A Continuous Effective Model of the Protein Dynamics

TL;DR

This paper introduces a continuous effective field theory model for protein dynamics, predicting geometric features and conformations, including helices and beta strands, with results aligning with observed protein behavior.

Contribution

It proposes a novel continuous curve-based model for protein conformations, capturing key features like helices and strands with a minimal parameter set.

Findings

Model predicts helical and strand-like configurations.

Predictions are compatible with experimental protein data.

Parameter controls the abundance of beta strands.

Abstract

The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins. In this letter we report a detailed study of the basic features of a version of the proposed model, which assumes proteins to be very long continuous curves. In the most appealing case, the model is based on a potential with a pair of minima corresponding to helical and strand-like configurations of the curves. It allows to derive several predictions about the geometric features of the molecules, and we show that the predictions are compatible with the phenomenology. While the helices represent the ground state configurations, the abundance of beta strands is controlled by a parameter, which can either completely suppress their presence in a molecule, or make them abundant. The few-parameter model investigated in the letter rather represents a universality class of protein molecules. Generalizations accounting for the discrete nature and inhomogeneity of the molecules presumably allow to model realistic cases.