The First Super-Microsecond Molecular Dynamics Simulation of a Protein-Ligand Complex: MUP/IBM

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One of the defining features of life is motion, and it is the ability of biological molecules like proteins to move and change shape - to function as 'molecular machines' - that underpins this. Most experimental methods to study biological molecules at the atomic scale - for example X-ray crystallography and NMR spectroscopy - can only provide static 'snapshots' of their structure. But starting with this information, computer simulation methods, particularly molecular dynamics simulations, allow us to visualise the dynamical motions of proteins and other biological molecules, enabling us to understand how these molecules 'work'. The problem is that these simulations require enormous amounts of computer power. Until recently, it was only possible to follow the motions of biological molecules for very short periods of time - a few billionths of a second. But the new UK supercomputer HECToR has the power to increase this to the microsecond (1 millionth of a second) timescale. This still sounds like a very small period of time, but actually within a microsecond a lot of important biological processes can occur. This project will study the dynamics of a small protein from mice that acts as a molecular sponge, soaking up molecules of the mouse's pheromones. This may sound quite esoteric but is actually a well-established 'testbed system' for understanding important processes like drugs binding to their targets, and so will provide very useful information to help with drug design and development.