Speaker
Description
We present our work on simulating the self-assembly of large protein systems, with a focus on the assembly of tobacco mosaic virus coat proteins into a helical shell. The size and timescales of these systems make all-atom molecular dynamics simulations unfeasible.
To tackle this, we constrain the proteins to a single conformation and introduce a coarse-grained energy model that includes van der Waals, electrostatic, and hydrophobic interactions. A key challenge is that the energy model needs to account for the rigidity assumption. This means that directly implementing physical interactions, like exact van der Waals radii or Poisson-Boltzmann electrostatics, is insufficient and requires additional considerations.
Our simulations are driven by the hybrid Monte Carlo algorithm to efficiently sample the Gibbs distribution of possible configurations. We discuss results from numerical experiments with different versions of the energy model. A key finding is that achieving high interaction specificity through the collective interplay of van der Waals, electrostatic, and hydrophobic interactions is essential for self-assembly.
