Two-component polypeptides modeled with effective pair potentials.
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.
Pliego-Pastrana
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Departamento de Física, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, 07000 México D.F., Mexico.
Carbajal-Tinoco
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MD
D000409:Alanine / Q000737:chemistry; D005998:Glycine / Q000737:chemistry; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011108:Polymers / Q000737:chemistry; D017434:Protein Structure, Tertiary
D010455:Peptides; D011108:Polymers; D000409:Alanine; D005998:Glycine