title: Distinguishing gramicidin D conformers through two-dimensional infrared spectroscopy of vibrational excitons.
abstract: Gramicidin D is a short peptide which dimerizes to form helical pores, adopting one of two conformations in the process. These conformations differ primarily in number of residues per turn and the hydrogen-bond registry between rungs of the helix. Using amide I 2D infrared (IR) and FTIR, we have demonstrated that it is possible to distinguish between the different conformers of gramicidin D in solution. We show that the spectra observed for this helical peptide bear no resemblance to the spectra of α- or 310-helices and that while the FTIR spectra appear similar to spectra of β-sheets, 2D IR reveals that the observed resonances arise from vibrational modes unlike those observed in β-sheets. We also present an idealized model which reproduces the experimental data with high fidelity. This model is able to explain the polarization-dependence of the experimental 2D IR data. Using this model, we show the coupling between the rungs of the helix dominates the spectra, and as a consequence of this, the number of residues per turn can greatly influence the amide I spectra of gramicidin D.
authors.affiliation: Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Stevenson
authors.affiliation: Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA.
authors.forename: Andrei
authors.initials: A
authors.lastname: Tokmakoff
mesh_terms: D006096:Gramicidin / Q000737:chemistry*; D006860:Hydrogen Bonding; D011487:Protein Conformation; D013055:Spectrophotometry, Infrared; D014732:Vibration
chemical_list: D006096:Gramicidin