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Seminar

Steered Molecular Dynamics Studies of Ligand Binding and Protein Unfolding

Monday, 3:00 pm
September 14, 1998
3269 Beckman Institute

Steered molecular dynamics (SMD) induces unbinding of ligands and conformational changes in biomolecules on time scales accessible to molecular dynamics simulations. Time-dependent external forces are applied to a system, and the responses of the system are analyzed. SMD has already provided important qualitative insights into biologically relevant problems ranging from the identification and characterization of ligand binding pathways to the study of distortion and unfolding of immunoglobulin and fibronectin type III domains. The SMD trajectories demonstrate in the latter case that inter-strand hydrogen bonds control the behavior of protein domains exposed to mechanical strain, whereas in proteins not intended to withstand mechanical strain such control (protection) does not exist. First attempts to deduce potentials of mean force by discounting irreversible work performed on the system will also be summarized.