Conformational study of alanine and alpha-aminoisobutyric psi [NHCO]-retroamide peptide analogues

Extended form of a retro-inverso peptide stabilized by beta-sheet unidirectional H-bonds: Crystallographic and NMR evidence

The crystallographic investigation of the retro-inverso peptide Bz-S-gAla-R-mAla-NHPh reveals an extended backbone conformation where the NH groups of the gem-diamino alkyl moiety and the CO groups of the malonyl residue face side by side. This extended conformation, presenting all carbonyls on opposite sides of the NH groups, is stabilized by interstrand H-bonds running in a single direction of the parallel beta-sheets that characterize the crystal packing. These sheets differ from the beta-sheets formed by native amino acids only. (1)H-NMR nuclear Overhauser effect spectroscopy (NOESY) experiments suggest that a conformation similar to that found in the crystal also prevails in dimethylsulfoxide solution. Previous potential energy calculations of gem-diamino alkyl (g) and malonyl (m) Ala residues predicted that extended forms were less stable than the helical ones because of strong electrostatic repulsions between the parallel polar groups. Similar arguments were invoked to give more weight to helical forms of the retro-peptide units in the proposal of packing models of some nylons in their crystalline polar regions. The present findings show that both g and m Ala residues can experience the extended conformation in the beta-sheet aggregation. The energy increase occurring in one strand, due to the parallel orientation of consecutive peptide dipoles, is more than compensated by favorable cooperative interactions among head-to-tail aligned peptide dipoles of facing strands, resulting in the formation of two C==O...H==N H-bonds per residue.

Conformational interconversions in peptide beta-turns: analysis of turns in proteins and computational estimates of barriers

The two most important beta-turn features in peptides and proteins are the type I and type II turns, which differ mainly in the orientation of the central peptide unit. Facile conformational interconversion is possible, in principle, by a flip of the central peptide unit. Homologous crystal structures afford an opportunity to structurally characterize both possible conformational states, thus allowing identification of sites that are potentially stereochemically mobile. A representative data set of 250 high-resolution (</=2.0 A), non-homologous protein crystal structures and corresponding variant and homologous entries, obtained from the Brookhaven Protein Data Bank, was examined to identify turns that are assigned different conformational types (type I/type II) in related structures. A total of 55 examples of beta-turns were identified as possible candidates for a stereochemically mobile site. Of the 55 examples, 45 could be classified as a potential site for interconversion between type I and type II beta-turns, while ten correspond to flips from type I' to type II' structures. As a further check, the temperature factors of the central peptide unit carbonyl oxygen atom of the 55 examples were examined. The analysis reveals that the turn assignments are indeed reliable. Examination of the secondary structures at the flanking positions of the flippable beta-turns reveals that seven examples occur in the loop region of beta-hairpins, indicating that the formation of ordered secondary structures on either side of the beta-turn does not preclude local conformational variations. In these beta-turns, Pro (11 examples), Lys (nine examples) and Ser (seven examples) were most often found at the i+1 position. Glycine was found to occur overwhelmingly at position i+2 (28 examples), while Ser (seven examples) and Asn (six examples) were amongst the most frequent residues. Activation energy barriers for the interconversion between type I and type II beta-turns were computed using the peptide models Ac-Pro-Aib-NHMe and Ac-Pro-Gly-NHMe within the framework of the AM1 semi-empirical molecular orbital procedure. In order to have a uniform basis for comparison and to eliminate the distracting influence of the deviation of backbone dihedral angles from that expected for ideal beta-turns, the dihedral angles phii+1 and psii+2 were fixed at the ideal values (phii+1=-60 degrees and psii+2=0 degrees). The other two angles (psii+1 and phii+2) were varied systematically to go from type II to type I beta-turn structures. The computational results suggest that there exists one stereospecific, concerted flip of the central peptide unit involving correlated single bond rotation that can occur with an activation barrier of the order of 3 kcal/mol. The results presented here suggest that conformational variations in beta-turns are observed in protein crystal structures and such changes may be an important dynamic feature in solution.

Effects of the phi[NHCO] retromodification on dehydroalanine dipeptide

The potential energy surface of the phi [NHCO] delta Ala dipeptide has been computed using ab initio quantum mechanical calculations at different theoretical levels. Three degenerate minima were found and characterized. The most favoured conformation is stabilized by an intramolecular hydrogen bonding interaction. The other two minima correspond to helical and malonamide-like conformations, being 4.6 kcal/mol and 6.9 kcal/mol less stable than the lowest energy conformation, respectively. Influence of solvent effects on the relative stabilities of the different conformations have been accounted using SCRF calculations. Two implicit solvent models have been considered: water and CCl4. The results indicate that in the both cases the conformation with an intramolecular hydrogen bonding interaction retains its lowest energy.

Recent developments in retro peptides and proteins--an ongoing topochemical exploration

Main-chain peptidomimetics based on peptide-bond reversal and inversion of chirality represent important structural alterations for peptides and proteins, and are highly significant for biotechnology; these modifications have been widely applied: the D-HIV-protease dimer cleaves only all-D substrate; an all-D-hexapeptide opioid is able to produce analgesia following intraperitoneal administration. Antigenicity and immunogenicity can be achieved by metabolically stable antigens such as all-D- and retro-inverso-isomers of natural antigenic peptides. Isomers, including the retro- and retro-inverso- forms, of hybrid peptides derived from cercropin A and melittin, maintain antimicrobial activity. Therefore, an insight is provided into structure-activity relationships and the rational design of biologically important isomeric peptides.