The role of the energy gap in protein folding dynamics

TL;DR

This paper investigates how the energy gap affects protein folding dynamics using a master equation approach, revealing that the gap can either accelerate or slow down folding depending on the transition model.

Contribution

It introduces a phenomenological model analyzing the impact of energy gaps on folding times with various transition probability models.

Findings

Increasing the energy gap can accelerate folding in some models.

In other models, a larger gap slows down the folding process.

The effect of the energy gap depends on the transition probabilities between states.

Abstract

The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The influence of the gap on the folding dynamics is studied, for various models of the transition probabilities between the different states of the protein. We show that for certain models, the relaxation to the native state is accelerated by increasing the gap, whereas for others it is slowed down .