Backbone side-chain interactions in peptides

IR, ¹H-NMR and X-ray experiments have been carried out on dipeptides with the Pro-Asp and Pro-Asn sequences protected on both ends by amide groups. The Pro-Asp dipeptide was investigated for the carboxylic, methyl ester and carboxylate forms of the Asp residue.In solution, all dipeptides are found to accommodate almost exclusively the I-turn conformation stabilized by an interaction between the Asp or Asn-NH and CO bonds. The I-turn percentage roughly parallels the basicity of the Asp or Asn side substituent, and decreases from Asp^- to Asn, and to Asp or Asp (OMe).The I-turn, stabilized by the interaction involving the Asp-CO site, is retained in the crystal structure of the Pro-Asp(OMe) dipeptide. The Pro-Asp and Pro-Asn dipeptides assume a II-turn conformation in the solid state and the polar Asp or Asn side-groups are involved in a complex network of intermolecular interactions.     

Crystal state conformation of three azapeptides containing the Azaproline residue,a β-turn regulator

The molecular structure of three protected AzaPro-containing peptides have been determined by x-ray diffraction: Z-AzaPro-NHiPr ( 1 ; Z: benzyloxycarbonyl), Z-AzaPro-L -Ala-NHiPr ( 2 ), and Boc-L -Ala-AzaPro-NHiPr ( 3 ; Boc: tert-butyloxycarbonyl). Starting from the key synthon benzyl-azaprolinate, compounds 1 , 2 , and 3 have been prepared by combined use of liquid phase peptide synthesis method and adequate isocyanates. In all peptides, the following geometric characteristics are retained: (a) pyramidal character of the two nitrogen atoms of the pyrazolidine ring; (b) pseudo cis conformation of the urethane ( 1 , 2 ) or tertiary amide ( 3 ) function preceding the AzaPro residue; (c) identical absolute values of the Azaproline residue torsion angles “?, ψ” respectively 111° and 23°. In compound 2 , the two nitrogen atoms of the pyrazolidine ring are R, R but the opposite S, S absolute configurations are observed in compound 3 . In the crystal, compound 3 adopts a folded structure similar to a type VI β-turn with a weak intramolecular i + 3 → i hydrogen bond, while an extended structure is observed in compound 2 . In the light of our findings, in a peptide chain and contrary to the Pro residue, an AzaPro residue should prevent the formation of any type of any type of β-turn with the residue following it but could accommodate a folded structure with a pseudo type VI βturn with the preceding residue. If confirmed, this would be of tremendous importance in the design of biologically active peptides and drugs. © 1993 John Wiley & Sons, Inc.     

The lepidopteran mitochondrial control region: structure and evolution

For several species of lepidoptera, most of the approximately 350-bp mitochondrial control-region sequences were determined. Six of these species are in one genus, Jalmenus; are closely related; and are believed to have undergone recent rapid speciation. Recent speciation was supported by the observation of low interspecific sequence divergence. Thus, no useful phylogeny could be constructed for the genus. Despite a surprising conservation of control-region length, there was little conservation of primary sequences either among the three lepidopteran genera or between lepidoptera and Drosophila. Analysis of secondary structure indicated only one possible feature in common--inferred stem loops with higher-than-random folding energies-- although the positions of the structures in different species were unrelated to regions of primary sequence similarity. We suggest that the conserved, short length of control regions is related to the observed lack of heteroplasmy in lepidopteran mitochondrial genomes. In addition, determination of flanking sequences for one Jalmenus species indicated (i) only weak support for the available model of insect 12S rRNA structure and (ii) that tRNA translocation is a frequent event in the evolution of insect mitochondrial genomes.      

Glutamine repeats and inherited neurodegenerative diseases: molecular aspects

Several dominantly inherited, late onset, neurodegenerative diseases are due to expansion of CAG repeats, leading to expansion of glutamine repeats in the affected proteins. These proteins are of very different sizes and, with one exception, show no sequence homology to known proteins or to each other; their functions are unknown. In some, the glutamine repeat starts near the N-terminus, in another near the middle and in another near the C-terminus, but regardless of these differences, no disease has been observed in individuals with fewer than 37 repeats, and absence of disease has never been found in those with more than 41 repeats. Protein constructs with more than 41 repeats are toxic to E. coli and to CHO cells in culture, and they elicit ataxia in transgenic mice. These observations argue in favour of a distinct change of structure associated with elongation beyond 37–41 glutamine repeats. The review describes experiments designed to find out what these structures might be and how they could influence the properties of the proteins of which they form part. Poly- -glutamines form pleated sheets of β-strands held together by hydrogen bonds between their amides. Incorporation of glutamine repeats into a small protein of known structure made it associate irreversibly into oligomers. That association took place during the folding of the protein molecules and led to their becoming firmly interlocked by either strand- or domain-swapping. Thermodynamic considerations suggest that elongation of glutamine repeats beyond a certain length may lead to a phase change from random coils to hydrogen-bonded hairpins. Possible mechanisms of expansion of CAG repeats are discussed in the light of looped DNA model structures.     

Rǒle des electrons π des fonctions amide et ester dans les peptides et depsipeptides

The IR data for the R¹ CO-O-CHR²-CO-NHR³ derivatives are interpreted in terms of a H…π interaction involving the N? H bond and the π orbitals of the ester function and giving rise to a high ν(C?O) frequency and a low ν frequency. The resulting molecular conformation corresponds to the angular values ? # ?90°, ψ # 0°. The H…π interaction in MeCO-L-Lac-NHMe is highly destabilized by water and aprotic solvents but is retained in methanol. Considering the high ν(C?O) ester or amide frequency of the middle function in β-folded depsipeptide or peptide sequences, it may be supposed that the residue indexed i + 2 in β turns experiences a H…π interaction which has a stabilizing effect on β turns. Some examples concerning valinomycin and some model compounds are discussed.     

Development of cell surface saccharides on embryonic pancreatic cells

Using a battery of seven lectin-ferritin conjugates as probes for cell surface glycoconjugates, we have studied the pattern of plasmalemmal differentiation of cells in the embryonic rat pancreas from day 15 in utero to the early postpartum stage. Our results indicate that differentiation of plasmalemmal glycoconjugates on acinar, endocrine, and centroacinar cells is temporally correlated with development and is unique for each cell type, as indicated by lectin-ferritin binding. Specifically, (a) expression of adult cell surface saccharide phenotype can be detected on presumptive acinar cells as early as 15 d in utero, as indicated by soybean agglutinin binding, and precedes development of intracellular organelles characteristic of mature acinar cells; (b) maturation of the plasmalemma of acinar cells is reached after intracellular cytodifferentiation is completed, as indicated by appearance of Con A and fucoselectin binding sites only at day 19 of development; conversely, maturation of the endocrine cell plasmalemma is accompanied by "loss" (masking) of ricinus communis II agglutinin receptors; and (c) binding sites for fucose lectins and for soybean agglutinin are absent on endocrine and centroacinar cells at all stages examined. We conclude that acinar, centroacinar, and endocrine cells develop from a common progenitor cell(s) whose plasmalemmal carbohydrate composition resembles most closely that of the adult centroacinar cell. Finally, appearance of acinar lumina beginning at approximately 17 d in utero is accompanied by differenetiation of apical and basolateral plasmalemmal domains of epithelial cells, as indicated by enhanced binding of several lectin-ferritin conjugates to the apical plasmalemmal, a pattern that persists from this stage through adult life.     

3H]BHDP as a novel and selective ligand for sigma1 receptors in liver mitochondria and brain synaptosomes of the rat

The binding profile of [(3)H]BHDP ([(3)H]N-benzyl-N'-(2-hydroxy-3,4-dimethoxybenzyl)-piperazine) was evaluated. [(3)H]BHDP labelled a single class of binding sites with high affinity (K(d)=2-3 nM) in rat liver mitochondria and synaptic membranes. The pharmacological characterization of these sites using sigma reference compounds revealed that these sites are sigma receptors and, more particularly, sigma1 receptors. Indeed, BHDP inhibited [(3)H]pentazocine binding, a marker for sigma1 receptors, with high affinity in a competitive manner. BHDP is selective for sigma1 receptors since it did not show any relevant affinity for most of the other receptors, ion channels or transporters tested. Moreover, in an in vitro model of cellular hypoxia, BHDP prevented the fall in adenosine triphosphate (ATP) levels caused by 24 h hypoxia in cultured astrocytes. Taken together, these results demonstrate that [(3)H]BHDP is a potent and selective ligand for sigma1 receptors showing cytoprotective effects in astrocytes.