FT-IR Spectroscopy and Density Functional Theory Calculations of ¹³C Isotopologues of the Helical Peptide Z-Aib₆-OtBu

Abstract

Isotope-edited FT-IR spectroscopy is a combined synthetic and spectroscopic method used to characterize local (e.g., residue-level) vibrational environments of biomolecules. We have prepared the 3(10) helical peptide Z-Aib6-OtBu and seven (13)C-enriched analogues that vary only in the number and position(s) of (13)C═O isotopic enrichment. FT-IR spectra of these eight peptides solvated in the nonpolar aprotic solvent dichloromethane have been collected and compared to frequency, intensity, and normal mode results of DFT calculations. Single (13)C enrichment of amide functional groups tends to localize amide I vibrational eigenmodes, providing residue-specific information regarding the local environment (e.g., hydrogen bonding or solvent exposure) of the peptide bond. Double (13)C enrichment of Z-Aib6-OtBu allows for examination of interamide coupling between two labeled amide functional groups, providing experimental evidence of interamide coupling in the context of 3(10) helical structure. Although the calculated and observed interamide couplings of Z-Aib6-OtBu are a few cm(-1) and less, the eight peptides exhibit distinct infrared spectra, revealing details of interamide coupling and residue level vibrational environments.

Understanding the Amide-II Vibrations in β-Peptides

“…As one type of important unnatural peptide, β-peptides are known to exhibit novel secondary and tertiary structures, and these peptides are potentially applicable in designing new drugs, in fabricating novel materials and biocompatible devices, as well as in solving the puzzle of protein folding. − It is thus of great importance to explore spectroscopic methods that are sensitive to the conformations of β-peptides. Infrared spectroscopy, including linear and nonlinear methods, has been known to be extremely sensitive to structures and structural distributions of α-peptides − and natural proteins that are composed of α-amino acids. − In this regard, the periodically appearing amide units (CONH) in the backbone of α-peptides, which have several infrared-active modes, have been primarily used as a conformational probe. Two of these modes are the amide-I and -II modes, whose vibrational frequencies are located in the 1600–1700 cm –1 and 1500–1600 cm –1 frequency regions, respectively.…”

Observation of α-Helical Hydrogen-Bond Cooperativity in an Intact Protein

“…Computational studies indicate that H-bond cooperativity plays an important role in α-helix stabilization. − This cooperativity is stipulated to originate from the electric dipole moment of the α-helix, i.e, as the helix grows, the electric dipole moment of the newly added peptide plane forms favorable electrostatic interactions with the peptide planes of the existing helix, thereby increasing their dipole moments through polarization which then strengthens the electrostatic interaction among all peptide planes in the helix . Whether or not analogous cooperativity applies to β-sheet formation is a function of the geometric details of any particular such structure and remains a matter of debate. − Cooperativity of α-helical H-bonding has been studied experimentally by multiple spectroscopic techniques, including time-resolved or 2D infrared spectroscopy − and T-jump fluorescence. − Only mass spectrometry has been proposed as a potential tool for studying cooperativity of H-bonding in intact proteins, relying on the exploitation of hydrogen/deuterium (H/D) exchange phenomena, , but to the best of our knowledge, no quantitative analysis of H-bond cooperativity of such data has yet been published. NMR spectroscopy is a particularly powerful tool for the study of H-bonding in biomolecules, which can be probed by chemical shifts, NMR analysis of pressure-induced unfolding, H-bond J couplings, − H/D fractionation factors, − and isotope shifts. ,, …”

Handedness preference and switching of peptide helices. Part II: Helices based on noncodedα‐amino acids

“…For (Aib) n homo‐peptides in helix‐supporting solvents (e.g. CDCl 3 ), the same conformation (3 10 ‐helix) is largely prevailing . Using Fourier transform infrared spectroscopy (FTIR) absorption and 1 H NMR, we established that populations close to 90% and 100% of 3 10 ‐helical conformers are attained at the hexamer and octamer level, respectively.…”