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Is Protein Folding Sub-Diffusive?

Authors
Journal
PLoS Computational Biology
1553-734X
Publisher
Public Library of Science
Publication Date
Volume
6
Issue
9
Identifiers
DOI: 10.1371/journal.pcbi.1000921
Keywords
  • Research Article
  • Biophysics/Experimental Biophysical Methods
  • Biophysics/Protein Folding
  • Biophysics/Theory And Simulation
  • Computational Biology/Molecular Dynamics
  • Physics/Interdisciplinary Physics
Disciplines
  • Biology

Abstract

Author Summary To understand dynamics of complex systems with many degrees of freedom, one often projects it onto one or several collective variables. Protein folding, the complex, concerted motion of a protein chain towards a unique three-dimensional structure, is one example of where such reduction of complexity is useful. It is usually assumed that the projected dynamics is diffusive. However, many experiments and simulations have shown that the projected dynamics is sub-diffusive, i.e., the mean square displacement grows slower than linear with time. It means that the dynamics has a memory; that the free energy surface together with diffusion coefficient do not properly define the dynamics; and that such projections cannot be used to accurately describe dynamics. Here, we show that if one carefully constructs the reaction coordinate by optimizing (maximizing) its free energy profile, one can use a simple (memory-less) diffusive description. Loosely speaking, when the complex dynamics is projected onto a simple coordinate, all the complexity of the original dynamics goes into the memory of the projected dynamics. If the dynamics is projected onto the (complex) optimum reaction coordinate, all the complexity of the original dynamics is in the reaction coordinate, and the projected dynamics is simple.

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