Freie Universität Berlin
Fachbereich Mathematik und Informatik
Adaptive Conformation Dynamics with Application to Rhodopsin Activation
Rare molecular events such as folding of proteins or nucleic acids, ligand binding, conformational changes or macromolecular aggregation are the basis of all life processes. Besides experimental techniques, molecular dynamics (MD) simulation is an established tool to analyze such processes. However, the usefulness of MD for investigating biological processes is limited by the sampling problem: Due to the high computational effort involved in simulating biomolecules at atomistic resolution, the accessible simulation times are much too short to find the biologically relevant conformations and make statistically reliable statements about transition rates. This problem also hinders the improvement of molecular models towards the reliable prediction of experimental observables. In the proposed work we will develop an adaptive conformation dynamics (ACD) which facilitates the simulation of slow biomolecular processes on small CPU clusters using atomistic models. This method will be applied in order to elucidate the detailed structural mechanism of the activation of the G-protein coupled receptor Rhodopsin.