(1980). Reverse Turns in Peptides and Protein. Critical Reviews in Biochemistry: Vol. 8, No. 4, pp. 315-399.

Reverse turns in peptides and proteins.

(1980). Intramolecularly Hydrogen-Bonded Peptide Conformation. Critical Reviews in Biochemistry: Vol. 9, No. 1, pp. 1-44.

Intramolecularly hydrogen-bonded peptide conformations.

Spectroscopic and crystallographic data are presented for a series of tetrapeptides and analogous depsipeptides that can form a minimal β-hairpin (two intramolecular hydrogen bonds). These model compounds have been used to test the hypothesis that “mirror image” β-turns promote β-hairpin formation. This hypothesis was inspired by a statistical survey of β-hairpins in globular proteins (Sibanda, B. L.; Thornton, J. M. Nature 1985, 316, 170), which showed that mirror image β-turns (type I‘ and type II‘), although rare in general, are very commonly associated with β-hairpins containing a two-residue loop between the strand segments. Each of our four-residue molecules contains proline at the second position, to promote a central β-turn. The β-turn is induced to be either “common” or “mirror-image”, relative to the outer residues, by choice of residue configuration (l vs d). In methylene chloride, end-capped tetrapeptide Ac−l-Val-d-Pro-d-Ala-l-Leu-NMe2 folds largely into the β-hairpin conformation, while the d...

Stereochemical Requirements for β-Hairpin Formation: Model Studies with Four-Residue Peptides and Depsipeptides

Polyproline II structure in proteins: Identification by chiroptical spectroscopies, stability, and functions

Methods for describing a discrete number of conformational states of amino acid residues in proteins are presented and used to investigate the topography of chain folding. The relative importance of short-range, medium-range and long-range interactions is discussed in the light of an analysis of the conformational states for the different amino acid residues in eight proteins of known structure. A prediction algorithm, which assigns four states to each residue of a protein chain (α-helix, extended structure, bend, or coil), has been developed from a consideration of both short- and medium-range interactions and applied to thirteen proteins of known three-dimensional structure. The prediction algorithm is simple to apply, and the assignment of α-helix and extended structure is considerably better than in most other predictive schemes. The prediction of chain reversal or bend regions was also better than with previous algorithms, but these assignments were not as good as those for α-helix and extended structure. The motivation for the development of this algorithm is not only to demonstrate the relative importance of short- and longer-range interactions but, more important, to begin to develop procedures for obtaining an approximate starting conformation for subsequent energy minimization to predict the three-dimensional structure of a protein. This procedure, as well as various other methods for the prediction of the backbone topography and conformational states of residues in proteins from the amino acid sequence, have been reviewed and evaluated by comparing the success of the methods to the success expected from a random assignment of conformational states.

Analysis of Conformations of Amino Acid Residues and Prediction of Backbone Topography in Proteins

Some experimental data are given on the infrared spectra between 3300 and 3500 cm−1 of dilute solutions in carbon tetrachloride of three types of model compounds: CH3−CONH-CH(R1)-CONH(R2), (I); CH3-CON(CH3)-CH(R1)-CONH(R2), (II) and CH3-CONH-CH(R1)-CON(R2)2, (III). In studying the N-H stretching bands, it was found that there are two types of intramolecular hydrogen bonds in these molecules; these result in two different cyclized conformations, C5 and C7, which contain respectively, five and seven atoms in the ring. By using model substances I, II, and III, in which the nitrogen atoms are unequally substituted, it is possible to identify the N-H stretching bands which are to be ascribed to the N-H oscillators included in the two different chelated conformations. It is found also that the stretching frequency of a free N-H oscillator depends upon the substituent on the nitrogen atom. Thus, it is possible to observe, with some of the model compounds I, four different absorption bands located at 3340, 3420, 3440, and 3460 cm−1. The first two are ascribed to the N-H oscillators included in the Hbonds which lock the C7 and C5 conformations; the last two correspond to free N-H which differ with the substituent on the nitrogen atom.

J. Lascombe

Papers

Etude, par spectroscopie infra-rouge, de la conformation de quelques composés peptidiques modèles