title: Rotational Brownian dynamics simulations of clathrin cage formation.
abstract: The self-assembly of nearly rigid proteins into ordered aggregates is well suited for modeling by the patchy particle approach. Patchy particles are traditionally simulated using Monte Carlo methods, to study the phase diagram, while Brownian Dynamics simulations would reveal insights into the assembly dynamics. However, Brownian Dynamics of rotating anisotropic particles gives rise to a number of complications not encountered in translational Brownian Dynamics. We thoroughly test the Rotational Brownian Dynamics scheme proposed by Naess and Elsgaeter [Macromol. Theory Simul. 13, 419 (2004); Naess and Elsgaeter Macromol. Theory Simul. 14, 300 (2005)], confirming its validity. We then apply the algorithm to simulate a patchy particle model of clathrin, a three-legged protein involved in vesicle production from lipid membranes during endocytosis. Using this algorithm we recover time scales for cage assembly comparable to those from experiments. We also briefly discuss the undulatory dynamics of the polyhedral cage.
authors.affiliation: Computational BioPhysics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.
authors.forename: Ioana M
authors.initials: IM
authors.lastname: Ilie
authors.affiliation: Computational BioPhysics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.
authors.forename: Wouter K
authors.initials: WK
authors.lastname: den Otter
authors.affiliation: Computational BioPhysics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.
authors.forename: Wim J
authors.initials: WJ
authors.lastname: Briels
mesh_terms: D000465:Algorithms; D002966:Clathrin / Q000138:chemical synthesis / Q000737:chemistry*; D009010:Monte Carlo Method; D012399:Rotation
chemical_list: D002966:Clathrin