Here I describe my work in developing a computer-modeling platform for simulating cellular organization and kinetics in a more realistic fashion than other existing technologies, and apply this technology to two large-scale biological systems, microtubule assembly and cytoplasmic crowding. This platform facilitates the multiscale approach in which the consequence of atomic details is measured on a bulk scale.
In the first application, I created a coarse-grain model for microtubule assembly derived from atomic-scale calculations. Specifically, I use high-resolution, all-atom Molecular Dynamics simulations to quantify critical interaction strengths and conformational dependencies thought to be central to the assembly process. I then incorporate these parameters into coarse-grain Brownian Dynamics simulations and kinetic simulations that can handle the large timescales required for MT assembly. My results show that the unassembled GDP-tubulin heterodimer exists in a continuum of conformations ranging between straight and bent, but, in agreement with existing structural data, suggests that an intermediate bent state has a lower free energy (by ~1 kcal/mol) and thus dominates in solution. In agreement with predictions of the lattice model of microtubule assembly, lateral binding of two tubulins strongly shifts the conformational equilibrium towards the straight state, which is then ~1 kcal/mol lower in free energy than the bent state. Finally, calculations of colchicine binding to a single tubulin dimer strongly shifts the equilibrium toward the bent states, and disfavors the straight state to the extent that it is no longer thermodynamically populated.
In the second application, I created a coarse-grain model of the bacterial protein cytoplasm. I developed automated ways of coarse- graining macromolecules based on experimental structures or homology models, and simulated proteins at a domain-level of resolution. My results show that an intermediate resolution model is sufficient to achieve the results of the high-resolution model. In addition, we show that incorporation of shape, while of no consequence in dilute solution, significantly transforms the energetic properties of crowded media via weak, nonspecific interactions. Providing a more complete understanding of excluded volume in vivo, our model is then applied to address the open questions of the effects of crowding on effective diffusion and association reactions.