Exploring the energy landscape of model proteins: a metric criterion for the determination of dynamical connectivity

Abstract

A method to reconstruct the energy landscape of small peptides is presented with reference to a 2d off--lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly connected pairs (DCP). As the mutual distance of DCP is typically much smaller than that of generic pairs, a metric criterion can be established to identify the great majority of DCP. Advantages and limits of this approach are thoroughly analyzed for three different heteropolymeric chains. A funnel--like structure of the energy landscape is found in all of the three cases, but the escape rates clearly reveal that the native configuration is more easily accessible (and is significantly more stable) for the sequence that is expected to behave as a real protein.

arXiv comment10 pages, 16 figures, submitted to Physical. Review. E

References in corpus (5)

• Simulated Tempering: A New Monte Carlo Scheme
• Saddles in the energy landscape probed by supercooled liquids
• Studies of an Off-Lattice Model for Protein Folding: Sequence Dependence and Improved Sampling at Finite Temperature
• Identification of Amino Acid Sequences with Good Folding Properties in an Off-Lattice Model
• Thermally activated processes in polymer dynamics

Cited by in corpus (5)

• Curvature of the energy landscape and folding of model proteins
• Free energy landscape of mechanically unfolded model proteins: extended Jarzinsky versus inherent structure reconstruction
• Geometry of the energy landscape and folding transition in a simple model of a protein
• A graph theoretical analysis of the energy landscape of model polymers
• Stochastic dynamics of model proteins on a directed graph