P. Pliego-Pastrana and M. D. Carbajal-Tinoco. 2.Two-components polypeptides modeled with effective pair potentials. (2006) The Journal of Physical Chemistry B 110, 24728-24733.
We present Monte Carlo simulations performed within a model based on a set of distance-dependent effective potentials which are used to describe the interactions between a pair of distinct amino acids. These effective potentials are extracted from experimental correlation functions through the Ornstein?Zernike equations and adequate closure approximations. We focus our attention on the sequences of two specific residues, namely, alanine and glycine. The studied sequences are (a) (Ala)12-(Gly)4-(Ala)12 and (b) three interacting chains of alternating alanines and glycines (with five residues per chain). The resulting structures are combinations of known secondary structures. More importantly, we verify that our simulated structures are in thermodynamic equilibrium by means of an estimation of the density of states.