10.1016/j.str.2005.05.013
M3 - Article
C2 - 16154089
AN - SCOPUS:24344440880
SN - 0969-2126
VL - 13
SP - 1321
EP - 1329
JO - Structure
JF - Structure
IS - 9
ER -