Docking and migration of carbon monoxide in nitrogenase: the case for gated pockets from infrared spectroscopy and molecular dynamics.
Evidence of a CO docking site near the FeMo cofactor in nitrogenase has been obtained by Fourier transform infrared spectroscopy-monitored low-temperature photolysis. We investigated the possible migration paths for CO from this docking site using molecular dynamics calculations. The simulations support the notion of a gas channel with multiple internal pockets from the active site to the protein exterior. Travel between pockets is gated by the motion of protein residues. Implications for the mechanism of nitrogenase reactions with CO and N2 are discussed.
†Department of Chemistry, University of California, Davis, California 95616, United States.
Leland B
LB
Gee
§InterX Inc., Berkeley, California 94710, United States.
Igor
I
Leontyev
†Department of Chemistry, University of California, Davis, California 95616, United States.
Alexei
A
Stuchebrukhov
†Department of Chemistry, University of California, Davis, California 95616, United States.
Aubrey D
AD
Scott
∥Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany.
Vladimir
V
Pelmenschikov
†Department of Chemistry, University of California, Davis, California 95616, United States.|‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.
Stephen P
SP
Cramer
D016948:Azotobacter vinelandii / Q000737:chemistry / Q000201:enzymology* / Q000378:metabolism; D001665:Binding Sites; D002248:Carbon Monoxide / Q000378:metabolism*; D020134:Catalytic Domain; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D008983:Molybdoferredoxin / Q000378:metabolism; D009591:Nitrogenase / Q000737:chemistry / Q000378:metabolism*; D010782:Photolysis; D013055:Spectrophotometry, Infrared
D008983:Molybdoferredoxin; D002248:Carbon Monoxide; D009591:Nitrogenase