Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
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Edited by Robin M. Hochstrasser, University of Pennsylvania, Philadelphia, PA (received for review July 21, 2004)
Abstract
A joint analysis of all-atom molecular dynamics (MD) calculations and picosecond time-resolved x-ray structures was performed to gain single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin after ligand dissociation reproduce the direction, amplitude, and time scales of crystallographically determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories. From 1,700 single-molecule trajectories, we identified and structurally characterized a conformational switch that directs dissociated ligands to one of two nearby protein cavities. Subsequent ligand migration proceeds through a network of transiently interconnected internal cavities, with passage between them involving correlated protein–ligand motions. The simulations also suggest how picosecond protein motions modulate the functional dissociation of oxygen and suppress the geminate recombination of toxic carbon monoxide.
Footnotes
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↵ * To whom correspondence may be addressed at: National Institutes of Health, 5 Memorial Drive, Bethesda, MD 20892-0520. E-mail: hummer{at}helix.nih.gov or anfinrud{at}nih.gov.
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Author contributions: G.H., F.S., and P.A.A. designed research; G.H., F.S., and P.A.A. performed research; G.H., F.S., and P.A.A. analyzed data; and G.H. and P.A.A. wrote the paper.
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This paper was submitted directly (Track II) to the PNAS office.
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Abbreviations: Mb, myoglobin; MbCO, Mb with carbon monoxide bound to the heme; MD, molecular dynamics.
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Freely available online through the PNAS open access option.
