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The Inherent Structure Landscape of a Protein
Naoko Nakagawa and Michel Peyrard
Proceedings of the National Academy of Sciences of the United States of America
Vol. 103, No. 14 (Apr. 4, 2006), pp. 5279-5284
Published by: National Academy of Sciences
Stable URL: http://www.jstor.org/stable/30048792
Page Count: 6
You can always find the topics here!Topics: Thermodynamics, Specific heat, Molecular dynamics, Trajectories, Simulations, Entropy, Modeling, Flux density, Free energy, Energy
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Using the Go 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.
Proceedings of the National Academy of Sciences of the United States of America © 2006 National Academy of Sciences