Continuum mechanical parameterisation of cytoplasmic dynein from atomistic simulation

•MD simulations of cytoplasmic dynein show stalk angular fluctuations are significant.•The measured dynamics can be well represented at a coarse-grained level using FFEA.•Continuum parameterisation captures the higher flexibility of the ATP-bound motor. Cytoplasmic dynein is responsible for intra-cellular transport in eukaryotic cells. Using Fluctuating Finite Element Analysis (FFEA), a novel algorithm that represents proteins as continuum viscoelastic solids subject to thermal noise, we are building computational tools to study the mechanics of these molecular machines. Here we present a methodology for obtaining the material parameters required to represent the flexibility of cytoplasmic dynein within FFEA from atomistic molecular dynamics (MD) simulations, and show that this continuum representation is sufficient to capture the principal dynamic properties of the motor.