Role of anisotropy for protein-protein encounter

TL;DR

This study investigates how protein anisotropy influences encounter rates during protein-protein interactions, revealing that steric effects dominate over diffusion anisotropy, with implications for understanding molecular recognition.

Contribution

The paper provides a quantitative analysis of anisotropy effects on encounter rates using Brownian dynamics simulations, highlighting the dominance of steric effects over diffusion anisotropy.

Findings

Encounter rate depends mainly on steric effects of aspect ratio.

Anisotropic diffusion has minimal impact on encounter rate.

Crossover times from anisotropic to isotropic diffusion are much smaller than encounter times.

Abstract

Protein-protein interactions comprise both transport and reaction steps. During the transport step, anisotropy of proteins and their complexes is important both for hydrodynamic diffusion and accessibility of the binding site. Using a Brownian dynamics approach and extensive computer simulations, we quantify the effect of anisotropy on the encounter rate of ellipsoidal particles covered with spherical encounter patches. We show that the encounter rate $k$ depends on the aspect ratios $\xi$ mainly through steric effects, while anisotropic diffusion has only a little effect. Calculating analytically the crossover times from anisotropic to isotropic diffusion in three dimensions, we find that they are much smaller than typical protein encounter times, in agreement with our numerical results.