Paper Citing NAMD - Abstract
Bagchi, Sayan; Falvo, Cyril; Mukamel, Shaul; Hochstrasser, Robin M.
2D-IR Experiments and Simulations of the Coupling between Amide-I and Ionizable Side Chains in Proteins: Application to the Villin Headpiece
JOURNAL OF PHYSICAL CHEMISTRY B, 113:11260-11273, AUG 13 2009
The carboxylate side chains of Asp and Glu have significant coupling with the amide states of the backbone of the Villin headpiece. In two-dimensional spectroscopy, cross peaks are observed between these side chains and the main amide-I band. To model the absorption of the side chains, the electric field variations of vibrational frequencies of a carboxylic acid group (neutral form, CH(3)-COOH) and a carboxylate group (ionized form, CH(3)-COO(-)) are parametrized by means of density functional theory calculations. Simulations indicate that the side chains significantly couple to only one or two amide-I modes out of all of the amino acid residues which makes them useful as spectroscopic markers, providing information about the local structural behavior of the protein. Both experiment and simulations show that the cross peaks between the carboxylate and the amide-I bands are significantly diminished above the melting temperature,
