Synchronization as a unifying mechanism for protein folding

TL;DR

This paper proposes that synchronization of peptide oscillations is a fundamental mechanism in protein folding, offering a unifying physical principle that explains folding kinetics, thermodynamics, and related biological phenomena.

Contribution

It introduces a novel hypothesis linking peptide synchronization to protein folding, using the Kuramoto model to unify various models and phenomena in the field.

Findings

Synchronization explains folding pathways and kinetics.

The model addresses Levinthal's paradox.

It provides insights into homology modeling and receptor recognition.

Abstract

Different models such as diffusion-collision and nucleation-condensation have been used to unravel how secondary and tertiary structures form during protein folding. However, a simple mechanism based on physical principles that provide an accurate description of kinetics and thermodynamics for such phenomena has not yet been identified. This study introduces the hypothesis that the synchronization of the peptide plane oscillatory movements throughout the backbone must also play a key role in the folding mechanism. Based on that, we draw a parallel between the folding process and the dynamics for a network of coupled oscillators described by the Kuramoto model. The amino acid coupling may explain the mean-field character of the force that propels an amino acid sequence into a structure through self-organization. Thus, the pattern of synchronized cluster formation and growing helps to solve the Levinthal's paradox.Synchronization may also help us to understand the success of homology structural modeling, allosteric effect, and the mechanism responsible for the recognition of odorants by olfactory receptors.