Conformational Temperature Characterizing the Folding of a Protein

TL;DR

This paper introduces a conformational temperature based on inherent structure analysis to characterize protein folding dynamics, revealing distinct temperatures for vibrational and configurational relaxation in nonequilibrium systems.

Contribution

It proposes a novel formalism to define and analyze conformational temperature, capturing slow relaxation processes in protein folding simulations.

Findings

Conformational temperature tracks the folding process over time.

Two distinct temperatures describe nonequilibrium states.

System reaches bath temperature upon equilibrium.

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.