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Int. J. Mol. Sci. 2009, 10(4), 1808-1823; doi:10.3390/ijms10041808

Uncovering the Properties of Energy-Weighted Conformation Space Networks with a Hydrophobic-Hydrophilic Model

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1
and
1,*
1
College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, P.R. China
2
College of Science, Yanshan University, Qinhuangdao, 066004, P.R. China
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These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Received: 14 January 2009 / Revised: 30 March 2009 / Accepted: 7 April 2009 / Published: 21 April 2009
(This article belongs to the Special Issue Protein Folding 2009)
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Abstract

The conformation spaces generated by short hydrophobic-hydrophilic (HP) lattice chains are mapped to conformation space networks (CSNs). The vertices (nodes) of the network are the conformations and the links are the transitions between them. It has been found that these networks have “small-world” properties without considering the interaction energy of the monomers in the chain, i. e. the hydrophobic or hydrophilic amino acids inside the chain. When the weight based on the interaction energy of the monomers in the chain is added to the CSNs, it is found that the weighted networks show the “scale-free” characteristic. In addition, it reveals that there is a connection between the scale-free property of the weighted CSN and the folding dynamics of the chain by investigating the relationship between the scale-free structure of the weighted CSN and the noted parameter Z score. Moreover, the modular (community) structure of weighted CSNs is also studied. These results are helpful to understand the topological properties of the CSN and the underlying free-energy landscapes.
Keywords: Protein Folding; Conformation Space; Complex Network Protein Folding; Conformation Space; Complex Network
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Lai, Z.; Su, J.; Chen, W.; Wang, C. Uncovering the Properties of Energy-Weighted Conformation Space Networks with a Hydrophobic-Hydrophilic Model. Int. J. Mol. Sci. 2009, 10, 1808-1823.

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