Diffusional dynamics of cytochrome c molecules in the presence of a charged surface

A new Brownian dynamics code was developed that is capable of computing trajectories of several spherical particles in the presence of a charged planar surface. The code takes into account electrostatic, van der Waals, and hydrodynamic interactions. In this work we describe the methods used in the program and show results from calculations for cytochrome c molecules interacting with a negatively charged lipid bilayer. This system is of particular biological interest since these molecules play a major role as electron carriers, e.g., in photosynthesis. The shape and charge distribution of cytochrome c molecules can be well approximated as spherical particles with an embedded monopole and dipole and can therefore easily be handled by the program. That level of approximation makes it possible to study large systems with many (up to 100) particles over time scales up to milliseconds, which would be computationally too expensive using detailed atomistic models.