Paper Citing NAMD - Abstract
Lam, A. R.; Moran, S. D.; Preketes, N. K.; Zhang, T. O.; Zanni, M. T.; Mukamel, S.
Study of the gamma D-Crystallin Protein Using Two-Dimensional Infrared (2DIR) Spectroscopy: Experiment and Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 117:15436-15443, DEC 12 2013
Cataracts is a misfolding protein disease in which one of the major components is the gamma D-crystallin protein. The conformational structure of the aggregated gamma D-crystallin and the interactions that cause aggregation are largely unknown. A recent experimental two-dimensional infrared (2DIR) spectroscopy study determined that the C-terminal domain has a high propensity to form beta-sheets whereas the N-terminal domain forms a disordered structure in the fiber state. We present a combined computational molecular dynamics and infrared spectroscopy study of the local dynamics of these domains. The computed 2DIR signals agree remarkably well with experiment. We show that the two domains, both of which have a Greek key structural fold, experience different electrostatic environments, which may be related to the fact that the C-terminal domain is more structurally stable than the N-terminal domain. We correlate the vibrational couplings to known energy dissipation mechanisms and reveal their origin.
