Conformational temperature characterizing the folding of a protein

Area of Science:

• Computational chemistry
• Biophysics
• Statistical mechanics

Background:

• Protein folding is a complex process involving intricate molecular dynamics.
• Understanding the configurational dynamics of proteins is crucial for comprehending their function.
• Existing models often simplify the multi-state nature of protein folding landscapes.

Purpose of the Study:

• To analyze the configurational dynamics of protein folding using molecular dynamics simulations.
• To introduce a novel concept of 'conformational temperature' to characterize the system's state.
• To differentiate between equilibrium and non-equilibrium states in molecular systems.

Main Methods:

• Analysis of time sequences from molecular dynamics simulations.
• Focus on the inherent structure landscape to capture configurational dynamics.
• Introduction of time-dependent energy and entropy for inherent structures.

Main Results:

• A new 'conformational temperature' is defined based on energy and entropy.
• Conformational temperature tracks slow relaxation processes, equilibrating to bath temperature.
• Non-equilibrium systems are characterized by two temperatures: one for vibrations, one for configurational relaxation.

Conclusions:

• The proposed formalism provides a dual-temperature description for non-equilibrium systems.
• Equilibrated systems are accurately described by a single temperature.
• The formalism is broadly applicable to systems with multiple metastable states, enhancing our understanding of complex molecular behavior.