The inherent structure landscape of a protein
- *Department of Mathematical Sciences, Ibaraki University, Mito, Ibaraki 310-8512, Japan; and
- †Laboratoire de Physique, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
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Communicated by Hans Frauenfelder, Los Alamos National Laboratory, Los Alamos, NM, January 8, 2006 (received for review April 14, 2005)
Abstract
Using the Gō model of a real protein, we explore the landscape of its metastable structures. First, we show how the inherent structure energy density can be obtained from the probability density determined by sampling molecular dynamics trajectories and quenching. The analysis of the inherent structure landscape can characterize the folding transition. Then we show how thermodynamics of the inherent states can be established to study the equilibrium properties of proteins. Our work brings some elements into the current discussion about the protein dynamical transition. The study uses a simplified model to illustrate the ideas, but, as the inherent structure landscape is much simpler than the free energy surface of the protein, it appears to be accessible for an all-atom model of a small protein, at the expense of much longer calculations.
Footnotes
- ‡To whom correspondence should be addressed. E-mail: nah{at}mx.ibaraki.ac.jp
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Author contributions: N.N. and M.P. performed research and wrote the paper.
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↵ § The results from thermodynamics in the inherent structure space are not affected by a possible lack of ergodicity at low temperature because they are established from a density of states deduced from simulations around the T f. Their accuracy is determined by the quality of the sampling of the phase space in the vicinity of the T f.
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Conflict of interest statement: No conflicts declared.
- Abbreviations:
- ISL,
- inherent structure landscape;
- Tf,
- folding temperature
Abbreviations:
- © 2006 by The National Academy of Sciences of the USA
