Secondary Structures in Phe-Containing Isolated Dipeptide Chains: Laser Spectroscopy vs Quantum Chemistry

Abstract

The intrinsic conformational landscape of two phenylalanine-containing protein chain models (-Gly-Phe- and -Ala-Phe- sequences) has been investigated theoretically and experimentally in the gas phase. The near UV spectroscopy (first ππ* transition of the Phe ring) is obtained experimentally under jet conditions where the conformational features can be resolved. Single-conformation IR spectroscopy in the NH stretch region is then obtained by IR/UV double resonance in the ground state, leading to resolved vibrational spectra that are assigned in terms of conformation and H-bonding content from comparison with quantum chemistry calculations. For the main conformer, whose UV spectrum exhibits a significant Franck-Condon activity in low frequency modes involving peptide backbone motions relative to the Phe chromophore, excited state IR spectroscopy has also been recorded in a UV/IR/UV experiment. The NH stretch spectral changes observed in such a ππ* labeling experiment enable us to determine those NH bonds that are coupled to the phenyl ring; they are compared to CC2 excited state calculations to quantify the geometry change upon ππ* excitation. The complete and consistent series of data obtained enable us to propose an unambiguous assignment for the gallery of conformers observed and to demonstrate that, in these two sequences, three conceptually important local structural motifs of proteins (β-strands, 27 ribbons, and β-turns) are represented. The satisfactory agreement between the experimental conformational distribution and the predicted landscape anticipated from the DFT-D approach demonstrates the capabilities of a theoretical method that accounts for dispersive interactions. It also shows that the flaws, inherent to a resonant two-photon ionization detection scheme, often evoked for aromatic chromophores, do not seem to be significant in the case of Phe.

Isolated Neutral Peptides

“…6 Conformational diversity in the Ac-Gly-Phe-NH 2 capped dipeptide. The R2PI spectrum (top panel), combined with fours IR/UV experiments (below) carried out on the UV bands marked with an asterisk provides evidence for the existence of four conformers in this system, whose apparent intensities in the UV spectrum (one major conformer A and three minor ones) are fairly correlated to the calculated Gibbs energies (A is the most stable by more than 4 kJ mol À1 ) [200] Isolated Neutral Peptidesquantum yields on isolated peptides [47,71,72,125,126]. The principle (Fig.…”

“…8) exhibits only two conformers; those two in which a steric hindrance appears when substituting Gly by Ala are rejected at energies too high to be observed. Put in other terms, γ D -turns and type II' β-turns are specific to Gly residues and are not observed in other natural residues because of the presence of a side chain [200].…”

“…Figure 6 shows the remarkable example of a 248 E. Gloaguen and M. Mons capped Gly-Phe sequence, where four conformations with different types of backbones are found: two f-7-7 (double γ-turn) extended conformations, differing by the chirality L or D of the turns, and two β-turn folded structures of types I and II'. The latter differ only by the backbone folding on the Gly residue, and share the same backbone conformation and side chain orientation on Phe [200]. This conformational diversity is clearly caused by the specific flexibility of the Gly conformation, which does not suffer from any steric hindrance produced by the absence of a side chain.…”

“…2.3 and 4.2). The sub-nanosecond lifetime estimated for the hydrates [200] suggests that photophysics effects deserve to be taken into consideration.…”

“…Figure 8 shows examples of these characteristics, which help a great deal to find the turn signature when hidden in a congested region dominated by another conformer (e.g. type I β-turns in Ala-Phe and Gly-Phe sequences [92,200]). Phe-Phe type I β-turn also provides a nice illustration, where the origin positions of each chromophore match well the typical positions of Phe transitions found for all the other type I β-turns:~35,500 and~35,560 cm À1 for Phe in first and second position of the sequence, respectively.…”