Modeling the Chain Entropy of Biopolymers: Unifying
Two Different Random Walk Models under One Framework |
Wayne Dawson*, Gota Kawai |
| Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan |
| *Corresponding author: |
Dr. 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,
E-mail: dawson@bi.a.u-tokyo.ac.jp |
|
| 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: ©2008 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. |
| 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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