Conformational studies of retro-inverso peptides: the crystal and molecular structure of the hydantoin from H-Ala-g-Ala-mGly-OBzl

Structural and functional studies on Ribonuclease S, retro S and retro-inverso S peptides

Ribonuclease S peptide and S protein offer a unique complementation system to understand the finer features of molecular recognition. In the present study the S peptide (1-16), and its retro and retro-inverso analogs have been analyzed for their structural and biological attributes. RPHPLC, CD, and NMR analyses have revealed that the physicochemical and conformational properties of the S peptide are distinct from those of its retro and retro-inverso analogs. On the functional side, while the S peptide complemented the S protein to give RNase activity, was recognized by anti-S peptide antibodies and induced T cell proliferation, neither the retro nor the retro-inverso S peptides could do so.

Force-field parametrization of retro-inverso modified residues: Development of torsional and electrostatic parameters

Torsional and the electrostatic parameters for molecular mechanics studies of retro-inverso modified peptides have been developed using quantum mechanical calculations. The resulting parameters have been compared with those calculated for conventional peptides. Rotational profiles, which were obtained spanning the corresponding dihedral angle, were corrected by removing the energy contributions associated to changes in interactions different from torsion under study. For this purpose, the torsional energy associated to each point of the profiles was estimated as the corresponding quantum mechanical energy minus the bonding and nonbonding energy contributions produced by the perturbations that the variation of the spanned dihedral angle causes in the bond distances, bond angles and the other dihedral angles. These energies were calculated using force-field expressions. The corrected profiles were fitted to a three-term Fourier expansion to derive the torsional parameters. Atomic charges for retro-inverso modified residues were derived from the rigorously calculated quantum mechanical electrostatic potential. Furthermore, the reliability of electrostatic models based on geometry-dependent charges and fixed charges has been examined.

Algorithmically designed peptides ameliorate behavioral defects in animal model of ADHD by an allosteric mechanism

This study exemplifies the use of three ADHD-relevant methodological innovations. (1) The use of novel, patented, computational peptide design techniques to generate peptides targeting the extra-cellular and para-transmembrane amino acid loops of the putatively ADHD-involved, D(2) dopamine receptor, D(2)DAR; (2) experimental evidence that these peptides in L-amino acid/ortho ordered or D-amino acid/reverse ordered (retro-inverso), D(2)DAR, hydrophobic eigenmode matched forms, evoked positive allosteric and indirect agonist influences on in vitro stably receptor transfected CHO and LtK cells and on in vivo, brain mediated activity; (3) a representative 15 residue all-D-amino acid, D(2) mode matched peptide, given parenterally, was found to "repair" a key aberrant ADHD behavioral characteristic in a standard animal model of ADHD, the Spontaneously Hypertensive Rat, SHR, relative to its progenitor species control, the Wistar-Kyoto rat, WKY. The representative, retro-inverso peptide, all-D-LLYKNKPRYPKRNRE, reversed SHR's relative deficiency in sensory motor gating (pre-pulse inhibition, PPI) while leaving SHR's nonselective attention (rearings), impulsive behavior (time in center), and activity level (timed total motor behavior) unchanged. Amphetamine also reversed SHRs sensory gating defect, but with significant increases in nonselective attention, impulsivity and hyperactivity. These preliminary results suggest the possibility of a new, "softer" pharmacological approach to ADHD: hydrophobic mode matched peptide allosteric augmentation of the activity of indigenous dopamine with respect to D(2)DAR mediated function, in place of stimulant drug-induced presynaptic dopamine release or impairment of dopamine uptake.

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.

Synthesis and anti-aggregatory activity of linear retro-inverso RGD peptides

Six retro-inverso tri- and tetrapeptide analogues of RGD were prepared and their anti-aggregatory activity was determined by platelet aggregation tests in comparison with the corresponding parent peptides. An efficient method for the introduction of a malonyl-aspartic residue into a peptide chain is described for the first time. A 2-3-fold decrease in potency or total loss of bioactivity was observed with the new peptides; structure-activity relationships are discussed.

Contribution of peptide backbone atoms to binding of an antigenic peptide to class I major histocompatibility complex molecule

Antigenic peptides are thought to bind to class I major histocompatibility complex (MHC) molecules through three modes of interaction: van der Waals interaction and, to a lesser extent, hydrogen bonding of anchor side chain atoms to residues comprising the binding pockets of the MHC molecule; hydrogen bonding of N- and C-termini to residues at the ends of the binding groove; and hydrogen bonding of peptide backbone atoms to residues lining the binding groove. To dissect the relative contribution of each of these interactions to class I MHC-peptide stability, a retro inverso (RI) analog of VSV-8. an H-2Kb restricted cytotoxic T lymphocyte (CTL) epitope and terminally modified variants of both VSV-8 and RI VSV-8 were synthesized and their ability to target H-2Kb bearing cells for CTL mediated lysis was compared. None of RI VSV-8 analogs elicited lysis of target cells by CTL specific for VSV-8 nor did they appear to compete with the native peptide for binding to H-2Kb. In contrast, terminally modified VSV-8 peptides elicited target lysis. These findings suggest that side chain topochemistry of the peptide is insufficient for stable peptide binding to H-2Kb; rather, hydrogen bonding of the peptide backbone atoms to H-2Kb side chain atoms appears to play a major role in the stability of the complex. Computer modeling confirmed that none of the RI analogs participate in the extensive hydrogen bonding network between the peptide backbone and the MHC molecule seen in the native structure.