Amide vibrations are delocalized across the hydrophobic interface of a transmembrane helix dimer

Proc Natl Acad Sci U S A. 2006 Nov 7;103(45):16740-5. doi: 10.1073/pnas.0608243103. Epub 2006 Oct 30.


The tertiary interactions between amide-I vibrators on the separate helices of transmembrane helix dimers were probed by ultrafast 2D vibrational photon echo spectroscopy. The 2D IR approach proves to be a useful structural method for the study of membrane-bound structures. The 27-residue human erythrocyte protein Glycophorin A transmembrane peptide sequence: KKITLIIFG(79)VMAGVIGTILLISWG(94)IKK was labeled at G(79) and G(94) with (13)C=(16)O or (13)C=(18)O. The isotopomers and their 50:50 mixtures formed helical dimers in SDS micelles whose 2D IR spectra showed components from homodimers when both helices had either (13)C=(16)O or (13)C=(18)O substitution and a heterodimer when one had (13)C=(16)O substitution and the other had (13)C=(18)O substitution. The cross-peaks in the pure heterodimer 2D IR difference spectrum and the splitting of the homodimer peaks in the linear IR spectrum show that the amide-I mode is delocalized across a pair of helices. The excitation exchange coupling in the range 4.3-6.3 cm(-1) arises from through-space interactions between amide units on different helices. The angle between the two Gly(79) amide-I transition dipoles, estimated at 103 degrees from linear IR spectroscopy and 110 degrees from 2D IR spectroscopy, combined with the coupling led to a structural picture of the hydrophobic interface that is remarkably consistent with results from NMR on helix dimers. The helix crossing angle in SDS is estimated at 45 degrees. Two-dimensional IR spectroscopy also sets limits on the range of geometrical parameters for the helix dimers from an analysis of the coupling constant distribution.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amides / chemistry
  • Amino Acid Sequence
  • Biophysical Phenomena
  • Biophysics
  • Dimerization
  • Glycophorins / chemistry*
  • Humans
  • Hydrophobic and Hydrophilic Interactions
  • In Vitro Techniques
  • Membrane Proteins / chemistry
  • Models, Molecular
  • Molecular Sequence Data
  • Peptide Fragments / chemistry
  • Protein Structure, Quaternary
  • Protein Structure, Secondary
  • Spectroscopy, Fourier Transform Infrared
  • Thermodynamics
  • Vibration


  • Amides
  • Glycophorins
  • Membrane Proteins
  • Peptide Fragments