l-Alanyl-l-alanine Conformational Changes Induced by pH As Monitored by the Raman Optical Activity Spectra

Abstract

Fine effects of the hydration, charge, and conformational structural changes in L-alanyl-L-alanine (Ala-Ala) dipeptide were studied with the aid of Raman and Raman optical activity (ROA) spectra. The spectra were recorded experimentally and analyzed by means of density functional computations. A 15 N and 13 C isotopically labeled analogue was synthesized and used to verify the vibrational mode assignment. Calculated shifts in vibrational frequencies for isotopically labeled molecule agreed well with the experiment. The assignment made it possible to scale computed vibrational frequencies and extract better structural information from the intensities. Solvent modeling with clusters obtained from molecular dynamics led to a qualitatively correct inhomogeneous broadening of Raman spectral lines but did not bring a convincing improvement of ROA signal when compared to a standard dielectric solvent correction. In comparison with the zwitterionic form, charged anionic and cationic dipeptides provided spectral variations that indicated different conformational behavior. Only minor backbone conformational change occurs in the cation, whereas the results indicate the presence of more anion conformers differing in the rotation of the NH 2 group and the backbone ψ-angle. These findings are in agreement with previous electronic circular dichroism (ECD) and NMR studies. The results confirm the large potential of the ROA technique for the determination of final details in molecular structure and conformation.

Quantum Mechanics Approach to Hydration Energies and Structures of Alanine and Dialanine

“…The conformation of dialanine has been the subject of many computational and experimental studies, since it is a useful model of long peptides, the behavior of which would be difficult to investigate. However, the reported findings may not be unique and are sometimes contradictory because their interpretation/conclusions are based on molecular dynamics calculations and/or quantum mechanics, the reliability of which is not guaranteed due to the enormous complexity of the peptide–water system.…”

“…Using NMR, UVCD, Raman, and Raman optical activity (ROA) spectroscopy combined with quantum chemical calculations, Bouř et al. suggested subtle changes in the structure of dialanine on pH change . In particular, their data support the dominance of one backbone conformer in solution for the zwitterion, while the cation may exist in an ensemble of similar conformers.…”

Formation and structure of the potassium complex of valinomycin in solution studied by Raman optical activity spectroscopy

“…33,34 Nowadays, computations of ROA intensities can be done with approximately the same effort as for the Raman intensities with popular software packages. 35,36 Nevertheless, the fine splitting of vibrational energy levels and the second-order intensity response properties determining the ROA spectrum require large basis sets and high-quality approximations, 37,38 which become prohibitive for larger molecules. Direct ROA simulations for peptides containing up to ten alanine residues have been reported so far.…”

Sensing site‐specific structural characteristics and chirality using vibrational circular dichroism of isotope labeled peptides

“…While most such isotopic labeling studies have emphasized use of IR methods, others have included Raman and VCD as well as newer multidimensional methods, including 2D-IR. 43,44,[50][51][52][53][54][57][58][59][60][61][62][63][64] This mini-review will discuss selected examples of applications of isotope labeling to determine chiral aspects of peptide secondary structure via VCD spectra with an emphasis on the role of local coupling of amides in peptides. Such isotopic VCD of peptides has tended to emphasize helices, due to their higher chiral impact on the spectra, but the methods are broadly applicable in principle.…”

“…These methods work best for oligopeptides where labeled residues can be inserted synthetically at known locations in the sequence and the relatively dilute labels are still sufficient for detection. While most such isotopic labeling studies have emphasized use of IR methods, others have included Raman and VCD as well as newer multidimensional methods, including 2D–IR . This mini‐review will discuss selected examples of applications of isotope labeling to determine chiral aspects of peptide secondary structure via VCD spectra with an emphasis on the role of local coupling of amides in peptides.…”