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Biomedical subjects

E Benedetti

Publications and source records attributed to E Benedetti.

At least 217 records · Page 12Linked to original sources
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↗
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↗
PubMed1980

Preferred conformation of the tert-butoxycarbonyl-amino group in peptides.

Structural parameters, derived from X-ray crystallographic data, have been compiled for amino acid and linear peptide derivatives which contain the N-terminal tert-butoxycarbonyl (Boc) group or its next higher homolog, the tert-amyloxycarbonyl group. The comparison of the geometry of the urethane group in Boc-derivatives with that of the peptide group shows small differences in bond angles about the trigonal carbon, because of altered interactions when a C alpha H group of a peptide unti is replaced by an ester oxygen. In contrast to the strong preference of the peptide bond for the trans form (except when it precedes proline), the urethane amide bond adopts both the cis and trans conformations in crystals. The cis urethane conformation is preferred in crystals of compounds with a tertiary nitrogen (such as Boc-Pro) or in structures stabilized by strong intermolecular interactions. Conformational energy computations on Boc-amino acid N'-methylamides indicate that the trans and cis conformations of the urethane amide bone have nearly equal energies (even for amino acids other than proline), in contrast to the peptide bond, for which the trans conformation has a much lower energy. The computed increase of the cis content in Boc-amino acid derivatives (as compared with the corresponding N-acetyl derivatives) is consistent with the observed distributions of conformations in crystal structures and with n.m.r. studies in solution. Usually, the substitution of a Boc for an N-acetyl end group does not alter the conformational preferences (as indicated by phi, psi values and relative energies) of the amino acid residue which follows the end group when the amide bond is trans. Particular conformations, however, can be stabilized by strong attractive interactions between some side chains (e.g. that of phenylalanine) the the bulky Boc end group.

Chemical Phenomena↗
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↗
PubMed1976

Structural characterization of thermal prebiotic polypeptides.

Thermal polycondensation of amino-acids as a possible prebiotic path of chemical evolution of life has been critically examined. The polymeric materials studied by nmr methods have scarce resemblance to natural peptidic material because beta, gamma and eplision peptide bonds largely predominate over a-peptide bonds.

Aspartic Acid↗
PubMed1971

Conformation of cyclolinopeptide a observed by circular dichroism.

A stereochemical investigation, by circular dichroism, of a synthetic nonapeptide (cyclolinopeptide A) in several organic and organic-sulfuric acid solvents is presented. From this examination, and results found for a conformationally rigid model compound, 1,7,7-trimethyl-3-azabicyclo [2.2.1] heptan-2-one(camphorolactam), it is concluded that cyclolinopeptide A may exist in several conformations in solution. None of these conformations is believed to be stabilized by intramolecular hydrogen bonds. Some details on an x-ray analysis of the cyclic nonapeptide are also presented.

Journal Article↗
PubMed1970

Crystal and molecular structure of n,n'-diethyl-n,n'-diphenylurea.

N,N'-diphenyl-N,N'-diethylurea (C(17)H(20)N(2)O) crystallizes in the space group P2(1)/c. The unit cell constants are: a = 10.42 +/- 0.01 A, b = 16.86 +/- 0.02 A, c = 10.66 +/- 0.001 A, beta = 125 degrees 16' +/- 5'; Z = 4, D(x) = 1.16 g.cm(-3), D(meas) = 1.16 +/- 0.01 g.cm(-3). Data for 1392 reflections were collected at room temperature on a Picker automated diffractometer. The crystal structure was solved by direct methods and refined by bloc-diagonalized matrix least-squares calculations. The molecule is characterized by a pseudo C(2) symmetry; both phenyl groups are trans with respect to the oxygen atom. The hybridization of the two nitrogen atoms is intermediate between trigonal and tetrahedral; the nonplanar distortion of the amide groups is about 30 degrees . The amide C-N bond lengths are 1.37 A.

Journal Article↗
PubMed1969

Flexibility of supposed "rigid" molecules: substituted 2,5-piperazinediones (diketopiperazines).

The relevant results of accurate X-ray analyses of both the trans-and the L-cis-3,6-dimethyl-2,5-piperazinediones (diketopiperazines) are reported. We note that a large variability of conformations for the ring system can be accomplished by coupling small bond-angle deformations with large variations of the internal rotation angles. The experimental molecular models are discussed in terms of these changes and in terms of nonbonded intramolecular interactions.

Journal Article↗
PubMedDate not supplied

Conformational analysis of the dipeptide taste ligand L-aspartyl-D-2-aminobutyric acid-(S)-alpha-ethylbenzylamide and its analogues by NMR spectroscopy, computer simulations and X-ray diffraction studies.

A dipeptide taste ligand L-aspartyl-D-2-aminobutyric acid-(S)-alpha-ethylbenzylamide was found to be about 2000 times more potent than sucrose. To investigate the molecular basis of its potent sweet taste, we carried out conformational analysis of this molecular and several related analogues by NMR spectroscopy, computer simulations and X-ray crystallographic studies. The results of the studies support our earlier model that an L-shape molecular array is essential for eliciting sweet taste. In addition, we have identified an aromatic group located between the stem and the base of the L-shape, which is responsible for enhancement of sweetness potency. In this study, we also assessed the optimal size of the essential hydrophobic group (X) and the effects of the chirality of the second residue toward taste.

Aminobutyrates↗