Computational Advances in Structural Biology

Abstract:

Tools such as cryo-electron microscopy and tomography are revealing new regimes of biology that have not yet been seen, such as the organization of protein complexes into subcellular architectures, and the co-ordinated activity of molecular motors. This requires new simulation tools to model and understand this experimental data in terms of biological function. We have developed a mesoscale modelling tool “Fluctuating Finite Element Analysis” that uses a combination of rod and tetrahedral finite elements to capture the dynamics of biomolecular complexes too large for atomistic (or conventional coarse-grained) simulations, which we are using to model molecular motors such as dynein and myosin. These novel simulations also require bespoke visualization tools, because the software available either is not appropriate for viewing protein structures (e.g. finite element engineering software) or for mesh-based trajectories (e.g. atomistic visualization tools such as VMD or Chimera).