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Protein Biology and Biophysics Network

Proteins are exciting — in vivo and in silico

Proteins are the stuff of life. Their function is determined by their structure and its capacity for flexible motion that is intrinsic to those structures. Nowadays, this mobility can be investigated by a number of experimental means which probe a very wide range of timescales and resolutions. These include high resolution methods such as X-ray and neutron diffraction, high field nuclear magnetic resonance spectroscopy, and mass spectrometry where atomic level resolution of mass and structures can be obtained for single molecules. Lower resolution methods such as FRET, IR spectroscopy, and biochemical probes (cross-linking) can also provide valuable, complementary information. A similarly wide range of timescales and resolutions can be probed in silico, with in general a trade-off between the level of detail in a simulation and the timescale or amplitude of motion that can be probed at a given computational expense – ranging from CPU-weeks or even months (for high-precision molecular dynamics) to minutes for elastic network modelling, rigidity analysis, etc. Hence simulations have become the approach of choice to predict structures of biomolecules and their assemblies, dynamics, energetics, molecular recognition, biochemical reactivity.

A network of experimentalists and computational modellers

This surge of new computational and experimental advancements in the field of structural biology has brought new tools for scientists to inquire into the nature of protein structure and their dynamics. At this point in time the techniques start to overlap significantly in their respective ranges of validity and a combined approach across different ranges, from the atomistic, to the molecular and on to coarse-grained and the meso-scale seems not only feasible, but quickly becomes a necessity. Here in Warwick, we have the critical mass of researchers and relevant expertise in nearly all techniques. Hence turning this necessity into reality at Warwick is what our network is about.