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Modeling the Chain Entropy of Biopolymers: Unifying Two Different Random Walk Models under One Framework | OMICS International | Abstract
ISSN: 0974-7230

Journal of Computer Science & Systems Biology
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Research Article

Modeling the Chain Entropy of Biopolymers: Unifying Two Different Random Walk Models under One Framework

Wayne Dawson* and Gota Kawai
Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan
Corresponding Author : Wayne Dawson
Bioinformation Engineering Laboratory,
Department of Biotechnology
Graduate School of Agriculture and Life Sciences
The University of Tokyo, 1-1-1 Yayoi
Bunkyo-ku, Tokyo 113-8657,
Email : [email protected]
Received December 18, 2008; Accepted January 31, 2009; Published February 03, 2009
Citation: Dawson W, Kawai G (2009). Modeling the Chain Entropy of Biopolymers: Unifying Two Different Random Walk Models under One Framework. J Comput Sci Syst Biol 2:001-023. doi:10.4172/jcsb.1000014
Copyright: © 2009 Dawson W, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Abstract

Entropy plays a critical role in the long range structure of biopolymers. To model the coarse-grained chain entropy of the residues in biopolymers, the lattice model or the Gaussian polymer chain (GPC) model is typically used. Both models use the concept of a random walk to find the conformations of an unstructured polymer. However, the entropy of the lattice model is a function of the coordination number, whereas the entropy of the GPC is a function of the root-mean square separation distance between the ends of the polymer. This can lead to inconsistent predictions for the coarse-grained entropy. Here we show that the GPC model and the lattice model both are consistent under transformations using the cross-linking entropy (CLE) model and that the CLE model generates a family of equations that include these two models at important limits. We show that the CLE model is a unifying approach to the thermodynamics of biopolymers that links these incompatible models into a single framework, elicits their similarities and differences, and expands beyond the models allowing calculation of variable flexibility and incorporating important corrections such as the worm-like-chain model. The CLE model is also consistent with the contact-order model and, when combined with existing local pairing potentials, can predict correct structures at the minimum free energy.

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