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At least 199 records · Page 11Linked to original sources
PubMed2002

Synthesis and conformational analysis of a pentasaccharide corresponding to the cell-wall polysaccharide of the Group A Streptococcus.

The synthesis and conformational analysis of a pentasaccharide corresponding to a fragment of the cell-wall polysaccharide (CWPS) of the bacteria Streptococcus Group A are described. The polysaccharide consists of alternating alpha-(1 --> 2)- and alpha-(1 --> 3)-linked L-rhamnopyranose (Rhap) residues with branching 2-acetamido-2-deoxy-D-glucopyranose (GlcpNAc) residues linked beta-(1 --> 3) to alternate rhamnose rings. The pentasaccharide is of interest as a possible terminal unit on the CWPS, for use in a vaccine. The syntheses employed a trichloroacetimidate glycosyl donor. Molecular dynamics (MD) calculations of the pentasaccharide with the force fields CVFF and PARM22, both in gas phase and with explicit water present, gave different predictions for the flexibility and preferred conformational space. Metropolis Monte Carlo (MMC) calculations with the HSEA force field were also performed. Experimental data were obtained from 1D transient NOE measurements. Complete build-up curves were compared to those obtained by full relaxation matrix calculations in order to derive a model of the conformation. Overall, the best fit between experimental and calculated data was obtained with MMC simulations using the HSEA force field. Molecular dynamics and MMC simulations of a tetrasaccharide corresponding to the Group A-variant polysaccharide, which differs in structure from Group A in lacking the GlcpNAc residues, were also performed for purposes of comparison.

Bacterial Vaccines↗
PubMedDate not supplied

[Conformational analysis of cysteine-containing peptides and prospects of their application to 213Bi chelating in antitumor therapy].

The method of conformational analysis was applied to the spatial structures of peptide analogues of phytochelatins and some fragments of metallothioneins: (Cys-Gly)3, (Cys-Gly)3Asp, (Cys-Gly)3Glu, (Cys-betaAla)3, (Cys-gammaGlu)3, and (Cys-Gly-Gly)3. All the possible low-energy conformations of the molecules were revealed and the role of intra- and inter-residual interactions in the formation of their spatial structures was determined. A different tendency of the molecules under study for acceptance of conformations favorable for binding bismuth ions was shown. Low-energy structures providing an optimum binding of bismuth ion were shown to be most frequent for (Cys-betaAla)3 peptide. Among the analogues of peptide fragments of the metallothioneins, lacking in natural peptides, low-energy pentapeptide CCXXC fragments (where X = Gln, Asn, Phe, Tyr, and Gly) were revealed. In the alpha-helical conformations of these pentapeptides, the distance between the sulfur atoms corresponds to that in Bi2S3. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2006, vol. 32, no. 3; see also http://www.maik.ru.

Animals↗
PubMed2002

Highly potent inhibitors of TNF-alpha production. Part II: metabolic stabilization of a newly found chemical lead and conformational analysis of an active diastereoisomer.

Design and synthesis of metabolically stabilized inhibitors of TNF-alpha production, which could be new drug candidates, are reported. Conformational analysis of an active diastereoisomer was performed based on biological evaluations of the conformationally fixed indane derivatives 17 and 18. Structure-activity relationships (SARs) based on biological evaluations of the optically active derivatives are also discussed. Full details including chemistry are reported.

Animals↗
PubMed1986

[Experimental and theoretical conformation analysis of the O-antigenic polysaccharide from Pseudomonas cepacia strain 3181. II. The polysaccharide].

The spatial structure of Pseudomonas cepacia 3181 polysaccharide in aqueous solution is discussed basing on the data of nuclear Overhauser effect, observed with preirradiation of anomeric protons of all 3 D-rhamnose residues in the repeat unit, and theoretical conformational analysis. It is shown that conformational states of the free disaccharides and corresponding disaccharide units of the polysaccharide are similar. All conformations of the polysaccharide may be described by one shape representing an extended structure with characteristic turns in the D-Rha alpha 1-2-D-Rha beta 1-3-D-Rha units.

Antigens, Bacterial↗
PubMed1987

Conformational analysis of 2-aminoindans and 2-(aminomethyl)indans in relation to their central dopaminergic effects and a dynamic dopamine receptor concept.

Conformational analyses on differently substituted 2-aminoindans of significant pharmacological interest were carried out by the molecular mechanics method (MM2). An X-ray structure of (R)-4-methoxy-2-aminoindan has shown the ammonium nitrogen [-)-D-tartaric acid salt) in an axial position. From comparison with other, highly potent, centrally acting dopamine (DA) receptor agonists, it can be predicted that the active enantiomer (R)-4-hydroxy-2-(di-n-propylamino)indan should have its nitrogen atom in an equatorial position. This places it close to the aromatic ring plane, which is one of several prerequisites for potent DA receptor agonism. MM2 correctly calculates (R)-4-methoxy-2-aminoindan and (R)-4-hydroxy-2-(dialkylamino)indan to be more stable in the N-axial and N-equatorial conformations, respectively. Conformational analysis of the dimethyl model compound of the moderately potent dopaminergic phenylpropylamine analogue 4-hydroxy-2-[(di-n-propylamino)methyl]indan was also carried out, in order to see if any conformations of this compound satisfy the requirements for dopaminergic agonism. Two such stable conformations were found.

Brain↗
PubMed1990

Conformational analysis and structure-activity relationships of selective dopamine D-1 receptor agonists and antagonists of the benzazepine series.

Comprehensive conformational analysis using molecular mechanics calculations (MM2(85)) has been carried out for the potent and selective dopamine D-1 receptor agonist 7,8-dihydroxy-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine (1; SK&F 38393), the antagonist 7-chloro-8-hydroxy-3-methyl-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine (8; SCH 23390), and several analogues, including conformationally constrained ones. Calculated conformational energies have been related to pharmacological and biochemical data in an attempt to identify the biologically active conformations of 1 and 8. It is concluded that the most probable receptor-bound conformation in both cases is a chair conformation with an equatorial phenyl ring and for 8 an equatorial N-methyl group. It is suggested that the orientation of the phenyl ring in the receptor-bound molecule does not deviate in terms of dihedral angles by more than about 30 degrees from the preferred phenyl group rotamer in which the planes of two aromatic rings are essentially orthogonal.

2,3,4,5-Tetrahydro-7,8-dihydroxy-1-phenyl-1H-3-ben↗
PubMedDate not supplied

[Conformational analysis of anti-arrhythmia agents of the lidocaine series and a model for the mechanism of their action].

After conformation analysis of a number of lidocaine-like antiarrhythmic molecules a simple model of their mode of action is suggested. It is proposed that the hydrophobic antiarrhythmic molecules after their absorption on cytoplasmic membranes concentrate due to polar interactions close to ionic channel proteins, then bind to these proteins and allosterically influence the process of ionic conductance.

Allosteric Regulation↗
PubMed1994

A possible missense mutation detected in the dystrophin gene by Double-Strand Conformation Analysis (DSCA).

A new and simple method for detecting point mutations is presented. The method, based on Double-Strand Conformation Analysis (DSCA) of PCR amplification products in polyacrylamide gel electrophoresis, was applied to 78 unrelated subjects affected with Duchenne or Becker muscular dystrophy and to 9 subjects suspected to be affected with an atypical dystrophinopathy. An A-->G substitution in the nucleotide 2525, which changes the codon for lysine to a codon for glutamic acid was detected in an 8-year-old boy, with normal neurological examination, but showing increased CK level and an abnormal EMG. The muscle biopsy was normal, without features of necrosis or regeneration. Immunoreactions with anti-dystrophin antibodies showed a normal distribution and intensity of the staining. A review of the dystrophin mutations detected so far is included.

Base Sequence↗
PubMed2002

Environmental mimic of receptor interaction: conformational analysis of CCK-15 in solution.

CCK-15, a peptide derived from the 115-membered CCK preprohormone, was the object of a comparative conformational analysis by NMR spectroscopy and molecular modeling methods. NMR data in several solvents demonstrate that the propensity of the peptide to fold into a helical conformation is intrinsic, not merely a consequence of the interaction with phosphatidylcholine micelles or with a putative receptor, as suggested by a previous study on CCK-8 (Pellegrini, M.; Mierke, D. Biochemistry 1999, 38, 14775-14783.). The prevailing CCK-15 conformer in a mixture 1,1,1,3,3,3-hexafluoroacetone/water reveals that the residues common to CCK-15 and CCK-8 assume very similar conformations. Our CCK-15 structure is consistent with the model of receptor interaction proposed by Pellegrini and Mierke and discloses possible novel interactions that involve a larger area of the putative receptor. The consensus structure between CCK-15 and CCK-8 shows a good superposition of the side chains of residues 12-14 with crucial moieties of two non-peptidic CCK-A antagonists.

Acetone↗
PubMed1990

Local interactions in peptides. 1H-1H, 13C-H coupling constants and calculations for the conformational analysis of N-acetyl-N'-methylamides of aliphatic amino acids.

We report the results of a joint NMR and theoretical investigation devoted to the conformational properties of N-acetyl-N'-methylamides of aliphatic amino acids with side chains of increasing bulkiness: Gly, Ala, Leu, Ile, and tert.Leu. In this series, determination of the coupling constants 3JHNC alpha H together with the coupling constants 3JC'NC alpha H (thanks to specific carbon-13 labeling of the N-acetyl carbonyl group) led to the derivation of alternative A, B, and C parameters in a Karplus-type relation expressing the dependence of 3JC'NC alpha H upon the phi dihedral angle. The value of the latter is found to increase regularly following the increase of the side-chain bulkiness. The theoretical conformational analysis is performed by applying the SIBFA procedure, which uses empirical formulas based on ab initio SCF computations. The conformational energy maps illustrate the progressive distortion of the backbone conformation incurred in the series Gly to tert.Leu. Theoretical values computed for 3JHNC alpha H and 3JC'NC alpha H are found to be in a good quantitative agreement with the experimental ones.

Alanine↗
PubMed1992

Conformational analysis of dopamine D-2 receptor antagonists of the benzamide series in relation to a recently proposed D-2 receptor-interaction model.

Conformational analysis using molecular mechanics calculations (MM2(87)) has been performed for four different types of benzamides which display high affinity for the dopamine D-2 receptor. In order to elucidate the conformation of the receptor-bound molecules, a previously described dopamine D-2 receptor-interaction model has been employed. We conclude that all four types of benzamides accommodated in the proposed receptor-interaction model are in low-energy conformations. An acyclic amide side chain is concluded to adopt an extended conformation in the receptor-bound benzamide. A phenylpyrrole analogue of the benzamides could similarly be fitted to the model. Using the receptor-interaction model, the enantioselectivity of benzamides with an N-ethyl-2-pyrrolidinylmethyl side chain could be rationalized in terms of different conformational energies of the receptor-bound enantiomers. Two different receptor sites for N-alkyl substituents are suggested.

Benzamides↗
PubMed1995

Single strand conformation analysis of two genes contained within the first intron of the neurofibromatosis type I gene in patients with multiple sclerosis.

Single strand conformation analysis has become the most widely used technique to screen large numbers of DNA samples for unknown mutations which may contribute to genetic susceptibility to disease. The method relies on the electrophoretic migration of a single strand of nucleic acid in a polyacrylamide gel being dependent on its conformation which is in turn dependent on its sequence. We have examined two closely related genes present in the first intron of the neurofibromatosis type I gene--the oligodendrocyte myelin glycoprotein (OMGP) gene and the ecotropic viral integration 2A (EVI2A) gene--in 36 patients with multiple sclerosis (MS) and 36 healthy controls. A single mutation was found in the OMGP gene which resulted in an amino-acid change of glycine to aspartic acid. This occurred in identical proportions (16.6%) in MS patients and controls. Two rare mutations were found in the EVI2A gene, one resulting in an arginine substituting for a glutamine (one control and one patient), the other in the replacement of a glycine with serine (one control only). A third common polymorphism was seen in 5'-untranslated region of the EVI2A gene, with 65% of patients and controls showing a T-->C transition in either a heterozygous or a homozygous form. This makes it unlikely that either of these genes is involved in genetic susceptibility to MS, but regions of these genes outside of the exonic sequences have not been examined.

Adult↗
PubMed1999

Conformational analysis of the biologically active cyclic analog of beta-casomorphin H-Tyr-cyclo[D-OrnPheProGly].

A biologically active analog of beta-casomorphin, H-Tyr-cyclo[D-OrnPheProGly], was studied by theoretical conformational analysis. Random sampling was used to search the conformational space of allowed dihedral angles. Among 53 low-energy conformers with different folding of the peptide cyclic moiety, only those were selected which correspond to the low-energy area of the model linear tripeptide Ac-D-AlaAlaPro-NHMe. This peptide was used as the main chain "template" for the D-OrnPheProGly fragment of the studied cyclopeptide molecule. Only 15 conformers were chosen as potentially biologically active structures. The conformational possibilities of the Phe residue were constrained to the combined (A + G) region of the Ala residue phi,psi-map for linear peptides.

Amino Acid Sequence↗
PubMed1998

Conformational analysis of [Met5]-enkephalin: solvation and ionization considerations.

[Met5]-Enkephalin has the sequence Tyr-Gly-Gly-Phe-Met. Only the extended conformation of the peptide has been observed by X-ray crystallography. Nuclear magnetic resonance spectroscopy supports the presence of a turn at Gly 3 and Phe 4 in dimethyl sulfoxide. In this study, the peptide conformational states and thermodynamic properties are understood in terms of ionization state and solvent environment. In the calculation, final conformations obtained from multiple independent Monte Carlo simulated annealing conformational searches are starting points for molecular dynamics simulations. In an aqueous environment given by the use of solvation free energy and the zwitterionic state, dominant structural motifs computed are G-P Type II' bend, G-G Type II' bend, and G-G Type I' bend motifs, in order of increasing free energy. In the calculation of the peptide with neutral N- and C-termini and solvation free energy, the extended conformer dominates (by at least a factor of 2.5), and the conformation of another low free energy conformer superimposes well on the pharmacophoric groups of morphine. Neutralization of charge and solvation induce and stabilize the extended conformation, respectively. A mechanism of inter-conversion between the extended conformer and three bent conformers is supported by phi/psi-scatter plots, and by the conformer relative free energies. An estimate of the entropy change of receptor unbinding is 8.3 cal K-1 mol-1, which gives rise to a -2.5 kcal/mol entropy contribution to the free energy of unbinding at 25 degrees C. The conformational analysis methodology described here should be useful in studies on short peptides and flexible protein surface loops that have important biological implications.

Energy Metabolism↗
PubMed2005

Conformational analysis of self-organized monolayers with scanning tunneling microscopy at near-atomic resolution.

We describe the synthesis and a novel approach to the conformational analysis of 2,2'-bipyridines (bpy) bearing aromatic rich Frechet-type dendritic wedges of the first and second generation as substituents. The evaporation of solutions of these new ligands on graphite surfaces under ambient conditions results in the formation of self-organized monolayers. Scanning tunneling microscopy (STM) investigations of the monolayers under ambient conditions (air, 298 K) gave images at submolecular and near-atomic resolution. The analysis of the STM images includes the following processes: (i) identification and reproduction of potential homoconformational domains, (ii) exclusion of improper data using quality criteria for drift and feedback artifacts, (iii) compilation of running averages and checking for averaging artifacts, (iv) analysis of three-dimensional and contour plots, (v) calculation of the HOMO properties of the free molecules, and (vi) final conformational assignment based on all accessible information. Following this procedure, two different conformations could be assigned to domains observed in the monolayers of the first-generation (G1) and second-generation (G2) dendritic compounds. Homoconformational domains are observed side-by-side. The different conformations arise from syn or anti arrangements at the ether substituents. An additional conformational effect is found upon treating the G1 domains with HCl gas, when a partial rearrangement of the bpy from trans to cis occurs, concomitant with protonation.

Journal Article↗
PubMed2001

Conformational analysis of DNA-trinucleotide-hairpin-loop structures using a continuum solvent model.

A number of trinucleotide sequences in DNA can form compact and stable hairpin loops that may have significance for DNA replication and transcription. The conformational analysis of these motifs is important for an understanding of the function and design of nucleic acid structures. Extensive conformational searches have been performed on three experimentally known trinucleotide hairpin loops (AGC, AAA, and GCA) closed by a four-base-pair stem. An implicit solvation model based on the generalized Born method has been employed during energy minimization and conformational search. In addition, energy-minimized conformers were evaluated using a finite-difference Poisson-Boltzmann approach. For all three loop sequences, conformations close to experiment were found as lowest-energy structures among several thousand alternative energy minima. The inclusion of reaction-field contributions was found to be important for a realistic conformer ranking. Most generated hairpin loop structures within approximately 5 kcal x mol(-1) of the lowest-energy structure have a similar topology. Structures within approximately 10 kcal x mol(-1) could be classified into about five structural families representing distinct arrangements of loop nucleotides. Although a large number of backbone torsion angle combinations were compatible with each structural class, some specific patterns could be identified. Harmonic mode analysis was used to account for differences in conformational flexibility of low-energy sub-states. Class-specific differences in the pattern of atomic fluctuations along the sequence were observed; however, inclusion of conformational entropy contributions did not change ranking of structural classes. For an additional loop sequence (AAG) with no available experimental structure, the approach suggests a lowest-energy loop topology overall similar to the other three loop sequences but closed by a different non-canonical base-pairing scheme.

Biophysical Phenomena↗