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Title: Graph representation of protein free energy landscape

The thermodynamics and kinetics of protein folding and protein conformational changes are governed by the underlying free energy landscape. However, the multidimensional nature of the free energy landscape makes it difficult to describe. We propose to use a weighted-graph approach to depict the free energy landscape with the nodes on the graph representing the conformational states and the edge weights reflecting the free energy barriers between the states. Our graph is constructed from a molecular dynamics trajectory and does not involve projecting the multi-dimensional free energy landscape onto a low-dimensional space defined by a few order parameters. The calculation of free energy barriers was based on transition-path theory using the MSMBuilder2 package. We compare our graph with the widely used transition disconnectivity graph (TRDG) which is constructed from the same trajectory and show that our approach gives more accurate description of the free energy landscape than the TRDG approach even though the latter can be organized into a simple tree representation. The weighted-graph is a general approach and can be used on any complex system.
Authors:
; ; ;  [1] ;  [2]
  1. Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610 (United States)
  2. Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, Massachusetts 01610 (United States)
Publication Date:
OSTI Identifier:
22251450
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 139; Journal Issue: 18; Other Information: (c) 2013 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; FREE ENERGY; MOLECULAR DYNAMICS METHOD; PROTEINS; THERMODYNAMICS