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.
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14 May 2014
Research Article|
May 12 2014
Studying protein assembly with reversible Brownian dynamics of patchy particles
Heinrich C. R. Klein;
Heinrich C. R. Klein
1Institute for Theoretical Physics,
Heidelberg University
, 69120 Heidelberg, Germany
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Ulrich S. Schwarz
Ulrich S. Schwarz
a)
1Institute for Theoretical Physics,
Heidelberg University
, 69120 Heidelberg, Germany
2BioQuant,
Heidelberg University
, 69120 Heidelberg, Germany
Search for other works by this author on:
a)
Electronic mail: [email protected]
J. Chem. Phys. 140, 184112 (2014)
Article history
Received:
December 20 2013
Accepted:
April 17 2014
Citation
Heinrich C. R. Klein, Ulrich S. Schwarz; Studying protein assembly with reversible Brownian dynamics of patchy particles. J. Chem. Phys. 14 May 2014; 140 (18): 184112. https://doi.org/10.1063/1.4873708
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