Curvature of the energy landscape and folding of model proteins

Abstract

We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical trajectories are the geodesics of the metric. Using numerical simulations, we show that the fluctuations of the curvature clearly mark the folding transition, and that this quantity allows to distinguish between polymers having a protein-like behavior (i.e., that fold to a unique configuration) and polymers which undergo a hydrophobic collapse but do not have a folding transition. These geometrical properties are defined by the potential energy without requiring any prior knowledge of the native configuration.

arXiv comment5 pages, 1 figure. Revised version accepted for publication in Physical Review Letters

References in corpus (9)

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• Geometric approach to the dynamic glass transition
• Riemannian theory of Hamiltonian chaos and Lyapunov exponents
• Geometry of dynamics, Lyapunov exponents and phase transitions
• Energy Landscape of a Model Protein
• Geometry of dynamics and phase transitions in classical lattice phi^4 theories
• Topological aspects of geometrical signatures of phase transitions
• Thermally activated processes in polymer dynamics
• Exploring the energy landscape of model proteins: a metric criterion for the determination of dynamical connectivity

Cited by in corpus (8)

• Phase transitions and configuration space topology
• Microcanonical versus Canonical Analysis of Protein Folding
• Multifractal Analysis of Polyalanines Time Series
• 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
• Geometry of the energy landscape of the self-gravitating ring
• Density of states of the $XY$ model: an energy landscape approach
• Selecting fast folding proteins by their rate of convergence