Propensity for local folding induced by the urea fragment in short-chain oligomers.

Examination of local folding and H-bonding patterns in model compounds can be extremely informative to gain insight into the propensity of longer-chain oligomers to adopt specific folding patterns (i.e. foldamers) based on remote interactions.

Conformational studies of proline-, thiaproline- and dimethylsilaproline-containing diketopiperazines.

As proline plays an important role in biologically active peptides, many analogues of this residue have been developed to modulate the proportion of cis and trans conformers. A correlation between the pyrrolidine ring shape and structural properties of proline has been established. Diketopiperazine (DKP) is the model of choice to study the influence of the proline ring modification.

Structural investigation of "cis" and "trans" vinylogous peptides: cis-vinylog turn in folded cis-vinylogous peptides, an excellent mimic of the natural beta-turn.

[structure: see text] Various sequences of modified peptides including those containing a cis- or trans-vinylogous residue have been studied using X-ray diffraction in the solid state and 1H NMR and IR spectroscopy in solution. A cis-vinylogous residue promotes an NH to CO intramolecular H-bond, closing a nine-membered pseudocycle that stabilizes a folded moiety that we proposed to name the cis-vinylogous turn. A trans-vinylogous residue involves an extended conformation.

Synthesis and structure of symmetrical bicyclic hexapeptides bridged by metathesis reaction.

[structure: see text] Bicyclic hexapeptides 1a-c were synthesized via an intramolecular ring-closing metathesis reaction on solid phase followed by an N- to C-terminal cyclization in solution. Structural elucidation showed that these compounds assumed a C2-symmetrical structure with two beta-turns. The trans-ethylene plane was found to occupy two positions in rapid interconversion.

Production of antibodies to alpha(181-192) peptides of neuronal nicotinic acetylcholine receptor coupled to protein carriers in different orientations.

The antibodies to nicotinic acetylcholine receptor alpha(181-192) synthetic peptides were elicited in rabbits and mice using the peptides conjugated to protein carriers in different orientations, either through C-terminal Cys (S-conjugates), or through amino groups (N-conjugates). S-conjugated peptides were less potent in eliciting peptide-specific antibodies compared to N-conjugates and this type of conjugation resulted in antibodies to the coupling reagent. However, the epitopes present in either S- or N-conjugated peptides appeared to be similar, indicating that amino acid residues, which form the epitope, were located in the middle part of the peptide and did not include both N- and C-terminal residues.

Alpha-aminoxy acids as building blocks for the oxime and hydroxylamine pseudopeptide links. Application to the synthesis of human elastase inhibitors.

The aminoxy acids NH2-O-C(alpha)HR-CO2H are much more easily obtained in the enantiomerically pure form than the analogous hydrazino acids NH2-NH-C(alpha)HR-CO2H, and it has been shown that the isosteric amidoxy psi[CO-NH-O] and hydrazide psi[CO-NH-NH] amide surrogates Induce two quite similar gamma-like folded structures. An aminoxy acid can also be N-coupled to a peptide aldehyde to give the aldoxime psi[CH = N-O] link or to a peptide ketone to form the ketoxime psi[CR= N-O] link. The former can be further reduced into the hydroxylamine psi[CH2-NH-O] link which gives rise to reduced amidoxy peptides.

Influence of silaproline on peptide conformation and bioactivity.

The analogue gamma-(dimethylsila)-proline, denoted silaproline (Sip), was synthesized in both enantiomerically pure forms by diastereoselective alkylation of a chiral glycine equivalent with use of Schöllkopf's bis-lactim ether method. The effect of replacing a proline residue in model peptides by this new proline surrogate has been examined in the crystal state by X-ray diffraction and in solution by IR absorption and NMR techniques. Silaproline and proline-containing sequences exhibit very similar conformational properties.

Characterization of the methionine sulfoxide reductase activities of PILB, a probable virulence factor from Neisseria meningitidis.

PILB has been described as being involved in the virulence of bacteria of Neisseria genus. The PILB protein is composed of three subdomains. In the present study, the central subdomain (PILB-MsrA), the C terminus subdomain (PILB-MsrB), and the fused subdomain (PILB-MsrA/MsrB) of N.

Structure of epitopes recognized by the antibodies to alpha(181-192) peptides of neuronal nicotinic acetylcholine receptors: extrapolation to the structure of acetylcholine-binding domain.

Using the alpha(181-192) peptides of neuronal nicotinic acetylcholine receptor (nAChR) and Ala-substituted peptide analogues, amino acid residues critical for specific monoclonal antibody (mAb) binding were identified. By means of 2D nuclear magnetic resonance (2D-NMR) analysis followed by molecular modeling, it was found that mAb binding resulted in stabilization of the free alpha3(181-192) peptide flexible conformation yielding an extended structure with residues 6-11 of the peptide being in direct contact with the Ab. Since the Ab binds the native AChR as well, it is suggested that the corresponding fragment of AChR alpha3 subunit is exposed to solution and also appears in extended conformation.

Unexpected stability of the urea cis-trans isomer in urea-containing model pseudopeptides.

In contrast to the situation observed in the crystal state, the urea moiety in N-Boc-N'-carbamoyl-gem-diaminoalkyl derivatives (single-residue ureidopeptides) 1-4 exclusively assumes a cis-trans conformation in solution. When R(3) = H, the resulting structure can be further stabilized by an intramolecular hydrogen bond that closes an eight-membered pseudocycle. The root-mean-square deviation calculated for heavy atoms between a peptide gamma-turn and the folded conformation that we propose to call urea turn is 0.

Preparative HPLC resolution of the CIS cyclohexane analogs of phenylalanine.

The analytical resolution of different derivatives of cis c(6)Phe (cyclohexane analogs of phenylalanine) was tested by HPLC using the mixed 10-undecenoate/3,5-dimethylphenylcarbamate of amylose bonded on allylsilica gel as the chiral stationary phase. The same chiral support has allowed the enantioseparation of racemate cis-4 on a semipreparative column (150 x 20 mm ID) with a mixture of n-hexane/2-propanol/chloroform as the mobile phase. Some 200-300 mg of the optically pure enantiomers were isolated and transformed into the N-benzyloxycarbonyl amino acids.

A silaproline-containing dipeptide.

The silaproline-containing dipeptide N-(3, 3-dimethyl-1-pivaloyl-1-aza-3-sila-5-cyclopentylcarbonyl)-L- alanine isopropylamide, C(17)H(33)N(3)O(3)Si, has two independent molecules in the asymmetric unit and each adopts a beta-II folded conformation, where the amide on the terminal C interacts intramolecularly with the pivaloyl O atom. The five-membered silaproline ring is C(beta)-puckered, an infrequent conformation for the homologous proline ring.

Piv-Propsi.

The pseudodipeptide, (S)-N-isopropyl [N-(pivaloyl)pyrrolidin-2-yl]methylaminooxyacetamide, C(15)H(29)N(3)O(3), adopts a global extended conformation with the hydroxylamine group in the g(+)/g(-) structure. The C-terminal amide NH interacts intramolecularly with the hydroxylamine O atom. Both NH bonds of each molecule are hydrogen bonded to the C-terminal amide carbonyl of a neighbouring molecule.

The position of the LysN epsilon H2-grafted antigens along the sequential oligopeptide carrier, Ac-(Aib-Lys-Aib-Gly)n (SOCn-II), influences the antibody recognition: application to the Sm main autoimmune epitope.

A sequential oligopeptide carrier of antigenic peptides is presented, incorporating two Aib residues in each repetitive moiety: Ac-(Aib-Lys-Aib-Gly)(n) (SOC(n) -II; n = 2-4). The conformational study, by (1)H-nmr, CD, and Fourier transform ir spectroscopy, indicated that the SOC(n) -II carrier displays a pronounced 3(10)-helix, compared to the Ac-(Lys-Aib-Gly)(n) (SOC(n) -I) carrier of the same approximately backbone length, previously reported. One of the dominant autoimmune epitopes of the Sm and U1RNP cellular components, the PPGMRPP sequence, was coupled to the Lys-N(epsilon)H(2) groups of the SOC(n) -II carrier and used as antigenic substrate for detecting anti-Sm/U1RNP autoantibodies in ELISA assays.

The third-dimensional structure of the complex between an Fv antibody fragment and an analogue of the main immunogenic region of the acetylcholine receptor: a combined two-dimensional NMR, homology, and molecular modeling approach.

Binding of autoantibodies to the acetylcholine receptor (AChR) plays a major role in the autoimmune disease Myasthenia gravis (MG). In this paper, we propose a structure model of a putative immunocomplex that gives rise to the reduction of functional AChR molecules during the course of MG. The model complex consists of the [G(70), Nle(76)] decapeptide analogue of the main immunogenic region (MIR), representing the major antigenic epitope of AChR, and the single chain Fv fragment of monoclonal antibody 198, a potent MG autoantibody.

Efficient access to all four stereoisomers of phenylalanine cyclopropane analogues by chiral HPLC.

Bonded polysaccharide-derived chiral stationary phases were found to be useful for the preparation of the four stereoisomers of the cyclopropane analogue of phenylalanine (c(3)Phe) as well as for the direct determination of the enantiomeric purity of c(3)Phe derivatives by HPLC. Three chiral stationary phases, consisting of cellulose and amylose derivatives chemically bonded on allylsilica gel, were tested. The mixed 10-undecenoate/3, 5-dimethylphenylcarbamate of cellulose, 10-undecenoate/3, 5-dimethylphenylcarbamate of amylose and 10-undecenoate/p-methylbenzoate of cellulose were the starting polysaccharide derivatives for CSP-1, CSP-2, and CSP-3, respectively.

Engineered glycolytic glyceraldehyde-3-phosphate dehydrogenase binds the anti conformation of NAD+ nicotinamide but does not experience A-specific hydride transfer.

Glycolytic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a NAD-dependent oxidoreductase which catalyzes the oxidative phosphorylation of d-glyceraldehyde-3-phosphate (G3P) to form 1, 3-diphosphoglycerate. The currently accepted mechanism involves an oxidoreduction step followed by a phosphorylation. GAPDH is classified as a B-specific oxidoreductase.

Solution structure of a retro-inverso peptide analogue mimicking the foot-and-mouth disease virus major antigenic site. Structural basis for its antigenic cross-reactivity with the parent peptide.

The antigenic activity of a 19-mer peptide corresponding to the major antigenic region of foot-and-mouth disease virus and its retro-enantiomeric analogue was found to be completely abolished when they were tested in a biosensor system in trifluoroethanol. This suggests that the folding pattern, which is alpha-helix in trifluoroethanol (confirmed by CD measurement), does not correspond to the biologically relevant conformation(s) recognized by antibodies. The NMR structures of both peptides were thus determined in aqueous solution.

Azaproline as a beta-turn-inducer residue opposed to proline.

Azaproline (AzPro) is an analogue of proline containing a nitrogen atom in place of the C(alpha)H group. AzPro has been introduced in various model peptides, and especially in the Boc-Ala-AzPro-Ala-NHiPr tripeptide. The structural consequence of that modification has been investigated in solution by using IR and 1H NMR, with reference to the cognate proline-containing peptide.

Anatomy of the antigenic structure of a large membrane autoantigen, the muscle-type nicotinic acetylcholine receptor.

The neuromuscular junction nicotinic acetylcholine receptor (AChR), a pentameric membrane glycoprotein, is the autoantigen involved in the autoimmune disease myasthenia gravis (MG). In animals immunized with intact AChR and in human MG, the anti-AChR antibody response is polyclonal. However, a small extracellular region of the AChR alpha-subunit, the main immunogenic region (MIR), seems to be a major target for anti-AChR antibodies.

Solution structures of the fibronectin-like Leishmania gp63 SRYD-containing sequence in the free and antibody-bound states--transferred NOE and molecular dynamics studies.

The anti-SRYD monoclonal antibody (mAbSRYD) raised against the IASRYDQL synthetic octapeptide, the 250-257 sequence of the Leishmania major surface glycoprotein gp63 recognizes both SRYD-containing peptides and the whole cognate major surface protein on intact parasites. Two SRYD-containing peptides, which antigenically and functionally mimic the RGDS sequence of fibronectin and efficiently inhibit parasite attachment to the macrophage receptors, were studied by two-dimensional transferred nuclear Overhauser effect experiments in the presence of mAbSRYD. The antibody-bound IASRYDQL octapeptide solution conformation was determined on the basis of 55 interproton-distance restraints, derived from NMR measurements.

Triphosgene: an efficient carbonylating agent for liquid and solid-phase aza-peptide synthesis. Application to the synthesis of two aza-analogues of the AChR MIR decapeptide.

The N alpha/C alphaH exchange in aza-peptides has the advantage of preserving the side chain. Bis(trichloromethyl)carbonate or triphosgene is a solid, stable phosgene substitute which retains its high reactivity. Temperature and coupling times are greatly reduced with reference to other usually recommended carbonylating agents, while purity and yield are increased.

X-ray structures of aza-proline-containing peptides.

The aza-analogue of proline (AzPro) contains a nitrogen atom in place of the CH alpha of the cognate residue. The resolution of the crystal structures of seven AzPro-containing peptides, presenting a set of ten AzPro motifs, reveals the structural properties of this particular aza-residue. Because of sterical hindrances, both nitrogen atoms are out of planarity, and the reduced electronic conjugation in the two AzPro-adjacent amide groups probably explains the longer amide bond distances and the weak proton-accepting character of the two pyrazolidine nitrogens.