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Protein Science (2007), 16:1101-1118. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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Molecular dynamics simulations of the native and partially folded states of ubiquitin: Influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics

David B. Kony, Philippe H. Hünenberger, and Wilfred F. van Gunsteren

Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland

(RECEIVED June 7, 2006; FINAL REVISION February 1, 2007; ACCEPTED February 7, 2007)

A series of explicit-solvent molecular dynamics simulations of the protein ubiquitin are reported, which investigate the effect of environmental factors (presence of methanol cosolvent in the aqueous solution, neutral or low pH value, room or elevated temperature) on the structure, stability, and dynamics of the protein. The simulations are initiated either from the native structure of the protein or from a model of a partially folded state (A-state) that is known to exist at low pH in methanol–water mixtures. The main results of the simulations are: (1) The ubiquitin native structure is remarkably stable at neutral pH in water; (2) the addition of the methanol cosolvent enhances the stability of the secondary structure but weakens tertiary interactions within the protein; (3) this influence of methanol on the protein structure is enhanced at low pH, while the effect of lowering the pH in pure water is limited; and (4) the A-state of ubiquitin can be described as a set of relatively rigid secondary structure elements (a native-like beta-sheet and native-like {alpha}-helix plus two nonnative {alpha}-helices) connected by flexible linkers.

Keywords: molecular dynamics; protein folding; partially folded state; ubiquitin; water–methanol mixture


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