Computer Science

Graph representation of protein free energy landscape

Document Type

Article

Abstract

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. © 2013 AIP Publishing LLC.

Publication Title

Journal of Chemical Physics

Publication Date

2013

Volume

139

Issue

18

ISSN

0021-9606

DOI

10.1063/1.4829768

Keywords

free energy landscapes, conformational dynamics, molecular dynamics, thermodynamics, computer simulation, Graph theory, peptides, proteins, Markov processes, statistical analysis

APA Citation

Li, M., Duan, M., Fan, J., Han, L., & Huo, S. (2013). Graph representation of protein free energy landscape. The Journal of Chemical Physics, 139(18).

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