Studying protein assembly with reversible Brownian dynamics of patchy particles
arXiv:1404.5827 · doi:10.1063/1.4873708
Abstract
Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex or the actin cytoskeleton is strongly determined by their spatial structure. Moreover it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly.
arXiv commentRevtex, 41 pages, 9 figures, includes some small corrections compared to first version
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Cited by in corpus (5)
- Particle-based membrane model for mesoscopic simulation of cellular dynamics
- Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics
- Role of dynamic capsomere supply for viral capsid self-assembly
- Dissipative self-assembly of patchy particles under nonequilibrium drive: a computational study
- Detailed Balance for Particle Models of Reversible Reactions in Bounded Domains