title: Structural classification of the amide I sites of a beta-hairpin with isotope label 2DIR spectroscopy.
abstract: We present a theoretical study of the possibility to use isotope label two-dimensional infrared (2DIR) spectroscopy to obtain site specific structural information in trpzip2. This small beta-hairpin peptide was designed as a model system for studying protein folding in beta-sheet structures. In order to unravel the folding mechanism, the surroundings of local sites should be characterized, which in principle is possible by using 2DIR in combination with isotope labeling. This requires a classification that correlates local structures to two-dimensional spectra. To this end, we provide the first spectral simulation of the isotope label spectra of all the amide I sites in trpzip2. We find that the anti-diagonal width of the 2DIR peak associated with a labelled site is a good measure of solvent exposure and the key parameter to distinguish between solvent exposed and internal sites. The diagonal widths are not particularly sensitive to this, but they do reveal the presence of slowly interconverting turn structures.
authors.affiliation: Center for Theoretical Physics and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
authors.forename: Santanu
authors.initials: S
authors.lastname: Roy
authors.forename: Thomas L C
authors.initials: TL
authors.lastname: Jansen
authors.forename: Jasper
authors.initials: J
authors.lastname: Knoester
mesh_terms: D000577:Amides / Q000737:chemistry; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D007553:Isotope Labeling; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013055:Spectrophotometry, Infrared
chemical_list: D000577:Amides; D010455:Peptides