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BP: Fachverband Biologische Physik
BP 22: Statistical Physics of Biological Systems III (with DY)
BP 22.7: Vortrag
Donnerstag, 29. März 2012, 16:30–16:45, H 1058
Brownian dynamics simulation with hydrodynamic interactions of crowded protein solutions — •Paolo Mereghetti1,2 and Rebecca Wade1 — 1Heidelberg Institute for Theoretical Studies (HITS) gGmbH, Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany — 2Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
The study of solutions of biomacromolecules provides an important basis for understanding the behavior of many fundamental cellular processes, such as protein folding, self-assembly, and signal transduction. We have developed the SDAMM Brownian dynamics simulation software to investigate the dynamic and structural properties of dilute protein solutions. In the model used, the proteins are treated as atomically detailed rigid bodies moving in a continuum solvent. The method showed good agreement with experimental data for proteins of concentrations up to 60 g/L even though hydrodynamic interactions were neglected. We here describe new developments of the simulation model to extend the range of applicability to protein solutions as concentrated as cell-like environments where the effect of hydrodynamic interactions cannot be neglected. To take hydrodynamic interactions into account, we use a mean field model and we apply the method to investigate the behaviour of concentrated solutions (up to 40% volume fraction) of normal and sickle cell hemoglobin, and of myoglobin. From these simulations, we assessed the effects of hydrodynamic interactions, short-range interactions and excluded volume effects on diffusion.