Conformational Temperature Characterizing the Folding of a Protein

Abstract

The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for inherent structures are introduced and from these quantities a conformational temperature is defined. The conformational temperature follows the time evolution of a slow relaxation process and reaches the bath temperature when the system is equilibrated. We show that the nonequilibrium system is described by two temperatures, one for fast vibration and the other for slow configurational relaxation, while the equilibrium system is by one temperature. The proposed formalism is applicable widely for the systems with many metastable states.

References in corpus (2)

• Observable-dependence of fluctuation-dissipation relations and effective temperatures
• Inherent Structures, Configurational Entropy and Slow Glassy Dynamics

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• Characterization of the low temperature properties of a simplified protein model
• Critical examination of the inherent-structure-landscape analysis of two-state folding proteins
• Golf-course and funnel energy landscapes: Protein folding concepts in martensites