Molecular Simulation of Proton Channels: Proton Gating in Influenza M2 Protein
The group is using molecular simulations to understand proton transfers in membrane bound proton pumps. Junior and senior undergraduate students at the University of Minnesota Rochester are learning basics strategies in atomistic simulations. The scope of the project is two-fold. First, students work on a scientific problem that has a significant relevance in their health science major. Second, they learn the basics of molecular modelling, from quantum chemical methods of small molecules using Gaussian software, to larger molecular dynamic simulations and statistical mechanical calculations with the Charmm suite of programs. As the students gain experience, they apply modeling techniques to the simulation of membrane-bound proteins, in particular, the influenza M2 protein proton pump. These models will become more computationally demanding and they must be run on the queue system. In particular, they students will be using QM/MM/Continuum models to investigate the effect of different protein residues in the proton transfer across the membrane. They will test different reaction coordinate models and different statistical techniques to compute the potential of mean force to test the validity of their models.