Network rigidity at finite temperature: Relationships between thermodynamic stability, the non-additivity of entropy and cooperativity in molecular systems

TL;DR

This paper introduces a statistical mechanical distance constraint model that explicitly incorporates network rigidity to explain thermodynamic stability, entropy non-additivity, and cooperativity in molecular systems, with applications to protein conformational transitions.

Contribution

The paper presents a novel distance constraint model that accounts for network rigidity and provides a quantitative framework for understanding entropy non-additivity and cooperativity in molecular systems.

Findings

Model accurately predicts alpha-helix to coil transition in peptides.

Network rigidity explains cooperativity and self-organization in molecular structures.

Model parameters fitted to Monte Carlo simulation data across different conditions.

Abstract

A statistical mechanical distance constraint model (DCM) is presented that explicitly accounts for network rigidity among constraints present within a system. Constraints are characterized by local microscopic free energy functions. Topological re-arrangements of thermally fluctuating constraints are permitted. The partition function is obtained by combining microscopic free energies of individual constraints using network rigidity as an underlying long-range mechanical interaction -- giving a quantitative explanation for the non-additivity in component entropies exhibited in molecular systems. Two exactly solved 2-dimensional toy models representing flexible molecules that can undergo conformational change are presented to elucidate concepts, and to outline a DCM calculation scheme applicable to many types of physical systems. It is proposed that network rigidity plays a central role in balancing the energetic and entropic contributions to the free energy of bio-polymers, such as proteins. As a demonstration, the distance constraint model is solved exactly for the alpha-helix to coil transition in homogeneous peptides. Temperature and size independent model parameters are fitted to Monte Carlo simulation data, which includes peptides of length 10 for gas phase, and lengths 10, 15, 20 and 30 in water. The DCM is compared to the Lifson-Roig model. It is found that network rigidity provides a mechanism for cooperativity in molecular structures including their ability to spontaneously self-organize. In particular, the formation of a characteristic topological arrangement of constraints is associated with the most probable microstates changing under different thermodynamic conditions.