Two-Dimensional Infrared Spectral Signatures of 3₁₀- and α-Helical Peptides

Abstract

Two-dimensional infrared (2D IR) spectra of Calpha-alkylated model octapeptides Z-(Aib)8-OtBu, Z-(Aib)5-L-Leu-(Aib)2-OMe, and Z-[L-(alphaMeVal)]8-OtBu have been measured in the amide I region to acquire 2D spectral signatures characteristic of 3(10)- and alpha-helical conformations. Phase-adjusted 2D absorptive spectra recorded with parallel polarizations are dominated by intense diagonal peaks, whereas 2D rephasing spectra obtained at the double-crossed polarization configuration reveal cross-peak patterns that are essential for structure determination. In CDCl3, all three peptides are of the 3(10)-helix conformation and exhibit a doublet cross-peak pattern. In 1,1,1,3,3,3-hexafluoroisopropanol, Z-[L-(alphaMeVal)]8-OtBu undergoes slow acidolysis and 3(10)-to-alpha-helix transition. In the course of this conformational change, its 2D rephasing spectrum evolves from an elongated doublet, characteristic of a distorted 3(10)-helix, to a multiple-peak pattern, after becoming an alpha-helix. The linear IR and 2D absorptive spectra are much less informative in discerning the structural changes. The experimental spectra are compared to simulations based on a vibrational exciton Hamiltonian model. The through-bond and through-space vibrational couplings are modeled by ab initio coupling maps and transition dipole interactions. The local amide I frequency is evaluated by a new approach that takes into account the effects of hydrogen-bond geometry and sites. The static diagonal and off-diagonal disorders are introduced into the Hamiltonian through statistical models to account for conformational fluctuations and inhomogeneous broadening. The sensitivity of cross-peak patterns to different helical conformations and the chain length dependence of the spectral features for short 3(10)- and alpha-helices are discussed.

Optimization of Model Parameters for Describing the Amide I Spectrum of a Large Set of Proteins

“…The shift of the intrinsic frequency due to interpeptide hydrogen bonds was modeled according to the method proposed by Ge and co-workers, 62 who found that the shifts of the amide I oscillator frequencies are well described by proportional relations to the Kabsch-Sander bond energies. 63 The electrostatic Kabsch-Sander energy of a hydrogen bond between C=O and NH groups is…”

Quantification of transition dipole strengths using 1D and 2D spectroscopy for the identification of molecular structures via exciton delocalization: Application to α-helices

“…Thus, transition dipoles are good indicators of peptide secondary structure, for example, since many individual amide I bonds are coupled together in betasheets and α-helices, creating strong transition dipoles. 22,[25][26][27] Of course, one can also detect coupling by the frequency separation, but frequency shifts are not always easily measurable. In the example above, the coupling caused each peak to shift by only 1.5 cm −1 , which may be difficult to experimentally detect considering that the linewidths of most condensed phase vibrational modes are >10 cm −1 .…”

Simulation of vibrational energy transfer in two-dimensional infrared spectroscopy of amide I and amide II modes in solution

“…The amide I mode has been the subject of most studies due to its strong intensity and the strong coupling between different amide I modes, which allow the use of this mode for structural determination. [18][19][20][21][22][23][24] Typically the spectra are obtained in heavy water in order to remove the strong water bend signal that is located in the same spectral region as the amide I band. This also results in the exchange of the acidic proton bound to nitrogen, and the resulting molecule is called NMA-d.…”