Theory and simulations for crowding-induced changes in stability of proteins with applications to $\lambda$ repressor

TL;DR

This paper develops a theoretical framework and simulations to understand how crowding particles influence protein stability, revealing a power-law relationship between crowding and melting temperature, with implications for cellular environments.

Contribution

The study introduces a theoretical model linking crowding effects to protein stability via the Flory exponent and confirms it with molecular simulations and analysis of prior data.

Findings

Melting temperature increase scales as a power law with crowding volume fraction.

Effective Flory exponent determines the strength of crowding effects.

Non-specific attractions can negate stabilization from depletion forces.

Abstract

Experiments and theories have shown that when steric interactions between crowding particles and proteins are dominant, which give rise to Asakura-Oosawa depletion forces, then the stabilities of the proteins increase compared to the infinite dilution case. We show using theoretical arguments that the crowder volume fraction ($\Phi_C$) dependent increase in the melting temperature of globular proteins, $\Delta T_m(\Phi_C) \approx \Phi_C^{\alpha}$ where $\alpha = \frac{1}{(3 \nu_{eff} - 1)}$. The effective Flory exponent, $\nu_{eff}$, relates the radius of gyration in the unfolded state to the number of amino acid residues in the protein. We derive the bound 1.25 $\le \alpha \le$ 2.0. The theoretical predictions are confirmed using molecular simulations of $\lambda$ repressor in the presence of spherical crowding particles. Analyses of previous simulations and experiments confirm the predicted theoretical bound for $\alpha$. We show that the non-specific attractions between crowding particles and amino acid residues have to be substantial to fully negate the enhanced protein stabilities due to intra protein attractive Asakura-Oosawa (AO) depletion potential. Using the findings, we provide an alternate explanation for the very modest (often less than 0.5 Kcal/mol) destabilization in certain proteins in the cellular milieu. Cellular environment is polydisperse containing large and small crowding agents. AO arguments suggest that proteins would be localized between large (sizes exceeding that of the proteins) crowders, which are predicted to have negligible effect on stability. {\it In vitro} experiments containing mixtures of crowding particles could validate or invalidate the predictions.