Dresden 2009 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 22: Transport Processes and Cellular Trafficking

BP 22.1: Vortrag

Donnerstag, 26. März 2009, 14:30–14:45, ZEU 260

Modelling anisotropy in protein encounter: a Langevin equation approach with reaction patches — •Jakob Schluttig and Ulrich S. Schwarz — University of Karlsruhe, Theoretical Biophysics Group, Kaiserstrasse 12, 76131 Karlsruhe, Germany

Protein association involves anisotropy for at least two reasons. First the shape of proteins might be non-spherical and thus their diffusion matrix is not necessarily diagonal. Second the association process itself is anisotropic because the binding interfaces are localized at specific positions on their surface. We implemented a Langevin equation approach with reaction patches which allows us to study these two effects [1]. For spherical proteins we find that encounter frequency scales linearly with protein concentration, thus proving that our microscopic model results in a well-defined macroscopic encounter rate. For specific systems of interest and appropriate choices for the size of the reaction patches, encounter rates are obtained within one order of magnitude of the experimentally measured association rates. The number of unsuccessful contacts before encounter decreases with increasing encounter rate and ranges from 20-9000. For spheroids, the principal diffusion coefficients are known analytically and do only sublinearly depend on the ratio ξ of the spatial dimensions. Furthermore the crossover from anisotropic to isotropic diffusion caused by rotational diffusion can be evaluated analytically. These analytical results suggest that the effect of varying ξ on the encounter rate is rather weak, as indeed confirmed by computer simulations.

[1] J. Schluttig et al., J. Chem. Phys. 129, 155106 (2008).