publication . Article . Other literature type . 2009

2D-IR experiments and simulations of the coupling between amide-I and ionizable side chains in proteins: application to the Villin headpiece.

Bagchi, Sayan; Falvo, Cyril; Mukamel, Shaul; Hochstrasser, Robin M.;
  • Published: 13 Aug 2009
Abstract
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...
Subjects
free text keywords: Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films, Absorption (pharmacology), Chemistry, Carboxylate, chemistry.chemical_compound, Spectroscopy, Electric field, Photochemistry, Crystallography, Stereochemistry, Carboxylic acid, chemistry.chemical_classification, Amide, Density functional theory, Side chain, Article
Abstract
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...
Subjects
free text keywords: Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films, Absorption (pharmacology), Chemistry, Carboxylate, chemistry.chemical_compound, Spectroscopy, Electric field, Photochemistry, Crystallography, Stereochemistry, Carboxylic acid, chemistry.chemical_classification, Amide, Density functional theory, Side chain, Article
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publication . Article . Other literature type . 2009

2D-IR experiments and simulations of the coupling between amide-I and ionizable side chains in proteins: application to the Villin headpiece.

Bagchi, Sayan; Falvo, Cyril; Mukamel, Shaul; Hochstrasser, Robin M.;