The number of structures in the Electron Microscopy Database (EMDB) is growing rapidly due to improvements in cryo-electron microscopy and tomography [1]. This database is complementary to the Protein Data Base (PDB), in that it contains volumetric information about the overall shape of a biomolecule, rather than fully atomistic structures. Fluctuating Finite Element Analysis (FFEA) [2] is a new computer simulation technique that simulates the dynamic behaviour of bio-molecular structures in the EMDB, in an analogous manner to the use of atomistic molecular dynamics trajectories based on structures deposited in the PDB. As FFEA uses a continuum representation of biomolecules it has no upper length-scale limit, and provides access to mesoscopic regimes (50-1000nm) inaccessible to more detailed modelling techniques.To model the action of molecular motors using FFEA, we account for atomistic processes such as ATP binding, hydrolysis and changes in protein secondary structure by including them as instantaneous events occurring at a given rate. Coupling the temperature driven dynamics of the motor with the probability that a transition will occur ensures that the internal strain energy influences the rate of the chemical processes driving the action of the motor. We are currently applying this coupled simulation to cytoplasmic dynein, which is a dimeric molecular motor involved in intracellular cargo transport, to study how mechanical communication and gating between the two subunits enables the motor to walk without moving backwards, stalling or releasing from the microtubule completely.[1] Kuehlbrandt, W., The Resolution Revolution, Science. 2014, 343(6178), 1443-4.[2] Oliver, R. C., Read, D. J., Harlen, O. G. And Harris, S. A., A stochastic finite element model for the dynamics of globular macromolecules, J. Comp. Phys. 2013, 239, 147-65.
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