Dynamic cluster formation determines viscosity and diffusion in dense protein solutions

Abstract

We develop a detailed description of protein translational and rotational diffusion in concentrated solution on the basis of all-atom molecular dynamics simulations in explicit solvent. Our systems contain up to 540 fully flexible proteins with 3.6 million atoms. In concentrated protein solutions (100 mg/mL and higher), the proteins ubiquitin and lysozyme, as well as the protein domains third IgG-binding domain of protein G and villin headpiece, diffuse not as isolated particles, but as members of transient clusters between which they constantly exchange. A dynamic cluster model nearly quantitatively explains the increase in viscosity and the decrease in protein diffusivity with protein volume fraction, which both exceed the predictions from widely used colloid models. The Stokes–Einstein relations for translational and rotational diffusion remain valid, but the effective hydrodynamic radius grows linearly with protein volume fraction. This increase follows the observed increase in cluster size and explains the more dramatic slowdown of protein rotation compared with translation. Baxter’s sticky-sphere model of colloidal suspensions captures the concentration dependence of cluster size, viscosity, and rotational and translational diffusion. The consistency between simulations and experiments for a diverse set of soluble globular proteins indicates that the cluster model applies broadly to concentrated protein solutions, with equilibrium dissociation constants for nonspecific protein–protein binding in the Kd ≈ 10-mM regime.

Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design

“…173 However, soluble proteins can self-associate in a crowded environment, and such self-association has been suggested to form transient and dynamic clusters in concentrated solutions. 28,174,175 Under these circumstances, a simplified coarsegrained (CG) representation of antibody molecules and their simulations can prove useful in the study of the viscosity behavior of concentrated antibody solutions.…”

Simulation of FUS protein condensates with an adapted coarse-grained model

“…While high computational costs still preclude their widespread use for simulating LLPS, they promise considerable insights into structures and interactions of biomolecules in (sub-systems of) phase-separated condensates [26][27][28][29] and how these give rise to materials properties. 30 Soft-matter approaches 31 provide access to the large length and long timescales relevant for phase separation, but may not resolve the detailed effects of protein chemistry and may not be transferable. Overcoming these two issues would require transferable models.…”

Potential and limits of a colloid approach to protein solutions

“…31 The importance of transient cluster formation on short time dynamics for short-range attractive particles has also been pointed out in other simulation studies. 152,153 With the extreme sensitivity of the local collective short-time diffusion to the exact interaction potential in patchy systems, it is clear that understanding and predicting protein dynamics in crowded environments on these short length scales requires a considerable future effort for conditions where the interactions are not primarily repulsive, but influenced by directional attractive contributions.…”