Berlin 2005 – scientific programme

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AKB: Biologische Physik

AKB 100: Poster Session I

AKB 100.81: Poster

Saturday, March 5, 2005, 16:45–18:45, Poster TU D

Analysis of the Protein-Protein Association Free Energy Studied by Brownian Dynamics Simulations — •Alexander Spaar — Center for Bioinformatics, Saarland University, Im Stadtwald, D-66041 Saarbrücken, Germany

We carefully analyzed the trajectories from Brownian Dynamics (BD) simulations in order to study protein-protein encounter on the example of barnase and barstar, a well characterized model system of electrostatically steered diffusional association. The individual positions and orientations of the proteins during all trajectories are stored in occupancy maps. By interpreting the occupancy maps as probability distributions and by defining a local entropy function we are able to compute the 6-dimensional entropy landscape for the encounter of the two proteins. Together with the configuration dependent electrostatic and desolvation energies, the association free energy is obtained as the sum of these terms. In the free energy profile along the reaction path, which is defined as the path along the minima in the free energy landscape a characteristic minimum at small distances shows up, suggesting this to be used as the definition of the encounter state. The association free energy profiles are compared for different ionic strength and temperature of the solvent.