Publication: Dissipative Dynamics and the Statistics of Energy States of a Hookean Model for Protein Folding
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Springer Science and Business Media LLC
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Abstract
A generic model of a random polypeptide chain, with discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues, reproduces the energy probability distribution of real proteins over a very large range of energies. We show that this system with harmonic interactions, under dissipative dynamics driven by random noise, leads to a distribution of energy states obeying a modified one-dimensional Ornstein-Uhlenbeck process and giving rise to the so called Wigner distribution. A tunably fine- or coarse-grained sampling of the energy landscape yields a family of distributions for the energies and energy spacings.
RevTeX, 24 pages, including 8 figures
RevTeX, 24 pages, including 8 figures
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Relaxation, Behavior, Statistical Mechanics (cond-mat.stat-mech), Biochemistry, molecular biology, Dissipative dynamics, Biophysics, FOS: Physical sciences, Biomolecules (q-bio.BM), Condensed Matter - Soft Condensed Matter, Universality, Charge-density waves, Quantitative Biology - Biomolecules, Spectrum, protein folding, FOS: Biological sciences, Soft Condensed Matter (cond-mat.soft), dissipative dynamics, Protein folding, Motions, Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.), Condensed Matter - Statistical Mechanics