Including H-Bonding and Lipid Exposure in Near-Atomic Level Folding Simulations of Helical Membrane Proteins: II. Applications to Single-Molecule Force Spectroscopy

Abstract

Single-molecule force spectroscopy (SMFS) is a powerful technique to study the unfolding of soluble and membrane proteins. Coarse-grained (CG) models expedite the MD simulations and allow for slower and more realistic extraction velocities and lower pulling forces for simulating SMFS experiments. These factors increase the likelihood of observing transient intermediates. We simulate the forced unfolding of membrane proteins using our CG model, Upside (1), incorporating new membrane potentials. Upside can reversibly fold some soluble proteins up to 97 AA in CPU-hours without the use of fragments or homology. Our membrane potentials are derived from statistics of known structures, accounting for burial depth in the membrane and side chain exposure levels. In the simulations of the forced unfolding of bacteriorhodopsin, we are able to reproduce the characteristic features displayed in experiments, including the unfolding of individual and pairs of helices, worm-like chain behavior of the elastic unfolded segments and the back-and-forth transitions between states with a comparable resolution as the experiments. The difference in the unfolding pathway are compared for the isolated monomer and in trimeric form. Our method is ready to be applied to other transmembrane protein systems including GlpG, halorhodopsin. (1) Jumper et. al, Trajectory-Based Parameterization of a Coarse-Grained Forcefield for High-Throughput Protein Simulation, http://www.biorxiv.org/content/early/2017/07/27/169326.