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

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. 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 singl