Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics
Prof. Cameron F Abrams (Drexel University) and Eric Vanden-Eijnden used a new molecular dynamics simulation method to investigate the conformational variability of large proteins, a problem of interest e.g. in drug design. The method was applied to two complex proteins, a subunit of GroEL, a protein that catalyzes folding of substrate proteins, and the HIV-1 envelope gp120, a protein responsible for the fusion of the virus with a target cell. In this second example, the method generates plausible all-atom models of the unliganded conformation of HIV-1 gp120, which was uncharacterized so far and may prove useful in the development of inhibitors and immunogens. The full article was published in the Proceeding of the National Academy of Science and can be found at http://www.pnas.org/content/early/2010/02/22/0914540107.abstract.