Berlin 2008 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 28: Molecular Recognition

BP 28.8: Vortrag

Freitag, 29. Februar 2008, 12:30–12:45, PC 203

Stochastic dynamics of protein assembly — •Jakob Schluttig and Ulrich Schwarz — University of Heidelberg, Bioquant, BQ 0013 BIOMS Schwarz, INF 267, D-69120, Heidelberg, Germany

The growing interest in structure and dynamics of protein assemblies requires the development of computer time-efficient modelling methods. In our approach, we combine efficient methods from stochastic dynamics with molecular information derived from all-atom simulations. In order to bridge these two fields, we use the concept of an encounter complex, which denotes an intermediate state of mutual entanglement separating the spatially completely separated reaction partners and the bound state. The stochastic transport process preceeding the formation of the encounter complex is described with a Langevin equation. The effect of anisotropic proteins and anisotropic intermediates is studied using non-diagonal mobility matrices. Long-ranged (electrostatic) interactions can be taken into account using appropriate drift terms. We apply our methods to several cases of biological interest, including bi-molecular reactions like barnase-bastar and large assemblies like viral capsids.