Adding Value to Nanodisc Determined Cryo-EM Membrane Protein Structures by Molecular Simulations

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Membrane proteins are an important class of protein found in cellular membranes which are responsible for a wide range of vital functions. Cryo-electron microscopy is a technique that is able to determine the structure of membrane proteins; it has undergone a recent revolution in the resolution of data it produces. In particular, the use of nanodiscs is allowing detailed understanding of membrane proteins in an environment that is more physiological than was used in previous methodologies. However, the resolution of these structures is still modest, typically 3 to 4.5 Å. Due to this many structures require repair and refinement through computational techniques such as modelling and molecular dynamics simulations. Molecular simulations can be used to reanimate the proteins so they are no longer static snapshots and instead are able to exhibit the dynamics and interactions that would be found in the cell. This allows the investigation of the properties and interactions of the components of the simulation system. This project aims to enrich the models produced by cryo-electron microscopy by developing new molecular dynamics protocols. WCUB, ENWW