Vibrational normal modes of folded prolyl‐containing peptides

Abstract

Normal mode analysis of standard β turns has been performed using the refined force field obtained from type‐II β‐turn‐like conformation frequencies. Effects of various potentials are discussed and theoretical predictions are compared to the experimental results of various authors.

Conformational investigations of two diastereoisomers of the tripeptide Nα‐Z‐Nϵ‐Bz‐Lys‐Ala‐Sar‐OBzl. 2. Infrared and Raman studies and normal modes analysis

“…For all the 9 (S, R) and the 10 (S, S) compounds, the NH alanyl group implied in the C7 structure has its amide III calculated in the 1275-1305 cm −1 range while the NH lysyl amide III mode is calculated between 1300 and 1320 cm −1 . These relative high frequencies for the amide III modes are in accordance with the observed or calculated frequencies of NH groups engaged in internal hydrogen bonds [10,[12][13][14]. Unfortunately, no deuterated species were available for both the (S, R) or (S, S) compounds and the experimental assignments remain difficult.…”

“…Keeping in mind that the benzamide group remains free (no amide A frequency under 3300 cm −1 ), several combinations are possible, but each of them contains at least a C7-like structure we could consider as a 'hard core' in which the alanine NH group is hydrogen bonded to the C = O ester of the Z group while the alanyl amide carbonyl remains free ( Figure 3). Generally in such a structure, the amide I mode of the free carbonyl group displays a sharp band [10,[12][13][14] at a relative high frequency. We choose the experimental 1688 cm −1 infrared band as the amide I frequency for the lysyl carbonyl group.…”

“…The 1634 cm −1 band is assigned to the stretching mode of the benzamide carbonyl moiety (1630 cm −1 in the solid state obtained from a film in CHCl 3 [11]. The NH group of the lysyl residue can then be hydrogen bonded to either the benzamide carbonyl (in a C10-type ring) or to the carbonyl ester group of the sarcosyl residue (in a C11-type ring) [10,[12][13][14]. Figure 4 displays the general scheme for this kind of structure.…”

Studies on proline‐containing tetrapeptide models of β‐turns

“…The contribution of a type B spectrum to the CD behavior of Cbz-Gly-Pro-Gly-Gly-OR (6a and 6b) in less polar solvents (Fig. 6) is attributed to the presence of a &turn type 11, as evidenced by the ir and nmr studies of Perly et al47 and Lagant et al 48 6. On the basis of CD studies presented here, it can be stated that it is unlikely that the presence of proline-containing &turns can be detected in proteins based on the analysis of the CD spectra of peptides or proteins.…”

Photoexcitation of Rhodopsin: Conformation Changes in the Chromophore, Protein and Associated Lipids as Determined by Ftir Difference Spectroscopy

“…1, most of the amide I and I1 changes present at the lumirhodopsin and meta I stages persist at meta 11. However, a new strong peak appears at 1686 cm-', a frequency characteristic of p-turns (Parker, 1983;Lagant et al, 1984). Such structure is expected to be present to a greater extent in the extramembrane regions of rhodopsin rather than the internal bilayer region since it nor-mally disrupts alpha-helices and is associated with Alterations in extramembrane regions of rhodopsin are also indicated by the appearance of the new peaks at 1767, 1749, and 1707 cm-', all of which exhibit D/H exchange induced frequency shifts and have been shown to originate from Asp and/or Glu groups (DeGrip et al, 1985).…”