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Multiple-Basin Energy Landscapes for Large-Amplitude Conformational Motions of Proteins: Structure-Based Molecular Dynamics Simulations

Kei-ichi Okazaki, Nobuyasu Koga, Shoji Takada, Jose N. Onuchic and Peter G. Wolynes
Proceedings of the National Academy of Sciences of the United States of America
Vol. 103, No. 32 (Aug. 8, 2006), pp. 11844-11849
Stable URL: http://www.jstor.org/stable/30051628
Page Count: 6
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Since scans are not currently available to screen readers, please contact JSTOR User Support for access. We'll provide a PDF copy for your screen reader.
Multiple-Basin Energy Landscapes for Large-Amplitude Conformational Motions of Proteins: Structure-Based Molecular Dynamics Simulations
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Abstract

Biomolecules often undergo large-amplitude motions when they bind or release other molecules. Unlike macroscopic machines, these biomolecular machines can partially disassemble (unfold) and then reassemble (fold) during such transitions. Here we put forward a minimal structure-based model, the "multiple-basin model," that can directly be used for molecular dynamics simulation of even very large biomolecular systems so long as the endpoints of the conformational change are known. We investigate the model by simulating large-scale motions of four proteins: glutamine-binding protein, 5100A6, dihydrofolate reductase, and HIV-1 protease. The mechanisms of conformational transition depend on the protein basin topologies and change with temperature near the folding transition. The conformational transition rate varies linearly with driving force over a fairly large range. This linearity appears to be a consequence of partial unfolding during the conformational transition.

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