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At least 307 records · Page 17Linked to original sources
PubMed1999

Conformational analysis of an alpha-galactosyl trisaccharide epitope involved in hyperacute rejection upon xenotransplantation.

alpha-Galactosyl epitopes are carbohydrate structures bearing an alpha-Gal-(1-->3)-Gal terminus (alpha-Gal epitopes). The interaction of these epitopes on the surface of animal cells with anti alpha-Gal antibodies in human serum is believed to be the main cause in antibody-mediated hyperacute rejection in xenotransplantation. In this paper, conformational analysis of an N-linked alpha-D-Galp-(1-->3)-beta-D-Galp-(1-->4)-beta-D-Glcp trisaccharide epitope was conducted in terms of each monosaccharide residue conformation, primary hydroxymethyl group configuration, and interglycosidic conformations. Selective 2D J-delta INEPT experiments have been carried out at three different temperatures to evaluate three-bond, long-range 13C-1H coupling constants for the crucial alpha-(1-->3) linkage. The NMR experimental data were complemented by theoretical calculations. The flexibility and dynamics of the trisaccharide have been studied by Metropolis Monte Carlo simulations. Ensemble-averaged three-bond, long-range 13C-1H coupling constants and nuclear Overhauser effects were in good agreement with the experimental data. The alpha-(1-->3) glycosidic linkage has shown a restricted flexibility as indicated by NMR spectroscopy and molecular modeling.

Galactose↗
PubMed1982

A conformational analysis of daunomycin considering D-ring repucker.

We present a complete molecule mechanics optimization of daunomycin. Two different D-ring puckers are found to be of comparable energy, consistent with NMR data, although only one of these low-energy structures has been observed by X-ray crystallography. Our results are more consistent with the previous conformational analysis of daunomycin by Neidle and Taylor (Neidle, S. and Taylor, G.L. (1979) FEBS Lett. 107, 348-354) than that of Nakata and Hopfinger (Nakata, Y. and Hopfinger, A.J. (1980) FEBS Lett. 117, 259-264).

Calorimetry↗
PubMed1990

Computer-aided conformational analysis based on NOESY signal intensities.

The basis for the development of a suite of programs that allow the user to determine motional features (the correlation time and the significance of segmental motion) and the optimum conditions for future experiments from a NOESY signal matrix is presented. This automated evaluation of NOESY data serves as the initial step of an iterative conformational analysis which uses the molecular model manipulation capabilities of modern graphics workstations. Incorporated in these programs is NOESYSIM, a calculation subroutine which uses a set of molecular coordinates (and a correlation time estimate) together with user entered experimental parameters (acquisition time, sweep width, mixing time and cycle repetition time) to generate an accurately calculated NOESY signal matrix reflecting those conditions and the specified conformational model. Conformational refinement then consists of iterative comparisons of the experimental signal matrix with a series (or systematically sampled set) of model coordinates corresponding to a dynamics' course, driven-minimization or torsional grid search. These procedures and developments are illustrated with examples including: solution conformations of prostanoids; studies of the folding preferences and media-dependent changes in conformation for peptide hormones; and the structure elucidation of a novel undecapeptide macrolide antibiotic (lysobactin). For larger molecules, even constrained grid searches have too high a dimensionality and one must resort to distance-constraint based minimizations. A novel procedure for deriving more accurate distance constraints (corrected for secondary NOEs) is detailed and a new strategy for conformation elucidation, based on this procedure, is outlined.

Amino Acid Sequence↗
PubMed1987

Conformational analysis of gramicidin-gramicidin interactions at the air/water interface suggests that gramicidin aggregates into tube-like structures similar as found in the gramicidin-induced hexagonal HII phase.

The energetics of interaction and the type of aggregate structure in lateral assemblies of up to five gramicidin molecules in the beta 6.3 helical conformation at the air/water interface was calculated using conformational analysis procedures. It was found that within the aggregate two types of gramicidin interaction occur. One leading to a linear organization with a mean interaction energy between monomers of -6 kcal/mol and one in a perpendicular direction leading to a circularly organization with a lower mean interaction energy of -10 kcal/mol. Extrapolation towards larger gramicidin assemblies predicts that gramicidin itself could form tubular structures similar to those found in the gramicidin-induced HII phase. The tryptophans appear to play an essential role in the tubular organization of the gramicidin aggregate, since they determine the cone shape of the monomer and contribute to the structure of the monomer and oligomer by stacking interactions. These results, which are discussed in the light of experimental observations of gramicidin self-association in model membranes and the importance of the tryptophans for HII phase formation, further support the view (Killian, J.A. and De Kruijff, B. (1986) Chem. Phys. Lipids 40, 259-284) that gramicidin is a first example of a new class of hydrophobic polypeptides which can form cylindrical structures within the hydrophobic core of the membrane.

Gramicidin↗
PubMed1985

Delineation and conformational analysis of two synthetic peptide models of antigenic sites on rodent cytochrome c.

Two regions of rodent cytochrome c, one within the first four residues of the molecule, which is N-acetylated, and one at a beta bend around residue 44, are known to be immunogenic and antigenic in rabbits. Using sequential peptide synthesis, we have determined the residues required for linear synthetic peptides within these sequences to bind to antibody raised in rabbits to intact rat cytochrome c. The residues that were important in binding the N-terminal peptides were N-acetylglycine at position 1 and valine at position 3. The smallest peptide sequence around residue 44 that would bind to antibodies was Gln-Ala-Ala-Gly-Phe. A theoretical conformational analysis of these peptides showed that the amino-terminal tetrapeptide adopts a wide statistical ensemble of conformational states and that the addition of residues beyond 41 and 45 in the other sequence does not appear to stabilize longer peptides in the native beta-bend conformation. Thus, the antigenicity conferred by Phe-46 and Gln-42 in this peptide is most likely due to the direct interaction of the side chains of these residues with the antibody binding site. The demonstration here that native conformation is not essential for antigenic peptides to bind to antibodies raised against the whole protein indicates that the association energy between antigen and antibody can be sufficient to induce conformation in conformationally flexible peptides. This supports the concept that anti-protein and anti-peptide antibodies may invoke conformational changes in cross-reactive protein antigens and may explain why longer peptides, which may adopt stable nonnative secondary structure, often do not bind to antibodies raised to the whole molecule.

Amino Acid Sequence↗
PubMed1996

Comparative conformational analysis of CCK-B agonist Boc-Trp-Phg-Asp-(1-Nal)-NH2 and CCK1-B antagonist Boc-Trp-Phg-Asp-(1-Nal)-N(Me)2 using 1HNMR spectroscopy and restrained molecular dynamics.

The tetrapeptide Boc-Trp-Phg-Asp-(1-Nal)-NH2 is a potent CCK-B agonist. Interestingly, bis-methylation of the C-terminal carboxamide group of this compound leads to Boc-Trp-Phg-Asp-(1-Nal)-N(Me)2 which behaves as a CCK-B antagonist in electrophysiological studies on hippocampal neurones (Corringer et al., 1993). In order to ascertain whether bismethylation of the terminal carboxamide group has an influence on the conformational preferences of the peptide, we have undertaken a comparative conformational analysis of the two tetrapeptides by the combined use of 2D NMR spectroscopy and restrained molecular dynamics. The solution conformation of the two peptides were examined by 1H NMR in a d6-DMSO/H2O (80:20) mixture. 1H-1H distance constraints, derived from 2D NOESY and ROESY experiments, were used as inputs for subsequent restrained molecular dynamics simulations. Comparison of the NMR and molecular modeling data indicates different conformational preferences for these two peptides. Interestingly, the aromatic side chains of the CCK-B antagonist Boc-Trp-Phg-Asp-(1-Nal)-N(Me)2 in its preferential conformation, overlap their corresponding moieties in the two non peptide CCK-B antagonists L-362,260 and LY-288,513. The differences in conformational behaviour of the studied tetrapeptides could, at least in part, account for their opposite agonist/antagonist profile, a findings which could serve for the design of new conformationally restricted CCK-B analogs.

Amino Acid Sequence↗
PubMed2006

Reference strand conformational analysis (RSCA) is a valuable tool in identifying MHC-DRB sequences in three species of Aotus monkeys.

The Aotus monkey has been of great value in the pre-clinical study of malaria vaccine candidates. Several components of this primate's immune system have been studied and they display great similarity to their human counterparts. Cloning and sequencing studies have revealed extensive sequence polymorphisms in Aotus MHC-DRB with very high similarities to several human allelic lineages, grouping at least nine distinct MHC-DRB lineages. As the efficacy of peptide vaccines in this animal model may be strongly influenced by exon 2 MHC-DRB polymorphism, the availability of a reliable and rapid MHC-DRB typing method for three species of Aotus (Aotus nancymaae, Aotus vociferans and Aotus nigriceps) is necessary. Reference strand conformational analysis (RSCA) was used here for differentiating the distinctive Aotus MHC-DRB sequences' mobility using five fluorescently labelled references proved to be very useful for resolving closely related sequences, establishing the number of sequences transcribed in a particular monkey and their identity. The RSCA method's reliability in terms of identifying Aotus MHC-DRB sequences will facilitate evaluating individual responsiveness to vaccines and prompt studies associating susceptibility/resistance to infectious agents or auto-immune disease, for which Aotus monkeys may be considered to be an appropriate animal model.

Amino Acid Sequence↗
PubMed2003

Introduction of 4(S)-oxazolidineacetic acid, 2-oxo (D-Oxac) motif in a polypeptide chain: synthesis and conformational analysis.

A four step synthesis of 4(S)-oxazolidineacetic acid, 2-oxo benzyl ester (D-Oxac-OBn) from L-Asp-OH in 45% overall yield is reported. The formation of by-products is completely avoided, by microwave irradiation and by the use of caesium carbonate as base. Moreover the synthesis and IR and 1H NMR conformational analysis of the tetramers Boc-L-Val-D-Oxac-L-Ala-OBn and Boc-L-Val-D-Oxac-Aib-L-Ala-OBn in solution is reported.

Amino Acid Sequence↗
PubMed1998

5-Substituted pyrimidines with a 1,5-anhydro-2, 3-dideoxy-D-arabino-hexitol moiety at N-1: synthesis, antiviral activity, conformational analysis, and interaction with viral thymidine kinase.

A new series of anhydrohexitol nucleosides are described. These compounds have a pyrimidine base moiety substituted in the 5-position with a chloro (1b), trifluoromethyl (1c), vinyl (1d), 2-thienyl (1e), ethynyl (1f) or propynyl (1g) substituent. The vinyl, propynyl, and, in particular, the 5-trifluoromethyl analogue showed potent activity against herpes simplex virus (HSV), 1c with a selectivity index of >16000 against HSV-1 and >1000 against HSV-2. Conformational analysis of anhydrohexitol nucleosides using computational methods indicates that these nucleosides occur in an equilibrium between the C1 and 1C form with a DeltaE of 5.9 kJ/mol. When the anhydrohexitol nucleoside is cocrystallized with the HSV-1 thymidine kinase it adopts a 1C conformation, which is opposite to the conformation found for the small molecule alone. The enzyme, apparently, induces a conformational change, and conformational flexibility of an anhydrohexitol nucleoside may be advantageous for recognition by viral enzymes.

Antiviral Agents↗
PubMed2000

Conformational analysis of 7-oxoacyl-L-alanyl-D-isoglutamines.

In a recent article (Planinsek, O., Srcic, S., 1999. Int. J. Pharm. 87, 199-207) some interesting physicochemical properties of a series N-(7-oxoacyl)-L-alanyl-D-isoglutamines with n=0-6 methylene groups between the terminal methyl and 7-oxo group were measured. In view of the practical importance of these N-acetylmuramyldipeptide(MDP) immunomodulator analogues and their interesting biological properties a detailed conformational analysis was undertaken for the series with n=3-6 methylene spacers between the 7-oxo and terminal methyl groups. The puzzle posed by the reversal of the measured water solubility and lipophylicity could be resolved by using the Monte Carlo approach to searching the conformational space of the molecules in this series. We have found that the increase in water solubility and drop in lipophylicity when the number of methylene groups is increased from 5 to 6 can be attributed to the change in predominant conformation in the conformational family as described by the Boltzmann distribution of conformations. Notwithstanding this, we point out the changes in biological response coupled to the nonlinearity of the physicochemical behaviour in the series.

Adjuvants, Immunologic↗
PubMed1993

QSAR and conformational analysis of the antiinflammatory agent amfenac and analogues.

The new nonsteroidal antiinflammatory drug (NSAID) arylacetic amfenac (2-amino-3-benzoylphenylacetic acid) and 19 substituted derivatives were studied in order to correlate the biological activities with the structure-related parameters. The geometry of amfenac in neutral and anionic form was totally optimized, starting from standard geometries and crystallographic data, using semiempirical AM1 and MNDO quantum-mechanical methods. Conformational analysis shows the existence of a rigid structure for rotations of the acetic acid chain (alpha degrees) and the central carbonyl group (gamma degrees) around the bonds with the phenylamine ring, whereas the carboxyl group (beta degrees) and the phenyl ring of the benzoyl group (delta degrees) can rotate almost freely. Electrostatic potential maps were analyzed and showed that the electrostatic orientation effect seems to make an important contribution to the binding of the active compounds to prostaglandin synthase. An electrostatic orientation model of the binding site is proposed. The frontier orbital charge distribution was also described for each compound. On the other hand, steric, electronic and hydrophobic (log P) parameters were calculated and QSAR analysis showed that the most significant parameter for the antiinflammatory activity was the pi-electron density of the HOMO orbital in the second aromatic ring. These results suggest a possible electronic charge transfer between the aromatic fragments and the receptor.

Anti-Inflammatory Agents, Non-Steroidal↗
PubMed2002

Frequency of HLA-DPB1 disparities detected by reference strand-mediated conformation analysis in HLA-A, -B, and -DRB1 matched siblings.

The role of HLA-DPB1 as transplantation antigen is controversial. The frequency and relevance of HLA-DPB1 mismatch in hematopoietic stem cell transplantation are unknown. To ascertain the rate of HLA-DBP1 mismatch in siblings that had been matched for HLA-A, -B, and -DRB1, reference strand mediated conformation analysis (RSCA) a high resolution HLA typing method was used. Locus-specific primers were used to amplify the HLA-DPB1 locus. The PCR product was then hybridized with two fluorescein-labeled references and the duplexes were analyzed after electrophoresis in a short polyacrylamide gel. Among the 113 pairs of individuals tested, six HLA-DPB1 mismatches were identified, which corresponds to a frequency of 5.31 % (95% confidence interval 3.20%-7.42 %).

Electrophoresis, Polyacrylamide Gel↗
PubMed1984

Synthesis, conformational analysis, and antiarrhythmic properties of 7-benzyl-3-thia-7-azabicyclo[3.3.1]nonan-9-one, 7-benzyl-3-thia-7-azabicyclo[3.3.1]nonane hydroperchlorate, and 7-benzyl-9-phenyl-3-thia-7-azabicyclo[3.3.1]nonan-9-ol hydroperchlorate and derivatives: single-crystal X-ray diffraction analysis and evidence for chair-chair and chair-boat conformers in the solid state.

The synthesis of the title ketone has been completed via a type of Mannich reaction starting from 4- thianone . An X-ray diffraction analysis has revealed that the solid system is a chair-boat conformer with the sulfur atom in the boat portion of the bicyclic ring compound. Wolff- Kishner reduction of the ketone group gave 7-benzyl-3-thia-7-azabicyclo [3.3.1]nonane, which was isolated as the hydroperchlorate . However, X-ray diffraction analysis of the salt showed this solid to be a chair-chair conformer. Addition of phenylmagnesium bromide to the ketone gave a tertiary alcohol with the C-C6H5 bond being equatorial with respect to the thiane ring and axial with respect to the piperidine ring. The reaction of the Grignard reagent with the ketone to give this alcohol seems to be very stereospecific. An X-ray analysis of the hydroperchlorate of the alcohol confirmed the system to be a chair-chair form in the solid. The title compounds were screened for antiarrhythmic activity in anesthetized mongrel dogs in which myocardial infarctions had been created when the left anterior descending coronary artery was ligated. Vagal-induced slowing of the sinus mode firing rate was used to determine the underlying ventricular automaticity in the dogs, which averaged 164 +/- 27 beats/min. Ventricular pacing was initiated to rates between 240 and 390/min. This technique resulted in the induction of rapid and sustained ventricular tachycardia. At doses of 3 and 6 mg/kg of body weight, 7-benzyl-3-thia-7-azabicyclo [3.3.1]nonane hydroperchlorate in alcohol (the solution was administered intravenously) was able to suppress markedly the induced ventricular tachycardia in five of six dogs. The compound also caused a 10-15% increase in blood pressure within a few minutes. The antiarrhythmic properties of this compound and others of related structure are discussed, and some comparison is made with the action of lidocaine in similar dog preparations.

Animals↗
PubMed2000

HLA-B44 subtyping in the Catalan population using reference strand mediated conformation analysis. Implications for the selection of unrelated bone marrow donors.

Cytotoxic T lymphocytes (CTLs) reactive against the disparity between HLA-B*4402 and HLA-B*4403 have been reported after unrelated donor bone marrow transplantation. These CTLs have been associated with acute graft-versus-host disease and graft rejection. This study describes the HLA-B44-subtyping in the Catalan population using reference-strand mediated conformation analysis. It has been performed on 297 unrelated HLA-B44+ cord blood units from the Barcelona Cord Blood Bank (Barcelona, Spain). We have found a predominance of HLA-B*4403 (66.04%) over HLA-B*4402 (33.02%), whereas the predominant HLA-B44 allele in Northern Europe and the United States is HLA-B*4402. This inverted proportion between HLA-B44 subtypes in Mediterranean populations compared with other Caucasian populations suggests that HLA-B44 subtyping should be performed when an HLA-B44+ unrelated donor marrow is identified.

Alleles↗
PubMed1998

Solution conformational analysis of amphiphilic helical, synthetic analogs of the lipopeptaibol trichogin GA IV.

The step-by-step synthesis by solution methods of the [Ser2,5,6,9, Leu-OMe11] analog of trichogin GA IV is described. The four Ser residues have been incorporated into the sequence as replacements of the naturally occurring Gly residues to increase the amphiphilicity of the 3D-structure of the lipopeptaibol. A detailed solution conformational analysis has been performed on this undecapeptide and its prototypical [Leu-OMe11] trichogin GA IV analog using FTIR absorption and CD spectroscopies, and two-dimensional NMR under a variety of experimental conditions, including a membrane-mimetic environment. Both peptides adopt a mixed 3(10)/alpha-helical structure, which in the micellar system was found to be less flexible for the Ser-containing analog. For both analogs permeability measurements revealed membrane-modifying properties comparable to those of the natural lipopeptaibol.

Anti-Bacterial Agents↗
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↗
PubMed2004

Synthesis and conformational analysis of novel N(OCH3)-linked disaccharide analogues.

N(OMe)-linked disaccharide analogues, isosteric to the corresponding natural disaccharides, have been synthesized by chemoselective assembly of unprotected natural monosaccharides with methyl 6-deoxy-6-methoxyamino-alpha-D-glucopyranoside in an aqueous environment. The coupling reactions were found to be chemo- and stereoselective affording beta-(1-->6) disaccharide mimics when using Glc and GlcNAc; in the case of Gal, the beta-anomer was prevalent (beta:alpha=7:1). An iterative method for the synthesis of linear N(OMe) oligosaccharide analogues was demonstrated, based on the use of an unprotected monosaccharide building block in which an oxime functionality at C-6 is converted during the synthesis into the corresponding methoxyamino group. The conformational analysis of these compounds was carried out by using NMR spectroscopy, ab initio, molecular mechanics, and molecular dynamics methods. Optimized geometries and energies of fourteen conformers for each compound have been calculated at the B3LYP/6-31G* level. Predicted conformational equilibria were compared with the results based on NMR experiments and good agreement was found. It appears that N(OMe)-linked disaccharide analogues exhibit a slightly different conformational behavior to their parent natural disaccharides.

Carbohydrate Conformation↗
PubMed1986

[Experimental and theoretical conformation analysis of the O-antigenic polysaccharide from Pseudomonas cepacia strain 3181. I. Disaccharide links].

Nuclear Overhauser effects, with preirradiation of glycoside bond anomeric protons, coupling constants 3J C3, H1' and 3J C1', H4 and linkage optical rotations A were measured for L-Rha beta 1-3-L-Rha alpha 1-OMe and L-Rha alpha 1-3-L-Rha alpha 1-OMe which are the models of the disaccharide units of the Pseudomonas cepacia polysaccharide. Theoretical conformational analysis was carried out in terms of a mechanical molecular model approximation. The spatial structures of these disaccharides as well as of D-Rha alpha 1-2-D-Rha beta 1-OMe in aqueous solutions were discussed basing on the obtained results.

Antigens, Bacterial↗