(253bo) Predicting Protein Dynamics in Complex Environments

Faller, R., UC Davis
A simulation model for proteins at the mass transport scale has been developed for the purpose of studying the separation of proteins based on isoelectric point and ionic strength. Coarse graining is required to investigate the mass trasport regimes of proteins using computational methods. The raspberry model for colloid particles is a rigid body defined by generic beads spready evenly over the surface. The hydrodynamics are resolved using lattice Boltzmann fluid. Spherical and ellipsoidal geometries have been constructed to validate the hydrodynamic characteristics of these colloid particles, namely, the effects of size, shape, and confinement on the diffusion tensor. The model has been extended to protein-shaped particles using the solvent accessible surface of a protein and charges assignment based on electrostatic potential mapping of the atomistic protein model. The computation effort is vastly reduced while maintaining accurate descriptions of the excluded volume, electrostatic, and hydrodynamic effects that dominate protein transport.