Biomedical subjects

M Saviano

Publications and source records attributed to M Saviano.

At least 55 records · Page 3Linked to original sources

PubMed1996

Bicyclic peptides as type I/type II beta-turn scaffolds.

We recently reported the rational design, synthetics, and structural characterization of the most potent and selective peptide-based neurokinin A antagonist thus far described: cyclo(Met1-Asp2-Trp3-Phe4-Dap5-Leu6)cyclo(2 beta-5 beta). Its bicyclic structure is characterized by a type I and a type II two beta-turn around Trp3-Phe4 and Leu6-Met1, respectively. In order to understand whether the two different beta-turned structures are determined by the bicyclic structure or by the amino acid type at the corner positions, we have synthesized the pseudo-symmetrical analogue cyclo(Phe1-Asp2-Trp3-Phe4-Dap5-Trp6)cyclo(2 beta-5 beta). The structural characterization in the crystal state and in solution, here reported, gives an experimental evidence that the backbone of the bicyclic structure is a rigid scaffold that can be used to build both a type I and type II beta-turn independently from the amino acid composition.

Crystallography, X-Ray↗

PubMed1996

Solvent-mediated conformational transition in beta-alanine containing cyclic peptides. VIII.

In the present paper we describe the solution nmr structural analysis and restrained molecular dynamic simulation of the cyclic pentapeptide cyclo-(Pro-Phe-Phe-beta-Ala-beta-Ala). The conformational analysis carried out in CD3CN and dimethylsulfoxide (DMSO) solutions by nmr spectroscopy was based on interproton distances derived from rotating frame nuclear Overhauser effect spectroscopy spectra and homonuclear coupling constants. A restrained molecular dynamic simulation in vacuo was also performed to build refined molecular models. The molecule is present in both solvent systems as two slowly interconverting conformers, characterized by a cis-trans isomerism around the beta-Ala5-Pro1 peptide bond. In CD3CN solution, the conformer with a ci5 peptide bond is quite similar to that observed in the solid state, while the conformer containing all trans peptide bonds is characterized by an intramolecular hydrogen bond stabilizing a C10- and a C13-ring structure. In DMSO solution, the trans isomer is partly similar to that observed in CD3CN solution while the cis isomer is different from that observed in the solid state. The effect of the solvent in stabilizing different conformations was also investigated in DMSO-CD3CN solvent mixtures.

Amino Acid Sequence↗

PubMed1996

Discovering protein secondary structures: classification and description of isolated alpha-turns.

Irregular protein secondary structures are believed to be important structural domains involved in molecular recognition processes between proteins, in interactions between peptide substrates and receptors, and in protein folding. In these respects tight turns are being studied in detail. They also represent template structures for the design of new molecules such as drugs, pesticides, or antigens. Isolated alpha-turns, not participating in alpha-helical structures, have received little attention due to the overwhelming presence of other types of tight turns in peptide and protein structures. The growing number of protein X-ray structures allowed us to undertake a systematic search into the Protein Data Bank of this uncharacterized protein secondary structure. A classification of isolated alpha-turns into different types, based on conformational similarity, is reported here. A preliminary analysis on the occurrence of some particular amino acids in certain positions of the turned structure is also presented.

Amino Acid Sequence↗

PubMed1996

NMR conformational studies on a synthetic peptide reproducing the [1-20] processing domain of the pro-ocytocin-neurophysin precursor.

The combined use of several nuclear magnetic resonance and restrained molecular dynamics techniques allowed the formulation of a molecular model for the preferred solution conformation of a synthetic peptide reproducing the [1-20] processing domain of the pro-ocytocin-neurophysin precursor. In the model, the conformation of the 20-membered tocin ring, with the two Cys1 and Cys6 residues bridged by a disulphide bond, is very close to that observed for isolated ocytocin in the solid state; in addition, a type II beta-turn is postulated for the 7-10 segment of the acyclic tail containing the Lys11-Arg12 processing site, and connecting ocytocin to the neurophysin domain, while the C-terminal 13-20 segment of the molecule is believed to assume a helical structure. This particular structural organization could be important in participating as the favorable conformation for optimal substrate-enzyme active site recognition and processing by specific endoproteases.

Amino Acid Sequence↗

PubMed1996

Unusual conformational preferences of beta-alanine containing cyclic peptides. VII.

In the present paper we describe the synthesis, purification, and single crystal x-ray analysis of the cyclic pentapeptide cyclo-(Pro-Phe-Phe-beta-Ala-beta-Ala). This compound crystallizes in the orthorhombic space group P2I2I2I from methanol and adopts in the solid state an unusual conformation characterized by a cis beta-Ala5-Pro1 peptide bond and by an intramolecular hydrogen bond stabilizing a C11-and a C12-ring structure. The C11 structure contains the Phe3 and the beta-Ala4 at the corner position of the turn; it is the first observation of a type II beta-turn enlargement due to the insertion of an extra methylene group of the beta-alanine residue. The rest of the molecule participates in a newly characterized C12-ring structure, which incorporates a beta-Ala residue at position i of the turn.

Amino Acid Sequence↗

PubMed1995

[Aib5,6-D-Ala8]-cyclolinopeptide A, grown from a benzene/acetonitrile mixture.

cyclo-(Prolyl-prolyl-phenylalanyl-phenylalanyl- alpha-aminoisobutyryl-alpha-aminoisobutyryl-isoleucyl-D-alan yl-valyl) ([Aib5,6-D-Ala8]-cyclolinopeptide A), grown from benzene/acetonitrile mixture, crystallizes with one acetonitrile and two water molecules. The molecular structure is almost identical to that obtained from methanol/water. The dimension of the solvent channels found in these structures is reduced in the present one, but the intramolecular hydrogen-bond pattern is preserved. The Pro1-Pro2 peptide unit is cis (omega = 8 degrees); all others are trans.

Acetonitriles↗

PubMed1995

Specific interaction between cyclophilin and cyclic peptides.

Cyclophilin A, a peptidyl-prolyl cis-trans is isomerase that catalyzes the otherwise slow isomerization of Xaa-Pro imidic bond, specifically binds the immunosuppressant cyclosporin A. Herein we report evidence on binding of cyclolinopeptide A and its synthetic analogue, [Aib5,6-D-Ala8]cyclolinopeptide, to bovine cyclophilin A. Binding experiments were monitored by fluorescence, CD, and second-derivative spectroscopies, evidencing no remarkable rearrangement of protein structure organization. The possibility that cyclolinopeptide A could act as a substitute of cyclosporin A in the immunosuppression modulation is also briefly discussed.

Amino Acid Isomerases↗

PubMed1995

Conformational studies of heterochiral peptides with diastereoisomeric residues: crystal and molecular structures of linear dipeptides derived from leucine, isoleucine, and allo-isoleucine.

The x-ray diffraction analyses of three N- and C-terminally blocked L,D dipeptides, namely t-Boc-D-Leu-L-Leu-OMe (1), t-Boc-L-Ile-D-aIle-OMe (2), and t-Boc-D-aIle-L-Ile-OMe (3) containing enantiomeric or diastereomeric amino acid residues have been carried out. The structures were determined by direct methods and refined anisotropically to final Rf actors of 0.077, 0.058, and 0.072 for (1), (2), and (3), respectively. Peptides 1-3 all assume a similar U-shaped structure with phi and psi torsion angles corresponding to one of the possible calculated minimum energy regions (regions E and G for L residues, and F*, D* and H* for D residues). The peptide backbones of 1-3 are almost superimposable [provided that the appropriate inversion of the chiral centers of (2) is made]. Side-chain conformations of Leu residues in peptide (1) are g- (tg-) for the L-Leu residue and the mirrored g+ (tg+) for the D-Leu residue; however, in peptides (2) and (3) the conformations of the isoconfigurational side chains of the Ile or allo-Ile residues are (g-t) t and (tg+) t for the L-Ile and the D-allo-Ile moieties, respectively. In all cases, these conformations correspond to the more populated conformers of beta-branched residues statistically found in crystal structures of small peptides. The results seem to indicate that, at least in short peptides with enantiomeric or diastereoisomeric residues, the change in chirality in the main-chain atoms perturbs the backbone conformation to a lesser extent and the side chain conformation to a greater extent.

Crystallography, X-Ray↗

PubMed1995

Bioactive peptides: conformational studies of [Tyr4] cyclolinopeptide A.

The solid state conformational analysis of [Tyr4] cyclolinopeptide A has been carried out by x-ray diffraction studies. The crystal structure of the monoclinic form, grown from a dioxane-water mixture [alpha = 9.849 (5) A, b = 20.752 (4) A, c = 16.728 (5) A, beta = 98.83 (3) degrees, space group P21, Z = 2], shows the presence of five intramolecular N-H...O = C hydrogen bonds, with formation of one C17 ring structure, one alpha-turn (C13), one inverse gamma-turn (C7), and two beta-turns (C10, one of type III and one of type I). The Pro1-Pro2 peptide unit is cis (omega = 5 degrees), all others are trans. The structure is almost superimposable with that of cyclolinopeptide A. The rms deviation for the atoms of the backbones is on the average 0.33 A.

Amino Acid Sequence↗

PubMed1995

The polypeptide 3(10)-helix as a template for molecular recognition studies. Structural characterization of a side-chain functionalized octapeptide.

A N alpha-blocked, Aib-rich octapeptide methylamide containing two N omega-benzoylated L-Lys residues at positions 3 and 6 was synthesized by solution methods and fully characterized. A solution and crystal-state conformational analysis, performed by using FT-IR, 1H NMR, CD, and X-ray diffraction techniques, showed that the peptide is folded into a regular, right-handed 3(10)-helix stabilized by seven consecutive N-H...O=C intramolecular H-bonds of the beta-turn III type. The two benzamidobutyl L-Lys side chains, located on the same side of the helix after one complete turn, generate a cleft the minimal width of which was found to be 3.47 A.

Amino Acid Sequence↗

PubMed1994

Bioactive peptides: solid state, solution and molecular dynamics studies of a cyclolinopeptide A-related cystinyl cyclopentapeptide.

The conformational analysis of [sequence: see text] the disulphide cyclopeptide-related cyclolinopeptide A, has been carried out by solid state methods using x-ray diffraction techniques, in solution by nmr, CD, ir spectroscopies, and by molecular dynamics (MD) analysis. The structure of the monoclinic form, obtained from ethanol (a = 11.303(2) A, b = 14.467(8) A, c = 12.355(2) A, beta(degree) = 109.40(1), space group P2(1), Z = 2) presents two transannular H bonds with the formation of one type VIa beta-turn involving the C = O of the urethane moiety and the Phe3 NH, and an intramolecular H bond between the C = O of urethane group and the Phe4 NH. In the solid state all the peptide bonds are in the trans configuration with the exception of a cis peptide bond occurring between the Cys1 and Pro2 residues; the linkage S-S assumes right-handed chirality. The conformational study in solution by nmr spectroscopy indicates that the peptide is very flexible and that some conformer families are present at room temperature both in polar and apolar solvents. CD studies confirm that this cyclic system tends to give rise to a complex mixture of quasi-isoenergetic conformations, favored by the flexibility of the disulphide bridge and by the isomerism of the Xxx-Pro bond. MD studies carried out in vacuo and in solution shows that the structure determined by solid state represents a energy minimum. All hydrogen bonds found in the crystalline state are correctly reproduced in vacuo and in solution simulations.

Amino Acid Sequence↗

PubMed1994

Defect peptide chemistry: perturbations in the structure of a homopentapeptide induced by a guest residue interrupting side-chain regularity.

The fully blocked pentapeptide Tfa-(Deg)2-L-Abu-(Deg)2-OtBu (Tfa: triflouroacetyl; Deg: C alpha, alpha-diethylglycine; Otbu: tert-butoxy) adopts in the crystal state a regular, right-handed 3(10)-helical structure stabilized by three N--H...O=C intramolecular 1 < 4 (or C10) H bonds, as determined by an x-ray diffraction analysis. However, a Fourier transform ir absorption and 1H-nmr study strongly supports the view that in deuterochloroform solution the four Deg residues at both termini of the peptide main chain are involved in successive, fully extended C5 forms. A comparison with the stable, fully developed, multiple C5 conformation of Tfa-(Deg)5-OtBu indicates that incorporation of an Abu guest residue, interrupting the side-chain uniformity of the host (Deg)5 homopeptide, while altering only marginally the conformation in a solvent of low polarity, is responsible for a dramatic perturbation of the crystal-state structure.

Amino Acid Sequence↗

PubMed1994

A crystal structure with features of an antiparallel alpha-pleated sheet.

A single-crystal x-ray diffraction analysis of Boc-L-Ala-D-aIle-L-Ile-OMe has been carried out. The analysis has shown (a) that the tripeptide molecules have in part an alpha-extended conformation, the torsion angles of the L-Ala and D-aIle residues being psi 1 = -75.1 degrees and psi 1 = -25.8 degrees and psi 2 = 67.3 degrees and psi 2 = 44.1 degrees, respectively, and (b) that the molecules are organized in rippled planes where they occur in relative antiparallel orientation linked together side by side by H bonds. This molecular organization of the tripeptide corresponds closely to that of an antiparallel alpha-pleated sheet, and likely constitutes the first example of a structure of this kind for which a characterization at the atomic level has been achieved. A molecular dynamics study has shown that the molecular conformation of the tripeptide in the crystalline state is determined primarily by intermolecular interactions.

Amino Acid Sequence↗

PubMed1994

Beta-alanine containing cyclic peptides with predetermined turned structure. V.

In the present paper we describe the synthesis, purification, single crystal x-ray analysis, and solution structural characterization by nmr spectroscopy, combined with restrained molecular dynamic simulations, of the cyclic hexapeptide cyclo-(Pro-Phe-beta-Ala-Phe-Phe-beta-Ala). The peptide was synthesized by classical solution methods and the cyclization of the free hexapeptide was accomplished in good yields in diluted methylenechloride solution using N,N-dicyclohexyl-carbodiimide. The compound crystallizes in the monoclinic space group P2(1) from methanol/ethyl acetate. The molecule adopts in the solid state a conformation characterized by cis beta-Ala6-Pro1 peptide bond. The alpha-amino acid residues are at the corner positions of turned structures. The Pro1-Phe2 segment is incorporated in a pseudo type I beta-turn, while Phe4-Phe5 is in a typical type I beta-turn. Assignment of all 1H and 13C resonances was achieved by homo- and heteronuclear two-dimensional techniques in dimethylsulfoxide (DMSO) solutions. The conformational analysis was based on interproton distances derived from rotating frame nuclear Overhauser effect spectroscopy spectra and homonuclear coupling constants. Restrained molecular dynamic simulation in vacuo was also performed to built refined molecular models. The molecule is present in DMSO solution as two slowly interconverting conformers, characterized by a cis-trans isomerism around the beta-Ala6-Pro1 peptide bond. This work confirms our expectations on the low propensity of beta-alanyl residues to be positioned at the corners of turned structure.

Amino Acid Sequence↗

PubMed1994

Beta-alanine containing cyclic peptides with turned structure: the "pseudo type II beta-turn." VI.

In the present paper we describe the synthesis, purification, single crystal x-ray analysis, and nmr solution characterization, combined with restrained molecular dynamic simulations, of the cyclic hexapeptide cyclo-(L-Pro-L-Phe-beta-Ala)2. The peptide was synthesized by classical solution methods and the cyclization of the free hexapeptide was accomplished in good yields in diluted methylene chloride solution using N,N-dicyclohexyl-carbodiimide. The compound crystallizes in the monoclinic space group P2(1) from methanol-dichloromethane solution. The two identical halves of the molecule adopt in the solid state two different conformations. One beta-Ala-L-Pro peptide bond is trans, while the second is cis. The molecule is present in dimethylsulfoxide d6 solutions as a mixture of conformational families. One of these corresponds to a C2 symmetrical molecule with both beta-Ala-Pro cis peptide bonds, while the second major conformation is very similar to that observed in the solid state. All Pro-Phe segments, both in the solid state and the symmetrical and unsymmetrical solution conformations, display phi, psi angles close to that of position i + 1 and i + 2 of type II beta-turns. In addition, the segments preceded by a trans beta-Ala-Pro peptide bond are characterized by a typical i<--i + 3 hydrogen bond, which is absent in the conformer containing a cis beta-Ala-Pro peptide bond. The latter conformation corresponds to a new structural domain we define as the "pseudo type II beta-turn."

Amino Acid Sequence↗

PubMed1994

Mixed conformation in C alpha, alpha-disubstituted tripeptides: x-ray crystal structures of Z-Aib-Dph-Gly-OMe and Bz-Dph-Dph-Gly-OMe.

We report here the synthesis and molecular structure in the solid state of fully protected tripeptides containing C alpha, alpha-diphenylglycine (Dph), namely Z-Aib-Dph-Gly-OMe (Aib: C alpha, alpha-dimethylglycine) and Bz-Dph-Dph-Gly-OMe. The molecular conformation around the Dph residue, containing two bulky substituents, is fully extended, while the Aib residue, containing two smaller groups on the C alpha atom, adopts the typical 3(10)/alpha-helical conformation. Gly residues, without substituents on the C alpha atom, show different conformational preferences. Each residue seems to behave, from a conformational point of view, independently from the presence of the other residues, and thus mixed local conformations (folded and extended) are present in the crystals. The nonconventional peptide synthesis, using the Ugi reaction, is also reported.

Amino Acid Sequence↗

PubMed1993

beta-Alanine containing peptides: gamma-turns in cyclotetrapeptides.

In the present paper we describe the synthesis, purification, single-crystal x-ray analysis, solution conformational characterization, and conformational energy calculations of the cyclic tetrapeptide cyclo-(beta-Ala-L-Pro-beta-Ala-L-Val). The peptide was synthesized by classical solution methods and the cyclization of the free tetrapeptide was accomplished in good yields in diluted methylene chloride solution using N,N-dicyclohexyl-carbodiimide. The compound crystallizes in the monoclinic space group P2(1) from ethanol with two independent molecules in the unit cell. All peptide bonds are trans. The nmr molecular conformation in the acetonitrile solution as well as that derived from the molecular dynamic simulation in vacuo is quite different from those observed in the solid state and is very similar to that previously observed for the parent compound cyclo- (beta-Ala-L-Pro-beta-Ala-L-Pro).

Amino Acid Sequence↗

PubMed1993

Bioactive peptides: conformational study of a cystinyl cycloheptapeptide in its free and calcium complexed forms.

The disulphide bridged heptapeptide Boc-Cys-Val-Pro-Pro-Phe-Phe-Cys-OMe has been synthesized by classical solution methods. An ion binding study showed the peptide's ability to complex calcium ions with definite stoichiometry. The solution conformation of the peptide in its free and calcium-complexed form has been investigated by CD and nmr. The model structure derived from nmr data has been energy minimized and the resulting structure investigated by molecular dynamics simulation in water. The structure of the equimolar peptide/Ca2+ complex in acetonitrile at room temperature shows the presence of two transannular hydrogen bonds, with the formation of two ring structures of the C10 (type VIa) and C14 type. One peptide unit (Pro-Pro) is cis, all others are trans.

Acetonitriles↗