Empirical amide I vibrational frequency map: Application to 2D-IR line shapes for isotope-edited membrane peptide bundles

Journal Article (Journal Article)

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-ξ 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. © 2009 American Chemical Society.

Full Text

Duke Authors

Cited Authors

  • Lin, YS; Shorb, JM; Mukherjee, P; Zanni, MT; Skinner, JL

Published Date

  • January 22, 2009

Published In

Volume / Issue

  • 113 / 3

Start / End Page

  • 592 - 602

International Standard Serial Number (ISSN)

  • 1520-6106

Digital Object Identifier (DOI)

  • 10.1021/jp807528q

Citation Source

  • Scopus