Paper Citing NAMD - Abstract
Legge, F.S.; Budi, A.; Treutlein, H.; Yarovsky, I.
Protein flexibility: Multiple molecular dynamics simulations of insulin chain B
BIOPHYSICAL CHEMISTRY, 119:146-157, JAN 20 2006
Multiple molecular dynamics simulations totaling more than 100 ns were performed on chain B of insulin in explicit solvent at 300 K and 400 K. Despite some individual variations, a comparison of the protein dynamics of each simulation showed similar trends and most structures were consistent with NMR experimental values, even at the elevated temperature. The importance of packing interactions in determining the conformational transitions of the protein was observed, sometimes resulting in conformations induced by localized hydrophobic interactions. The high temperature simulation generated a more diverse range of structures with similar elements of secondary structure and populated conformations to the simulations at room temperature. A broad sampling of the conformational space of insulin chain B illustrated a wide range of conformational states with many transitions at room temperature in addition to the conformational states observed experimentally. The T-state conformation associated with insulin activity was consistently present and a possible mechanism of behavior was suggested. (c) 2005 Elsevier B.V. All rights reserved.
