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At least 73 records · Page 4Linked to original sources
PubMed1990

1H NMR assignments and conformational analysis of the oligoribonucleotides CA, CAU, CAUG, ACAUG, and UCAUG: observation of pyrimidine H5-H1' long-range scalar couplings.

Conformational analysis and 1H NMR spectral assignments have been carried out using COSY and RELAY methods for a series of related oligoribonucleotides including two pentamers with 5'-dangling bases. Intraresidue long-range five bond scalar coupling was observed between pyrimidine H5 and H1' protons in the COSY-45 spectra and this feature was useful for both assignment purposes and conformational analysis. The ribose ring conformations were predominantly C3'-endo with the C2'-endo population increasing at the 3'-terminus. The 5'-dangling bases were not stacked efficiently, exhibiting lower % C3'-endo values than their 3'-nearest neighbors. Backbone torsion angle population. beta t, gamma +, epsilon t, were determined using 1H-1H, 1H-31P, and 13C-31P coupling constants. From beta t and gamma + populations the U3-G4 step in CAUG was found to be less efficiently stacked than the C1-A2 and A2-U3 steps. This observation in solution is consistent with the fiber diffraction A-RNA model (S. Arnott, D.W.L. Hukins, S.D. Dover, W. Fuller and A.R. Hodgson, J. Mol. Biol. 81, 107-122, 1973) which also predicts poor stacking in a U-G dinucleotide. The epsilon t populations were greater than 65% for all C3'-O3' bonds and consistent with a right-handed A-RNA helix.

Base Sequence↗
PubMed2005

Structure determination and conformation analysis of symmetrical dimers.

Conformational and stereochemical analysis of six new symmetrical dimers was performed using proton-proton vicinal coupling measured from (1)H NMR and (13)C satellites of (1)H NMR signals, natural abundance (13)C-edited nuclear overhauser effect (NOE) experiments, comprehensive NOE analysis and molecular modeling. The (13)C satellite analysis and (13)C-edited NOE experiments were carried out to extract spectral information between equivalent protons. Molecular modeling was applied for estimations of three-dimensional parameters of the studied dimers, which were subsequently used to generate a set of theoretical NOE for each possible conformation. The J-coupling, (13)C-edited NOE and quantitative NOE analyses showed the predominance of gauche conformation for three dimers, whereas a mixture of gauche and anti conformations (45:55) for three other dimers was established by quantitative NOE analysis. X-ray crystallographic study confirmed the stereochemistry of one of the dimers and revealed a discrepancy in conformation stability between liquid and solid states.

Carbon Isotopes↗
PubMed1983

Conformational analysis of the calcium-antagonist gallopamil.

Conformational analysis of gallopamil was performed in order to gain insight into the molecular determinant of its calcium-antagonistic property. Whereas the neutral form of gallopamil was characterized by a single, largely predominant configuration, the protonated form of the drugs yielded several conformers, some of which were characterized by a readily accessible ionized site. The capacity of gallopamil to inhibit ionophore-mediated calcium translocation in a two-phase bulk system was inversely related to the pH of the aqueous phase. These findings indicate that the capacity of gallopamil to interfere with the transport of cations is critically dependent on the availability of a protonated configuration of the drug.

Calcimycin↗
PubMed1985

Channel structures in synthetic polypeptides with alternating configurations. Conformational analysis of poly(DL-proline).

Theoretical conformational analysis of L,D alternating sequences of poly alpha-amino acids is reported in connection with the ability of naturally occurring peptide and depsipeptide having alternating configurations to increase selectively the ion permeability across membranes. The most stable structures of poly(DL-proline), of which the conformational variability is practically limited to the choice between cis and trans conformations of the peptide bonds, were characterized. The all-trans conformation results in a flat helical structure possessing the main features for acting as an ion channel across membranes as actually found experimentally. Random cis-trans conformational sequences provide an alternative mechanism of ion transport intermediate between the ion channel and the ion carrier.

Journal Article↗
PubMedDate not supplied

[Spatial organization of the globular fragment of calmodulin. 2. Conformational analysis of packing of two domains].

Theoretical conformational analysis of possible packing of two alpha-helical strands has been performed for the amino-acid sequence of N-terminal domains of CaM. It has been shown, that side chains of the antiparallel alpha-strands can interpenetrate and form a structure of the "knobs into holes" type. Such packing is profitable in the energy terms and can serve as an element of supersecondary structure, named "alpha-barrel". A possible conformational mechanism of CaM activation by Ca2+ is discussed in terms of the proposed model.

Amino Acid Sequence↗
PubMed1989

Conformational analysis of enkephalin analogs containing a disulfide bond. Models for delta- and mu-receptor opioid agonists.

Conformational analysis of the cyclic opioids H-Tyr-D-Pen-Gly-Phe-D-Pen-OH (DPDPE) and H-Tyr-D-Cys-Gly-Phe-D-Cys-OH (DCDCE) have been performed using the AMBER program. DPDPE is considerably more selective for delta-receptors than DCDCE. Using the RNGCFM program, a large number of ways were found to close the 14-membered disulfide-containing ring structure. However, intramolecular hydrogen bonds were only possible in gamma-turn and inverse gamma-turn conformations centered on the glycine residue which were associated with opposite chiralities of the disulfide bond. With the cyclic part of the molecules in either a gamma-turn or inverse gamma-turn, a systematic conformational analysis was performed on the tyrosine and phenylalanine sidechains. This showed that conformers with the tyrosine and phenylalanine phenyl rings in the vicinity of the disulfide bond were preferred due to attractive van der Waals forces. For DPDPE, however, this was only possible with a positive dihedral angle for the disulfide bond due to the presence of the beta-carbon methyls of Pen2. In contrast, these preferred conformers were possible with both chiralities of the disulfide bond in DCDCE. Conformational entropies and free energies were computed from the translational, rotational, and vibrational energy levels available to each conformer. The conformational entropies were found to vary significantly and to result in a re-ordering of the lowest energy minima. Based on these conformational differences in DPDPE and DCDCE and their differing pharmacological selectivities, tentative conformational preferences for delta- and mu-receptor opioid peptides are proposed.

Disulfides↗
PubMed1992

Enkephalin is a competitive antagonist of cholecystokinin in the gastrointestinal tract, as predicted from prior conformational analysis.

Prior calculations based on ECEPP (Empirical Conformational Energies for Peptides Program) of the low energy minima for cholecystokinin (CCK) and Met-enkephalin have demonstrated that significant structural features of these two peptides are identical. This result suggested the possibility that Met-enkephalin, as well as other enkephalin analogues of similar structure, could associate with receptors for CCK. To test this theoretical result, we examined the ability of Met-enkephalin and its analogues to bind to peripheral CCK receptors in the rat gastrointestinal tract; in particular, we measured the ability of the opiate peptide to inhibit the effects of CCK in a physiological assay system which we have previously characterized: CCK-induced contraction of the isolated rat pyloric sphincter. We find that Met-enkephalin is an antagonist of the CCK-8-induced contraction, with a IC50 of 110 nM. Furthermore, antibodies against CCK were found to cross-react with Met-enkephalin and its analogues in a manner which suggests a distinct structure-activity relationship. These experimental results strongly support the theoretical results of conformational analysis showing structural similarity between enkephalin and CCK. They further suggest that enkephalins could modulate the response of CCK systems under physiological conditions.

Amino Acid Sequence↗
PubMed2003

Resolution of complex feline leukocyte antigen DRB loci by reference strand-mediated conformational analysis (RSCA).

The DRB genes of the domestic cat are highly polymorphic. Studies based on clonal sequence analysis have suggested the existence of two distinct loci within individual animals and good evidence for 24 distinct FLA-DRB alleles. This variability, the complexity of clonal sequence analysis and its susceptibility to PCR-induced artefacts has represented a bottleneck to further progress. In this study we have applied reference strand-mediated conformational analysis (RSCA) to FLA-DRB. This protocol has been shown to be highly reproducible. Using five reference strands including two derived from non-domestic felines, we could distinguish 23 FLA-DRB alleles. We used RSCA to explore genetic polymorphism of FLA-DRB in 71 cats including 31 for which clonal sequence analysis was also available. On average, RSCA identified 0.9 more alleles within cats than clonal sequence analysis. Reference strand-mediated conformational analysis was also able to identify animals containing new alleles that could be targeted for sequence analysis. Analysis of allele patterns showed clear evidence for different allele distributions between breeds of cats, and suggested the Burmese breed may have highly restricted FLA-DRB polymorphism. Results from two families provided clear evidence for variation in the number of DRB genes on different haplotypes, with some haplotypes carrying two genes and some containing three. This study highlights the utility of RSCA for the resolution of complex amplicons containing up to six distinct alleles. A simple, rapid method for characterizing FLA-DRB makes possible studies on vaccine response and susceptibility/resistance to viral infections, which are a significant clinical problem in cats.

Alleles↗
PubMed1995

Conformational analysis of dolastatin 10: an NMR and theoretical approach.

A solution conformational analysis of dolastatin 10, a powerful antineoplastic agent, has been carried out by means of nmr techniques and theoretical calculations. 1H mono- and bidimensional nmr experiments, as well as 1H-13C heterocorrelated spectra, have been performed on CD2Cl2 solutions. The most interesting nmr data is a huge shielding of the aCH(25) proton of the Dov residue, suggesting the presence of an interaction between the N-terminal and the aromatic C-terminal ends of the molecule. The possibility of a head-to-tail intermolecular association having been discarded, the presence of a series of preferred folded conformation has been hypothesized. Conformational theoretical analysis supports the nmr hypothesis of a folded peptide-like molecule, and a series of possible conformers in good agreement with the experimental data have been analyzed.

Amino Acid Sequence↗
PubMed1997

Conformational analysis of Amphotericin B.

Within a theoretical approach to the problem of antifungal action of Amphotericin B (AmB), a conformational analysis of the neutral and zwitterionic form of this antibiotic in vacuo was performed by the MM2P and AM1 methods. The analysis was carried out with regard to the mutual orientation of the macrolidic and glycosidic fragments of the molecule, which is defined by the phi and psi steric angles. This orientation defines the overall shape of the molecule and is postulated to be important for the antifungal action of the drug. As a result of the MM2P calculations, phi, psi steric energy and population maps were prepared. Several conformers were found on these maps but only two of them (one each for the zwitterionic and the neutral forms of the antibiotic) were previously observed experimentally for isolated molecules. Our other calculated conformers were not observed experimentally but we propose that they may also appear in the AmB channel structure. The results of our conformational analysis were compared with experimental NMR data (nuclear Overhauser effects between selected hydrogen atoms) obtained previously. New structural information obtained for AmB in the present work will be useful for building a molecular model of AmB-target interactions as well as for designing new derivatives of AmB.

Journal Article↗
PubMed1985

Semi-empirical conformational analysis of propranolol interacting with dipalmitoylphosphatidylcholine.

A semi-empirical conformational analysis is used to compute the conformation of (+)-propranolol inserted in dipalmitoylphosphatidylcholine. In a first step, the minimal conformational energy of the isolated molecule at the hydrocarbon-water interface is calculated as the sum of the contributions resulting from the Van der Waals, the torsional, the electrostatic and the transfer energies. Five pairs of conformers of minimal energy are determined. They are compared to data available from other experimental approaches. In a second step, they are assembled with dipalmitoylphosphatidylcholine at the interface. Although propranolol is considered in its protonated form, the electrostatic interaction with dipalmitoylphosphatidylcholine is negligible as compared to the Van der Waals interaction. The area occupied per propranolol molecule is between 0.53 and 0.64 nm2/molecule. In the most probable modes of insertion of propranolol into the lipid layer, the naphthyl moiety of the compound interacts with the lipid acyl chains. The protonated amino group is located in the vicinity of the phosphate residue possibly causing an electrostatic interaction.

Chemical Phenomena↗
PubMed1998

Stepping through an RNA structure: A novel approach to conformational analysis.

Drawing from the growing database of complex three-dimensional RNA structures, a systematic method has been developed for classifying and analyzing the variety of conformations adopted by nucleic acids. This method is based on the development of a reduced representation for nucleic acid backbone conformation, simplifying the formidable eight-dimensional problem that has long complicated nucleic acid conformational analysis. Two pseudotorsion angles (eta and theta) have been defined, based on the selection of two appropriate pivot points along the RNA backbone, P and C4'. These pseudotorsions, together with a complete library of conventional torsion angles, can be calculated for any RNA structure or all-atom model using a new program called AMIGOS. Having computed eta and theta pseudotorsions for each position on an RNA molecule, they can be represented on a two-dimensional plot similar to the phi-phi plots that have traditionally been used for protein conformational analysis. Like a Ramachandran plot, clusters of residues appear at discrete regions on an eta-theta plot. Nucleotides within these clusters share conformational properties, often belonging to the same type of structural motif such as A-platforms, sheared tandem purine-purine pairs and GNRA tetraloops. An eta-theta plot provides a two-dimensional representation of the conformational properties of an entire RNA molecule, facilitating rapid analysis of structural features. In addition to the utility of eta-theta plots for intuitive visualization of conformational space, the pseudotorsional convention described here should significantly simplify approaches to macromolecular modeling of RNA structure.

Algorithms↗
PubMed1984

[Conformation analysis of a mixed hemoglobin-glutathione disulfide].

Theoretical conformational analysis was carried out for a mixed disulfide of hemoglobin with glutathione. The conformational mobility of the beta-subunit C-terminal fragment in methemoglobin and deoxyhemoglobin either with free or glutathione-blocked reactive SH-groups was examined. The most stable conformations of the mixed disulfide were delineated. Its spatial structure was shown to be dependent on the hemoglobin state prior to the S-S bond formation: a disulfide made with deoxyhemoglobin had more closely interwoven hemoglobin and glutathione chains than the methemoglobin-derived disulfide. However, in both cases disulfide formation brought about the alterations in the spatial structure of hemoglobin as well as glutathione. The changes in the hemoglobin biochemical properties accompanying the association with glutathione were rationalized in the frames of the mixed disulfide structural analysis.

Disulfides↗
PubMedDate not supplied

Pharmacology of the hypoglycaemic sulphonylurea gliquidone. III. Conformational analysis.

The hypoglycaemic sulphonylurea gliquidone was found, by conformation analysis, to display a U-shaped configuration, with hydrophobic cycles placed at the extremity of each branch and a peptidic bond placed at the bottom of the U. This configuration is similar to that recently observed with the hypoglycaemic sulphonylureas glimepiride and glibenclamide and non-sulphonylurea hypoglycaemic agents of the meglitinide family, such as S3075, repaglinide, A-4166 and KAD-1229. The identification of a conformation common to these various hypoglycaemic drugs may provide an imprint of their binding site at the level of the B-cell sulphonylurea receptor.

Hypoglycemic Agents↗
PubMed1995

Application of two-dimensional NMR spectroscopy and molecular dynamics simulations to the conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of Streptococcus group A.

This paper describes the use of a protocol for conformational analysis of oligosaccharide structures related to the cell-wall polysaccharide of Streptococcus group A. The polysaccharide features a branched structure with an L-rhamnopyranose (Rhap) backbone consisting of alternating alpha-(1-->2) and alpha-(1-->3) links and D-N-acetylglucosamine (GlcpNAc) residues beta-(1-->3)-connected to alternating rhamnose rings: [formula: see text] Oligomers consisting of three to six residues have been synthesized and nuclear magnetic resonance (NMR) assignments have been made. The protocol for conformational analysis of the solution structure of these oligosaccharides involves experimental and theoretical methods. Two-dimensional NMR spectroscopy methods (TOCSY, ROESY and NOESY) are utilized to obtain chemical shift data and proton-proton distances. These distances are used as constraints in 100 ps molecular dynamics simulations in water using QUANTA and CHARMm. In addition, the dynamics simulations are performed without constraints. ROE build-up curves are computed from the averaged structures of the molecular dynamics simulations using the CROSREL program and compared with the experimental curves. Thus, a refinement of the initial structure may be obtained. The alpha-(1-->2) and the beta-(1-->3) links are unambiguously defined by the observed ROE cross peaks between the A-B',A'-B and C-B,C'-B' residues, respectively. The branch-point of the trisaccharide CBA' is conformationally well-defined. Assignment of the conformation of the B-A linkage (alpha-(1-->3)) was problematic due to TOCSY relay, but could be solved by NOESY and T-ROESY techniques. A conformational model for the polysaccharide is proposed.

Carbohydrate Conformation↗
PubMed1997

19-nor-10-azasteroids, a new class of steroid 5 alpha-reductase inhibitors. 2. X-ray structure, molecular modeling, conformational analysis of 19-nor-10-azasteroids and comparison with 4-azasteroids and 6-azasteroids.

19-Nor-10-azasteroids are a new class of 5 alpha-reductase inhibitors whose activity depends on the presence of the bridgehead N-10 atom conjugated with the 4-en-3-one moiety in the A ring. The X-ray structure of 19-nor-10-azasteroid 1 has been determined and it is compared with the X-ray structure of testosterone. A complete conformational analysis of these compounds has been performed, determining the number and energy of the possible conformers, as well as the molecular flexibility of the 10-azasteroidal skeleton. Thus, MM2* molecular mechanics calculations and AM1 semiempirical energy refinements revealed that 19-nor-10-azasteroids 1-3 have four possible conformations with very small energy differences and that they are very flexible molecules. The conformational analysis has been extended to testosterone (4), which also showed conformational flexibility, with three different conformations, and to 6-azasteroid 5 and 4-azasteroid 6, for which only two thermally accessible conformations have been found. Compared to 19-nor-10-azasteroids 1-3, azasteroids 5 and 6 appear to be more rigid structures. By a best fit analysis of all conformers of 1-5 with the global minimum of testosterone (4-I) it has been found that the lowest energy conformers of 1, 3, and 5 are very close to the structure of 4-I, and among the conformers of 2, the best similarity has been observed for the highest energy conformer 2-IV.

5-alpha Reductase Inhibitors↗
PubMedDate not supplied

[Spatial structure of myelopeptides: I. Conformational analysis of MP-1, MP-2, and MP-3].

Theoretical conformational analysis was used to study the spatial structure and conformational properties of myelopeptides, bone-marrow peptide mediators. The low-energy conformations of three hexapeptides MP-1 (Phe-Leu-Gly-Phe-Pro-Thr), MP-2 (Leu-Val-Val-Tyr-Pro-Trp), and MP-3 (Leu-Val-Cys-Tyr-Pro-Gln) were found, the values of dihedral angles of the backbone and side chains of the amino acid residues constituting these peptides were determined, and the energies of intra- and interresidual interactions were estimated.

Amino Acid Sequence↗