Geometry of the energy landscape and folding transition in a simple model of a protein

Abstract

A geometric analysis of the global properties of the energy landscape of a minimalistic model of a polypeptide is presented, which is based on the relation between dynamical trajectories and geodesics of a suitable manifold, whose metric is completely determined by the potential energy. We consider different sequences, some with a definite protein-like behavior, a unique native state and a folding transition, and the others undergoing a hydrophobic collapse with no tendency to a unique native state. The global geometry of the energy landscape appears to contain relevant information on the behavior of the various sequences: in particular, the fluctuations of the curvature of the energy landscape, measured by means of numerical simulations, clearly mark the folding transition and allow to distinguish the protein-like sequences from the others.

to appear in Physical Review E

References in corpus (5)

• Phase transitions and configuration space topology
• Reconstructing the free energy landscape of a mechanically unfolded model protein
• Curvature of the energy landscape and folding of model proteins
• 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 (5)

• Hidden Symmetries of Dynamics in Classical and Quantum Physics
• Hidden symmetries of Eisenhart-Duval lift metrics and the Dirac equation with flux
• A graph theoretical analysis of the energy landscape of model polymers
• Geometry of the energy landscape of the self-gravitating ring
• Selecting fast folding proteins by their rate of convergence