Structural Mechanics and Protein Flexibility
Simon Guest (University of Cambridge)
Thursday 29th April, 2010 14:00-15:00 326, Maths Department
Proteins are large molecules, typically containing thousands of atoms, which often have both a structural and a mechanical function, i.e., their biological function requires the protein to change conformation, and this change will typically occur over biological time-scales of milliseconds to seconds. However, both direct observation and simulation of such conformational changes is difficult. Occasionally, it is possible to crudely observe the motion associated with a protein complex, but usually the detailed determination of protein shape is done by X-ray diffraction of protein crystals, and naturally during this process the protein is locked in one conformation within the crystal. Simulation of protein molecules with molecular dynamics is also problematic; these are large molecules, and it is typically only feasible to model time-scales of pico- or nano-seconds - no-where near the milliseconds or seconds required. This talk will describe an alternative way of simulating protein motion, through the use of tools originally developed to simulate deployable structures. The detailed force-field models of a molecular dynamics simulation are replaced with a simple set of rigid constaints, and the possible motions of the protein are then explored. The method provides useful insight into how a protein may behave, and also the possible internal 'secondary structures' that have evolved.