Empirical Amide I Vibrational Frequency Map: Application to 2D-IR Line Shapes for Isotope-Edited Membrane Peptide Bundles <sup>†</sup>

TitleEmpirical Amide I Vibrational Frequency Map: Application to 2D-IR Line Shapes for Isotope-Edited Membrane Peptide Bundles
Publication TypeJournal Article
Year of Publication2009
AuthorsLin Y-S, Shorb J.M, Mukherjee P., Zanni MT, Skinner J.L
Secondary TitleThe Journal of Physical Chemistry B
Volume113
Issue3
Pagination592 - 602
Date Published01/2009
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-ζ 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.

URLhttp://pubs.acs.org/doi/abs/10.1021/jp807528q
DOI10.1021/jp807528q
Short TitleJ. Phys. Chem. B