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Biomedical subjects

G M Bonora

Publications and source records attributed to G M Bonora.

At least 55 records · Page 3Linked to original sources
PubMed1983

Structure of N-tert-butyloxycarbonyl-D-leucyl-L-phenylalanylethanolamide. An N alpha-protected analogue of the COOH-terminal dipeptide of linear gramicidins.

Solid state conformational analysis of N-tert-butyloxycarbonyl-D-leucyl-L-phenylalanylethanolamide (t-Boc-D-Leu-L-Phe-EA), an N alpha-protected analogue of the COOH-terminal dipeptide of linear gramicidins, carried out by x-ray diffraction, has indicated that the molecules are characterized by an N-H...O = C intramolecularly hydrogen-bonded chain reversal of the beta-turn II' type. One of the two independent molecules in the asymmetric unit shows an additional intramolecular hydrogen bond of the O-H...O = C type, linking the hydroxyl function of the COOH-terminal ethanolamide moiety to the carbonyl oxygen of the urethane N-protecting group. This is the first experimental evidence for a beta-turn conformation fused with the oxy analogue of an alpha-turn. The results of an investigation in a solvent of low polarity (deuteriochloroform), using infrared absorption and 1' nuclear magnetic resonance, strongly support the view that an intramolecularly hydrogen-bonded beta-turn conformation is the most populated conformation of t-Boc-D-Leu-L-Phe-EA molecules at high dilution. In the self-association process, taking place at high concentration, the urethane and peptide NH groups are involved as hydrogen-bonding donors.

Amino Acid Sequence↗
PubMed1983

First observation of a beta-turn conformation fused with the oxy-analogue of an alpha-turn: the molecular structure of a model peptide of the C-terminal part of gramicidin A.

The molecular structure of N-tert-butyloxycarbonyl-D-leucyl-L-phenylalanyl ethanolamide (t-Boc-D-Leu-L-Phe-EA), a protected analogue of the C-terminal dipeptide of the membrane-active linear antibiotic gramicidin A, has been determined by X-ray diffraction. One of the two independent molecules in the asymmetric unit is characterized by a chain reversal stabilized by an intramolecular, three-centre, double hydrogen bonding. It represents the first experimental evidence for a beta-turn conformation fused with the oxy-analogue of an alpha-turn.

Chemical Phenomena↗
PubMed1983

Protected 1-3 segment of the peptaibol antibiotics alamethicin and hypelcin. Solid-state and solution study of a stereochemically constrained linear peptide.

A study of the modes of folding and self-association of Z-Aib-L-Pro-Aib-OMe (the protected 1-3 segment of the peptaibol antibiotics alamethicin and hypelcin) in the solid state was performed using i.r. absorption and X-ray diffraction. The stereochemically constrained tripeptide molecules adopt a 4 leads to 1 intramolecularly H-bonded form (beta-turn), where the single intramolecular H-bond is found between the peptide N-H group of the Aib3 residue and the urethane C = O group of the N-blocking benzyloxycarbonyl moiety. This folded structure is stabilized by an intermolecular H-bond between the urethane N-H group of the Aib1 residue and the peptide C = O group of the Pro2 residue of a symmetry related molecule. According to the i.r. absorption data, in CH2Cl2 and TMP solutions the same intramolecularly H-bonded form occurs as that found in solid state. Compared to the situation in the solid state, in CH2Cl2 and TMP solvation of the urethane N-H group replaces self-association (through the same N-H group). The results are also discussed in relation to those obtained for other protected -Aib-X-Aib- (X = Aib, L-Ala, L-Val) tripeptide segments of peptaibol antibiotics.

Alamethicin↗
PubMed1983

Bioorganic stereochemistry. A study of the peptide oxazolones from Z-(Aib)n-OH (n = 2-4) in the solid state.

An investigation of the preferred conformations and modes of self-association of the peptide oxazolones from Z(-Aib-)n-OH (n = 2-4) in the solid state has been performed by infrared absorption. More detailed information on the peptide oxazolone from Z(-Aib-)3OH(2) has been obtained using X-ray diffraction. In this compound the conformations of the first two Aib residues differ substantially, only the N-terminal one being found in the usual 3(10)-(or alpha-) helical region of the Ramachandran map. The C = N-bond of the oxazolone group is not conjugated with the lactone moiety. A very weak intermolecular interaction occurs between the urethane N-H and the carbonyl group of the oxazolone ring.

Aminoisobutyric Acids↗
PubMed1983

Conformational characteristics of homo-oligopeptides of O-benzyl-L-tyrosine.

Conformational studies of X[-L-Tyr(Bzl)-]n-series bound to polyethyleneglycol (X = H2, Nps; n = 3-8) in the solid state and in solvents of different polarities and capabilities of forming hydrogen bonds are reported. By using i.r. absorption, the occurrence of the beta-structure in the higher oligomers in the solid state was established. By means of i.r. absorption and CD the onset of that ordered conformation in solution was assessed as a function of chain length. The effects induced by the presence of the N-protecting group and added base, and by changing the nature of solvent on the conformational preferences of the [-L-Tyr(Bzl)-]n homo-peptides were also examined. The 2-nitrophenylsulphenyl chromophoric derivative of the alpha-amino group is proposed as a circular dichroism sensor for beta-structure in peptides.

Chemical Phenomena↗
PubMed1982

Peptaibol antibiotics: a study on the helical structure of the 2-9 sequence of emerimicins III and IV.

Solution conformations of the protected 2-9 segment of the peptaibol antibiotics emerimicins III and IV [alpha-aminoisobutyric acid (Aib)]3-L-Val-Gly-L-Leu-(Aib)2 and the related short sequences benzyloxy-(Aib)3-L-Val-OMe and benzyloxy-(Aib)3-L-Val-Gly-OMe have been investigated by circular dichroism studies. For the latter two compounds the structural preferences in the solid state have been assayed by x-ray diffraction analyses. The experimental data described here, along with those previously reported, support the view that the shortest Aib-containing segments (from tri- through pentapeptides) adopt the 3(10)-helical structure both in solution and in the solid state. In contrast, the octapeptide appears to adopt the alpha-helical structure in solution. The role of peptide chain length and specific amino acid sequences in stabilizing either of the two helical structures and hence their possible implications on the nature of the channel formed by peptaibol antibiotics in the membrane are also briefly outlined.

Alkylation↗
PubMed1982

Nuclear magnetic resonance of protamines. A 13C relaxation study of the three main fractions of clupeine.

The three main fractions of clupeine, the protamine extracted from herring sperm, have been investigated by 13C nuclear magnetic resonance techniques. The dynamic behaviour, examined through the evaluation of the spin lattice relaxation times (T1) of individual carbon resonances assigned to both backbone and side chains, reveals interesting features. The relaxation times of backbone alpha-carbons, interpreted on the basis of an axially symmetric ellipsoid, point to the clupeine fractions as being essentially extended in aqueous solution. These times remain constant along the polypeptide chain and are of the order of 0.16 +/- 0.02 s. Conversely, the side chains show different flexibilities in the presence of monophosphate counterions, thus demonstrating a diverging behaviour which may be biologically relevant. In particular, the side-chain flexibilities of fraction YI decrease, while those of fractions Z and YII are either constant or increase. Comparison of these data with the viscosity measurements helps in explaining the viscosity changes observed in the presence of phosphate.

Amino Acid Sequence↗
PubMed1981

Structure of N-acetyl-D-alanyl-D-alanine hydrate. An analogue of the COOH-terminal segment of peptidoglycan of bacterial cell walls.

The solid state conformational analysis of Ac-D-Ala-D-Ala-OH.H2O, carried out by infrared absorption and X-ray diffraction, has indicated that the molecules are not extended in a regular beta conformation, but rather that they are partially folded, the phi, psi torsional angles of the COOH-terminal residue in particular being in the region of the left-handed alpha helix of the Ramachandran map. The acetylamino and peptide groups ar found in the usual trans conformation, the latter, however, exhibiting a deviation from rigid planarity. Only intermolecular hydrogen bonds occur in the crystal state. The solution conformational analysis, performed by infrared absorption and CD, has revealed that the amount of intramolecular N--H ... O==C hydrogen-bonded folded forms, if any, should be extremely small, even in deuteriochloroform at high dilution. In water, solvated, unordered species largely predominate.

Bacteria↗
PubMed1981

Preparation and conformational study of clupeine fragments.

Fragments of clupeines, YI, YII, and Z of divergent chain length and different amino acid composition were prepared by digestion with thermolysin and a mixture of carboxypeptidases A and B, and their conformational preferences examined as a function of pH, added salts, presence of a helix-supporting solvent, and temperature. All these highly basic oligopeptides adopt an essentially unordered conformation in aqueous solution. 2-Chloroethanol supports in various amounts the onset of the right-handed alpha-helical form in the carboxy-peptidase fragments.

Amino Acid Sequence↗
PubMed1981

Interaction of the three main components of clupeine with glycosaminoglycans.

The interactions between each of the three main components of clupeine (YI, YII and Z) and the glycosaminoglycans chondroitin sulfate, heparin and hyaluronic acid were studied with circular dichroism spectroscopy. The induced dichroism is a measure of relative complex stability, which increases with the number of sulfate groups on the glycosaminoglycan. Measuring the induced dichroism as a function of mole ratio of disaccharide to arginine establishes the stoichiometry of the complexes. For a given glycosaminoglycan, the induced dichroism depends on the clupeine, increasing the order YI less than YII less than Z.

Chondroitin Sulfates↗
PubMed1979

Protamines. II. Circular dichroism study of the three main components of clupeine.

The three main components YI, YII, and Z of clupeine, a protamine from herring, have been purified and characterized. The conformational preferences of clupeines have been examined as a funciton of pH, temperature, added salts, and presence of structure-disrupting agents and helix-supporting solvents using circular dichroism. It was found that these small basic proteins assume predominantly an unordered conformation in aqueous solution. Addition of counter ions, in particular perchlorate, and 2-chloroethanol induces in various amounts the onset of the right-handed alpha-helical conformation. Urea favors the statistical coil state. It was also demonstrated that in the 0.1--4.0 . 10(-1) M range, in contrast to clupeines YI and Z, the circular dichroic properties of the YII component do not seem to be sensitive to the addition of mono- and diphosphate.

Amino Acids↗
PubMed1979

13C Nuclear magnetic resonance of protamines. The three main components of clupeine.

The three main components (called YI, YII and Z) of clupeine a protamine from herring have been isolated and characterized by 13C nuclear magnetic resonance. Resonance belonging to the many different amino acid carbon atoms are observable and assigned. The effect of urea on the clupeine fractions points to the molecules being essentially in extended form in 2H2O solutions. Unusual properties of clupeine fractions can be observed in the presence of phosphate. Two of the fractions, i.e. YI and Z, show that a partial folding occurs in some well-defined whereas fraction YII remains essentially unaltered.

Animals↗
PubMed1979

Conformational analysis of N-(tert.-amyloxycarbony-L-proline in the solid state and in solution.

The solid-state conformational analysis of t-AOC-L-Pro-OH has indicated that the molecules are not folded up to form an oxy-C7 peptide conformation, but rather that they are held together through intermolecular O-H .... 0 = C (urethane) hydrogen bonds. The tertiary amide bond is in the cis configuration. In solvents of high polarity strongly solvated species largely predominate. In cyclohexane solution non-associated and associated (involving the carboxyl C = O as the proton acceptor) species are simultaneously present. Obviously, the extent of association increases with increasing solute concentration. The amount of the oxy-C7 form, if any, should be extremely small. It is also demonstrated that CD measurements alone can lead to an incorrect picture of the conformational preferences of amino acid derivatives and small peptides in solution.

Adsorption↗
PubMed1979

X-ray study on homo-oligopeptides t-BOC-(D-Ala)7-OMe and HCl.H(D-Ala)7-OMe.

Observations of extended peptide chains, whose direction is perpendicular to the fiber axis (cross-beta-structures) have hitherto been confined to fibrous proteins and to some synthetic polydisperse polypeptides of rather low molecular weight. This structure has now been found in some monodisperse linear homo-oligopeptides with aliphatic hydrocarbon side chains. X-ray diffraction photographs of t-Boc-(D-Ala)7-OMe and HCl.H(D-Ala)7-OMe show characteristic reflections for this form. In addition, the good orientation of suitably prepared specimens has enabled a fairly complete determination of the unit cell of the heptapeptides to be made. t-Boc-(D-Ala)7-OMe and HCl.H(D-Ala)7-OMe molecules are packed in a monoclinic lattice with a = 4.80, b = 34.5, c = 5.82 A, beta = 65.6 degrees and a = 4.80, b = 29.5, c = 5.82 A, beta = 65.6 degrees, respectively. It has not been possible to establish whether the arrangement of the chains within the sheets is parallel or antiparallel.

Molecular Conformation↗
PubMed1979

Protamines. III. Synthesis of the tetradecapeptide corresponding to the C-terminal sequence 52--65 of galline.

The synthesis of peptides containing blocks of arginyl residues is proposed through amidination of the corresponding ornithyl analogs. In order to test this strategy the ornithyl analog of the C-terminal sequence 52--65 of galline was synthesized by the conventional method. The amidination reaction, performed on fragments of different length and ornithyl-residue content, quantitatively converts ornithines into arginines. The strategy proposed may represent a powerful tool for the synthesis of protamines and other basic proteins.

Amidines↗
PubMed1978

beta sheet formation by L-methionine oligopeptides.

Monodispersed N- and C-protected linear homo-oligomethionines (n = 2- -7) are studied by measurements of circular dichroism in the vacuum ultraviolet region. In the solid state higher members of the series take up a beta-conformation in which both parallel and antiparallel chain arrangements are present. The strong beta-forming tendency of the methionine residue is demonstrated.

Chemical Phenomena↗