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PubMedDate not supplied

Genotypic characterization of an MHC class II locus in lake trout ( Salvelinus namaycush) from Lake Superior by single-stranded conformational polymorphism analysis and reference strand-mediated conformational analysis.

This study compares the genotypic information provided by reference strand-mediated conformational analysis and single-stranded confirmational polymorphism (SSCP) analysis for the major histocompatibility complex (MHC) II locus in lake trout. For this study 80 wild-caught animals from the Apostle Islands of Lake Superior were genotyped using both RSCA and SSCP analysis. Their genotypes were recorded using both methods and compared. The genotypic information provided by the 2 methods was essentially the same although some inconsistencies were observed. Both methods detected approximately 65 genotypes, and both were able to distinguish heterozygous and homozygous animals. The analyses determined that only approximately 20% of alleles were shared between 2 morphologically different populations within the sample set, and identified the dominant alleles. SSCP analysis was quicker, simple, and more robust than RSCA. SSCP analysis using fluorescence technologies could be the method of choice for future genotypic analysis of the MHC II locus in salmonids.

Animals↗
PubMed1991

Computational analysis of conformational behavior of cholecystokinin fragments. I-CCK4, CCK5, CCK6 and CCK7 molecules.

A conformational analysis has been performed on several peptide fragments (CCK4 to CCK7) of the cholecystokinin neuromodulator. The Monte-Carlo Metropolis method was used to explore the conformational space of all these flexible units and different electric charge distributions were introduced in order to mimic pH effects. Results agree reasonably well with experimental data from NMR and fluorescence experiments. The CCK4 fragment displays a peculiar conformational behavior when compared to all other longer peptides with short range interaction between the Trp and Phe aromatic side-chains. Several H-bonded conformers including C- or beta-turns are found for CCK5 to CCK7. These findings are correlated to the central and peripheral actions of these compounds and hypotheses concerning the best possible templates for each one are discussed.

Amino Acid Sequence↗
PubMed1992

Analysis of conformationally restricted models for the (1----6)-branch of asparagine-linked oligosaccharides by n.m.r.-spectroscopy and HSEA calculation.

The conformational preferences of the trisaccharide, beta-D-GlcpNAc-(1----2)-alpha-D-Manp-(1----6)-beta-D-GlcpOR (1) have been investigated by n.m.r.-spectroscopy and HSEA calculation. The fixed omega-angle bicyclic analogs 2 and 3, models for the gt and gg rotamers, respectively, of 1, were furthermore examined with the same techniques in an attempt to deduce which of the conformations accessible to 1 was recognized and glycosylated by the enzyme GlcNAc-transferase-V, which acts on a component of the (1----6)-arm of glycoproteins. Only the gg bicyclic 3 was found to be reactive with the enzyme and this study concludes, based on conformational analysis, that 1 as well as the natural Asn-linked oligosaccharide are recognized by GlcNAc-transferase-V in only one of the two local minimum energy conformations energetically accessible to these molecules in their gg rotamer.

Asparagine↗
PubMed1987

Analysis of conformational parameters in nucleic acid fragments. I. Single crystals of nucleosides and nucleotides.

A study has been undertaken of conformational parameters in single crystal structures of nucleosides and nucleotides using the techniques of helical conformational analysis. A "quasi-helix" was generated from the geometry of base-paired structures, using published data extracted from the Cambridge structural database. A total of 54 base-pairs were found in these structures, for each of which were calculated hydrogen bond parameters, propeller twist, buckle and C1'-C1' separations. These were analysed according to various classifications. Propeller twists are found to show a wide range of values and the magnitude of twist appears to be unrelated to hydrogen bond parameters or C1'-C1' separation. The values of the buckle parameter vary over a smaller range of values and are unrelated to propeller twist magnitude. There is found to be a greater tendency to form homo-base-pairs among compounds containing adenine bases.

Base Composition↗
PubMedDate not supplied

Comparison of conformation-sensitive gel electrophoresis and single-strand conformation polymorphism analysis for detection of mutations in the BRCA1 gene using optimized conformation analysis protocols.

In order to develop a selective mutation screening strategy for BRCA1, one of the gene responsible for hereditary predisposition to breast cancer, we analysed by single-strand conformation polymorphism (SSCP) and conformation-sensitive gel electrophoresis (CSGE) a cohort of 20 Bulgarian breast cancer patients, prescreened for nonsense mutations by the protein truncation test. By assaying the complete coding sequence of the gene applying both methods, we were able to detect 12 sequence alterations: 11 nucleotide substitutions and one deletion. Two of the alterations are intronic polymorphisms, the rest are exon sequence variants. Of the 12 polymorphisms identified, 11 are described and one is new. All sequence changes were detected by CSGE and eight of them were also shown by SSCP analysis. There was no sequence alterations which could be detected by SSCP analysis only. We propose that because of the specificity of most sequence variants detected (nucleotide substitutions) and the comparatively high percentage of AT content of the BRCA1 gene (58.4%), CSGE turned out to be the more sensitive technique in our assay. This observation is in agreement with other accepted analysis strategies for BRCA1 and it may prove useful for mutation screening of AT-rich, multi-exon genes.

Adult↗
PubMed1994

Absolute configuration and biological activity of mequitamium iodide enantiomers.

The enantiomers of 1-methyl-3-(10H-phenothiazine-10-ylmethyl)-1-azoniabicyclo[2 ,2,2]octane iodide (1) were prepared by chiral chromatographic resolution of the precursor mequitazine (2). The (+)-(S)-enantiomer 1b is 10-fold more potent than (-)-(R)-enantiomer 1a as a histamine antagonist, while the two enantiomers show the same antimuscarinic activity in vitro. The absolute configuration of the more active dextrorotatory isomer has been determined by X-ray analysis. Conformational analysis and molecular modeling suggest that the (+)-(S)-enantiomer can adopt a conformation similar to that attributed to the receptor binding conformers of classical antihistamines.

Acetylcholine↗
PubMed1998

Molecular mechanics studies on the conformations of 2',3'-dideoxy-2',3'-didehydroguanine nucleoside, D4G.

Conformational energy calculations have been presented on guanine nucleoside in which the furanose ring is replaced by 2',3'-dideoxy-2',3'-didehydrofuran using molecular mechanics and conformational analysis. Conformational energies have been evaluated using the MM2 and AMBER94 force field parameters at two different dielectric constants. The results are presented in terms of isoenergy contours in the conformational space of the glycosidic (chi) and C4'-C5' (gamma) bonds torsions. In general, the chi-gamma interrelationships differ from the corresponding plots for unmodified nucleosides and nucleotides, reported previously. Consistency of the calculated preferred conformations with the x-ray data is sensitive to the force field employed.

Calorimetry↗
PubMed1989

Designing molecules: specific peptides for specific receptors.

Peptides are the largest class of mediators of intercellular communication in the central nervous system. These molecules pose special problems in design for potential medical applications because of the high degree of flexibility, lack of high receptor selectivity, and ready biodegradation or clearance. The global and local use of conformational constraints has overcome these difficulties. Structure-biological activity relationships, molecular modeling, conformational analysis, conformational calculations, and molecular dynamics simulations can all be used to derive suitable lead structures and conformational models. Often, a single, constrained peptide analogue can be designed, which will have many of the desired biological and biophysical properties, and will serve as a template. Peptide analogues with high potency, exquisite receptor selectivity, and biological stability can be obtained. The approach is illustrated by the design of cyclic enkephalin-agonist analogues with exceptional delta-opioid-receptor selectivity, and of constrained somatostatin analogues that have become opioid peptides and possess potent opioid antagonist activities and exceptional selectivity for mu-opioid receptors.

Chemical Phenomena↗
PubMed1999

Role of proximal His93 in nitric oxide binding to metmyoglobin. Application of continuum solvation in Monte Carlo protein simulations.

Monte Carlo protein simulations with continuum solvation were used to explore the conformational mobility of NO within the active site of metmyoglobin. To the best of our knowledge this is the first application of a continuum solvation model for exploring protein binding sites. The usefulness of the Monte Carlo conformational analysis was demonstrated in comparative molecular dynamics simulations. Analysis of conformer populations revealed that Monte Carlo conformational analysis is more effective in mapping the relevant region of the potential surface. Distribution of low-energy conformers obtained for the metmyoglobin-NO complex was found to depend on the orientation of proximal His93. Different charge distributions corresponding to the two experimentally verified possible torsions of this proximal residue result in strong binding of NO or its release to a nearby hydrophobic trap. Conformer populations obtained by Monte Carlo conformational analysis were grouped into three main families: one, with the NO directly bound to the iron, appears when the CA-CB-CG-CD2 torsion of His93 is at its ligand binding value (-113 degrees); and two conformers exist where NO is trapped in a nearby hydrophobic pocket, the same cavity that was determined to be the geminate trap of CO in ferrous Mb as a result of the torsional flip of His93 to its ligand releasing state (-125 degrees). Based on this analysis, we suggest that the electrostatic rearrangement coupled to the conformational fluctuation of the proximal His leads to the geminate trapping of the ligand. Conformational rearrangement of the proximal side would provide the possibility of rebinding of the ligand to Fe.

Animals↗
PubMed1997

Comparative Analysis of the Conformations of Symmetrically and Asymmetrically Deca- and Undecasubstituted Porphyrins Bearing Meso-Alkyl or -Aryl Groups.

Conformational analysis of highly substituted porphyrins has potential implications for modeling the behavior of macrocycles in tetrapyrrole-containing protein complexes and during catalytic reactions. In order to study the influence of different substituent patterns on the conformation of the porphyrin macrocycle, a series of metal free and nickel(II) decasubstituted porphyrins bearing aryl or ethyl groups at opposite meso positions and alkyl groups at the pyrrole positions have been synthesized and characterized by X-ray crystallography. Crystal structures of the free-base porphyrins with 5,15-diaryl substituents showed negligible out-of-plane distortion but a large amount of in-plane distortion along the 5,15-axis accompanied by large bond angle changes similar to those previously seen for related porphyrins with 5,15-dialkyl substituents. Nickel(II) complexes of the 5,15-diaryl-substituted porphyrins show planar or modestly nonplanar conformations, suggesting that these complexes are not intrinsically nonplanar, whereas a complex with 5,15-diethyl substituents has a very ruffled conformation similar to those observed for related complexes with other metals. The nickel(II) complexes are also elongated along the 5,15-axis in a qualitatively similar but less dramatic fashion than are the free-base porphyrins. Spectrosopic studies ((1)H NMR, optical, and resonance Raman spectroscopy) suggest that conformations similar to those determined by X-ray crystallography are present in solution for the 5,15-dialkyl- and 5,15-diaryl-substituted porphyrins. Several asymmetric nickel(II) and metal-free deca- and undecasubstituted porphyrins containing both aryl and alkyl meso-substituents were also investigated. Metal-free 5,15-disubstituted porphyrins with one aryl and one alkyl group showed considerably elongated porphyrin cores, whereas nickel(II) complexes of porphyrins with 5,10- or 5,10,15-substitution patterns showed very nonplanar structures consisting mainly of ruffle and saddle type distortions.

Journal Article↗
PubMed2005

Synthesis of 26,27-bisnorcastasterone analogs and analysis of conformation-activity relationship for brassinolide-like activity.

Three castasterone (CS) derivatives with varied side-chain moieties, 26,27-bisnorcastasterone (20S-bisnorCS), 20-epi-26,27-bisnorcastasterone (20R-bisnorCS), and 21,26,27-trisnorcastasterone (trisnorCS), were synthesized stereoselectively from either stigmasterol or dehydroisoandrosterone. The 50% effective doses (ED50, nmol/plant) in the concentration-response curve for brassinolide-like activity in the rice lamina inclination assay were determined to be 0.020 nmol (pED50 = 10.7) for 20S-bisnorCS, 3.2 nmol (pED50 = 8.5) for 20R-bisnorCS, and 2.0 nmol (pED50 = 8.7) for trisnorCS. An analog containing an ester linkage between the steroid and the side-chain moiety of 20S-bisnorCS was also synthesized and its activity was evaluated to be 3.2 nmol (pED50 = 8.5), being equipotent to 20R-bisnorCS and trisnorCS. The activity of 20S-bisnorCS was 1/40 that of CS. The conformation analysis was conducted using a systematic search, showing that the activity decreases with an increase in the degree of freedom of the side chain of the steroidal skeleton.

Brassinosteroids↗
PubMed1995

A reinvestigation towards the conformation of methyl alpha-D-mannopyranosyl-(1-->6)-alpha-D-mannopyranoside by a combined ROE and molecular dynamics analysis.

Conformational analysis of alpha-D-Man p-(1-->6)-alpha-D-Man p1-OMe, by a combination of extensive molecular dynamics calculations in water and ROE buildup series, afforded two main minima, namely, phi/psi = 95/-178 and phi/psi = 140/-185. Transitions between these minima are observed, which have not previously been demonstrated using other approaches. In contrast to literature data for the glycosidic linkage, describing equal populations of both the gg and the gt rotamers, it was found that the gg conformer is present to ca. 96%. The non-reducing mannosyl unit showed approximately a 1:1 ratio for the gg:gt equilibrium, in accordance with earlier reports.

Carbohydrate Conformation↗