Mimicking the First Turn of an α-Helix with an Unnatural Backbone: Conformation-Specific IR and UV Spectroscopy of Cyclically Constrained β/γ-Peptides

Abstract

The folding preferences of two capped, constrained β/γ-dipeptide isomers, Ac-βACPC-γACHC-NHBn and Ac-γACHC-βACPC-NHBn, (designated βγ and γβ, respectively), have been investigated using single- and double-resonance ultraviolet and infrared spectroscopy in the gas phase. These capped β/γ-dipeptides have the same number of backbone atoms between their N- and C-termini as a capped α-tripeptide and thus serve as a minimal structural unit on which to test their ability to mimic the formation of the first turn of an α-helix. Resonant two-photon ionization and UV-UV hole-burning spectroscopy were performed in the S0-S1 region, revealing the presence of three unique conformations of βγ and a single conformation of γβ. Resonant ion-dip infrared spectra were obtained in the NH stretch region from 3300 to 3500 cm(-1) and in both the amide I and amide II regions from 1400 to 1800 cm(-1). These infrared spectra were compared to computational predictions from density functional theory calculations at the M05-2X/6-31+G(d) level, leading to assignments for the observed conformations. Two unique bifurcated C8/C13 H-bonded ring structures for βγ and a single bifurcated C9/C13 H-bonded ring structure for γβ were observed. In all cases, the H-bonding patterns faithfully mimic the first full turn of an α-helix, most notably by containing a 13-membered H-bonded cycle but also by orienting the interior amide group so that it is poised to engage in a second C13 H-bond as the β/γ-peptide lengthens in size. The structural characteristics of the β/γ-peptide version of the 13-helix turn are compared with the α-helix counterpart and with a reported crystal structure for a longer β/γ-peptide oligomer.

Isolated Neutral Peptides

“…In these cases, one has to rely on the interpretation of the IR spectrum to figure out whether conformational selectivity is achieved or whether several species are simultaneously present. It should be noted that sequences deprived of UV chromophore can also been investigated by introducing so-called UV-tags which can be covalently [105,107,127,[131][132][133][134][135][136][137][138][139][140][141][142][143][144][145] or non-covalently bound, as in peptide-toluene complexes (Gloaguen E, Mons M, unpublished results). The assumption that the desired UV chromophore (often a phenyl ring) is weakly interacting with the rest of the molecule turned out to be a relatively seldom situation, owing to the huge flexibility of the peptides.…”

“…Vibrational couplings make the interpretation less easy, and confident assignments rely on a large spectral range (the whole amide I-III regions), especially when spectral resolution is limited, usually 1% of the IR frequency for a freeelectron source [48,54,55,66,69,79,80,82,83,95,97,105,108,131,132,136,141,142]. Difference frequency generation from table-top OPOs [52,64,90,104,120,126,127,137,139,144,145] has become a valuable alternative source to FELs, providing spectral resolutions in the cm À1 range, and solid conformational assignments have emerged from studies combining amide I/II and amide A spectral ranges (Fig. 1b).…”

“…More recently, other peptides, with longer spacers between amide bonds, i.e. β-and γ-peptides, having respectively two or three methylene spacers between their peptide bonds, have been investigated, either alone or in combination between them or with alpha peptides [52,104,122,123,[125][126][127][128][143][144][145]. More flexible C11, C8 and C6 H-bonded structures in β-peptides as compared to their C10, C7 and C5 equivalents in the regular α-peptide are a general characteristic of these species.…”

“…As another consequence of the increased flexibility provided by flexible spacers between amide groups, amide staking became possible and has indeed been revealed as a new shaping interaction on γ-peptides [125][126][127][128]. In turn, cyclic spacers bring more constraints which leave fewer folding choices for the peptide chain [143][144][145], paving the way for a controlled folding of larger species.…”

Franck–Condon-like Progressions in Infrared Spectra of Biological Molecules

“…[kg] 2 1 cm s m kg s 2 (8) where M is the reduced mass of the harmonic oscillator and c is the speed of light. We fixed the reduced mass at 5.5 au, which corresponds to the effective reduced mass of the torsional vibration in the ground electronic state of conformer A, extracted from the harmonic analysis at the M052X/6-31++G** level of theory.…”