title: Empirical amide I vibrational frequency map: application to 2D-IR line shapes for isotope-edited membrane peptide bundles.
abstract: The amide I vibrational mode, primarily associated with peptide-bond carbonyl stretches, has long been used to probe the structures and dynamics of peptides and proteins by infrared (IR) spectroscopy. A number of ab initio-based amide I vibrational frequency maps have been developed for calculating IR line shapes. In this paper, a new empirical amide I vibrational frequency map is developed. To evaluate its performance, we applied this map to a system of isotope-edited CD3-zeta membrane peptide bundles in aqueous solution. The calculated 2D-IR diagonal line widths vary from residue to residue and show an asymmetric pattern as a function of position in the membrane. The theoretical results are in fair agreement with experiments on the same system. Through analysis of the computed frequency time-correlation functions, it is found that the 2D-IR diagonal widths are dominated by contributions from the inhomogeneous frequency distributions, from which it follows that these widths are a good probe of the extent of local structural fluctuations. Thus, the asymmetric pattern of line widths follows from the asymmetric structure of the bundle in the membrane.
authors.affiliation: Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.
authors.forename: Y-S
authors.initials: YS
authors.lastname: Lin
authors.forename: J M
authors.initials: JM
authors.lastname: Shorb
authors.forename: P
authors.initials: P
authors.lastname: Mukherjee
authors.forename: M T
authors.initials: MT
authors.lastname: Zanni
authors.forename: J L
authors.initials: JL
authors.lastname: Skinner
mesh_terms: D000465:Algorithms; D000577:Amides / Q000737:chemistry*; D003198:Computer Simulation; D007554:Isotopes; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D013055:Spectrophotometry, Infrared
chemical_list: D000577:Amides; D007554:Isotopes; D008565:Membrane Proteins; D010455:Peptides