Molecular Dynamics Simulations of GGBP

Using IMPACT, I am performing umbrella-potential sampling and replica exchange molecular dynamics simulations of GGBP. In the absence of crystallographic data, one can steer the protein conformation and systematically search for and minimize the energy of conformational structures along a sensible pathway. Once the minimized structures are obtained, molecular dynamics simulations will populate the structures, and from the relative populations, one can extract the potential of mean force on a two-dimensional (theta, phi) coordinate system. Shown in the image are contour plots of the populations (~ PMFs) of ribose binding protein (RBP), which is nearly homologous to GGBP. The top contour is ribose-free and the bottom contour is ribose-bound. There are clearly three distinct populations as we observed in bulk fluorescence measurements of GGBP. The contour plots are from Prof. Ron Levy's publication:

Ravindranathan, K. P.; Gallicchio, E.; Levy, R. M., "Conformational Equilibria and Free Energy Profiles for the Allosteric Transition of the Ribose-binding Protein", Journal of Molecular Biology 353, 196–210 (2005). Molecular Biology 1965, 12, 88–118.