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At least 289 records · Page 16Linked to original sources
PubMed1980

An hypothesis concerning the molecular structure of the nicotinic acetylcholine receptor.

An hypothesis is presented concerning the molecular structure of the nicotinic acetylcholine receptor at the neuromuscular junction based on the actual amino acid sequence of the N-terminal segment of the alpha-subunit and the Chou and Fasman prediction of secondary structure from the primary sequence. This is mainly in the form of two alpha-helices cross-linked by four ionically bound complementary amino acids (arg/lys to glu). This structure (R) is complementary to a wide range of ACh agonists and to the antagonist beta-erythroidine. If the ionic cross-links are disrupted the two segments can separate by 2-3 A. This new conformation (R1) is now complementary to antagonists of the type of histrionicotoxin. A further separation (approximately 8 A) gives a conformation complementary to antagonist of the type of decamethonium. Experiments to test the hypothesis are suggested.

Acetylcholine↗
PubMed2005

Molecular structure of magnesium dibromide: an electron diffraction and quantum chemical study.

The molecular structure of magnesium dibromide was investigated by high-level computational techniques and gas-phase electron diffraction. The vapor consisted of about 88% monomeric and 12% dimeric species at the electron diffraction experimental conditions at 1065 K. The geometrical parameters and vibrational characteristics of monomeric, dimeric, and trimeric magnesium dibromide species were determined by computations. Very high level computations with extended basis sets and relativistic pseudopotentials on bromine were needed to reach an agreement between computed and estimated experimental equilibrium geometries for the monomer. For both the dimer and the trimer, different geometrical arrangements were tested. Their ground-state structures have halogen bridges with four-membered ring geometries and D2h and D2d symmetry, respectively. Thermodynamic parameters have also been calculated.

Journal Article↗
PubMed2006

The molecular structure and a Renner-Teller analysis of the ground and first excited electronic states of the jet-cooled CS2 + molecular ion.

The A 2Pi(u) - X 2Pi(g) electronic band system of the jet-cooled CS2 + ion has been studied by laser-induced fluorescence and wavelength-resolved emission techniques. The ions were produced in a pulsed electric discharge jet using a precursor mixture of carbon disulfide vapor in high-pressure argon. Rotational analysis of the high-resolution spectrum of the 2Pi32 component of the 0(0) 0 band gave linear-molecule molecular structures of r0" = 1.5554(10) A and r0' = 1.6172(12) A. Renner-Teller analyses of the vibronic structure in the spectra showed that the ground-state spin-orbit splitting (A = -447.0 cm(-1)) is much larger than that of the excited state (A = -177.5 cm(-1)), but that the Renner-Teller parameters are of similar magnitude and that a strong nu1 - 2nu2 Fermi resonance occurs in both states. Previous analyses of the vibronic structure in the ground and excited states of the ion from pulsed field-ionization-photoelectron data are shown to be substantially correct.

Journal Article↗
PubMed1991

Molecular structure of double reciprocal translocations: significance in B-cell lymphomagenesis.

The molecular structure of reciprocal translocations associated with low grade and high grade non-Hodgkin's lymphomas occurring together was analysed in two tumors. Sequential biopsies documented histological transformation of a large cell lymphoma to an immunoblastic lymphoma bearing t(14;18)(q32;q21) and t(8;22)(q24;q11). A second tumor, a small non-cleaved cell lymphoma, demonstrated a t(8;14)(q24;q11) as well as t(18;22)(q21;q11). DNA analysis from these tumors showed rearrangements at the Ig heavy chain, kappa and lambda light chains, BCL2 and c-MYC loci. Utilizing multiple enzyme digests and different probes spanning the BCL2, c-MYC and Ig genes, mapping of DNA break-points was performed. In both these tumors primary translocation events dysregulating the BCL2 or c-MYC were identified to have occurred in a pre-B-cell. Based on these results and those published previously, a sequence of B-cell development during which somatic recombination errors lead to the genesis of specific translocations is proposed. From these studies it is inferred that secondary dysregulation of a c-MYC in a lymphoma tumor carrying dysregulated BCL2 gene leads to rapid progression to high grade disease.

Biopsy↗
PubMed2005

Molecular structures of Se(SCH3)2 and Te(SCH3)2 using gas-phase electron diffraction and ab initio and DFT geometry optimisations.

The molecular structures of Se(SCH(3))(2) and Te(SCH(3))(2) were investigated using gas-phase electron diffraction (GED) and ab initio and DFT geometry optimisations. While parameters involving H atoms were refined using flexible restraints according to the SARACEN method, parameters that depended only on heavy atoms could be refined without restraints. The GED-determined geometric parameters (r(h1)) are: rSe-S 219.1(1), rS-C 183.2(1), rC-H 109.6(4) pm; angleS-Se-S 102.9(3), angleSe-S-C 100.6(2), angleS-C-H (mean) 107.4(5), phiS-Se-S-C 87.9(20), phiSe-S-C-H 178.8(19) degrees for Se(SCH(3))(2), and rTe-S 238.1(2), rS-C 184.1(3), rC-H 110.0(6) pm; angleS-Te-S 98.9(6), angleTe-S-C 99.7(4), angleS-C-H (mean) 109.2(9), phiS-Te-S-C 73.0(48), phiTe-S-C-H 180.1(19) degrees for Te(SCH(3))(2). Ab initio and DFT calculations were performed at the HF, MP2 and B3LYP levels, employing either full-electron basis sets [3-21G(d) or 6-31G(d)] or an effective core potential with a valence basis set [LanL2DZ(d)]. The best fit to the GED structures was achieved at the MP2 level. Differences between GED and MP2 results for rS-C and angleS-Te-S were explained by the thermal population of excited vibrational states under the experimental conditions. All theoretical models agreed that each compound exists as two stable conformers, one in which the methyl groups are on the same side (g(+)g(-) conformer) and one in which they are on different sides (g(+)g(+) conformer) of the S-Y-S plane (Y = Se, Te). The conformational composition under the experimental conditions could not be resolved from the GED data. Despite GED R-factors and ab initio and DFT energies favouring the g(+)g(+) conformer, it is likely that both conformers are present, for Se(SCH(3))(2) as well as for Te(SCH(3))(2).

Electrons↗
PubMed2002

Study on the screening of molecular structure parameter in QSAR model.

Based on the analysis of information flow through the Artificial Neural Network (ANN), a new screening rule of the molecular structure parameter in Quantitative Structure-Activity Relationship (QSAR) was presented by comparing of the values of connection weights and biases of the ANN model. The result showed that model quality and prediction ability of QSAR model, which was constructed by screening structural parameter with ANN, were better than by the method with MLR. The method established the foundation for further study in the mechanism research of the bio-toxicity of organic chemicals.

Animals↗
PubMedDate not supplied

Rheological properties and molecular structure of tunicate cellulose in LiCl/1,3-dimethyl-2-imidazolidinone.

Solution properties and molecular structure of tunicate cellulose (TC), an animal cellulose from Halocynthia roretzi, were investigated in terms of rheological and dilute solution properties. The solvent used is 8 wt % LiCl/1,3-dimethyl-2-imidazolidinone (DMI). A solution of dissolving pulp (DP), derived from plant, was also used for comparison. The weight-average molecular weight, Mw, and the limiting viscosity number, [eta], of the TC were evaluated to be 413 x 10(6) and 2645 mL/g, respectively. The TC solution showed the same concentration dependence of GN (GN=5.49 x 10(6)phiw(2.1)4 Pa; phiw: weight fraction of cellulose in solution; GN: plateau modulus) as the DP solution and, moreover, also as the solution of cotton linter (CC) in 8 wt % LiCl/N,N-dimethylacetamide (DMAc). This exponent of 2.1(4) indicates that network structure by entanglements was formed in these solutions. According to the theory of Fetters et al., moreover, such identity means that all of these celluloses have the identical chain structure though their biological origins are far different. On the other hand, the phiw-dependence of eta0-etas (eta0=zero shear rate viscosity of solution; etas=solvent viscosity) was different between the TC and the DP solution in the semidilute regime: the TC solution exhibited eta0-etas proportional, variant phiw(7.5) and the DP solution eta0-etas proportional, variant phiw4. According to the theory of Doi-Edwards, this exponent of 4 (the DP solution) indicates that the DP behaves as flexible polymers in the solution. In contrast, the dependence for the TC solution seems unexplainable on the basis of molecular theories. This difference probably signifies the difference in the relaxation process or mechanism in entanglement systems.

Animals↗
PubMed2001

Simultaneous prediction of aqueous solubility and octanol/water partition coefficient based on descriptors derived from molecular structure.

It has been shown that water solubility and octanol/water partition coefficient for a large diverse set of compounds can be predicted simultaneously using molecular descriptors derived solely from a two dimensional representation of molecular structure. These properties have been modelled using multiple linear regression, artificial neural networks and a statistical method known as canonical correlation analysis. The neural networks give slightly better models both in terms of fitting and prediction presumably due to the fact that they include non-linear terms. The statistical methods, on the other hand, provide information concerning the explanation of variance and allow easy interrogation of the models. Models were fitted using a training set of 552 compounds, a validation set and test set each containing 68 molecules and two separate literature test sets for solubility and partition.

1-Octanol↗
PubMed1991

Molecular structure of cytochrome c2 isolated from Rhodobacter capsulatus determined at 2.5 A resolution.

The molecular structure of the cytochrome c2, isolated from the purple photosynthetic bacterium Rhodobacter capsulatus, has been solved to a nominal resolution of 2.5 A and refined to a crystallographic R-factor of 16.8% for all observed X-ray data. Crystals used for this investigation belong to the space group R32 with two molecules in the asymmetric unit and unit cell dimensions of a = b = 100.03 A, c = 162.10 A as expressed in the hexagonal setting. An interpretable electron density map calculated at 2.5 A resolution was obtained by the combination of multiple isomorphous replacement with four heavy atom derivatives, molecular averaging and solvent flattening. At this stage of the structural analysis the electron densities corresponding to the side-chains are well ordered except for several surface lysine, glutamate and aspartate residues. Like other c-type cytochromes, the secondary structure of the protein consists of five alpha-helices forming a basket around the heme prosthetic group with one heme edge exposed to the solvent. The overall alpha-carbon trace of the molecule is very similar to that observed for the bacterial cytochrome c2, isolated from Rhodospirillum rubrum, with the exception of a loop, delineated by amino acid residues 21 to 32, that forms a two stranded beta-sheet-like motif in the Rb. capsulatus protein. As observed in the eukaryotic cytochrome c proteins, but not in the cytochrome c2 from Rsp. rubrum, there are two evolutionarily conserved solvent molecules buried within the heme binding pocket.

Amino Acid Sequence↗
PubMed2005

Molecular structure in soil humic substances: the new view.

A critical examination of published data obtained primarily from recent nuclear magnetic resonance spectroscopy, X-ray absorption near-edge structure spectroscopy, electrospray ionization-mass spectrometry, and pyrolysis studies reveals an evolving new view of the molecular structure of soil humic substances. According to the new view, humic substances are collections of diverse, relatively low molecular mass components forming dynamic associations stabilized by hydrophobic interactions and hydrogen bonds. These associations are capable of organizing into micellar structures in suitable aqueous environments. Humic components display contrasting molecular motional behavior and may be spatially segregated on a scale of nanometers. Within this new structural context, these components comprise any molecules intimately associated with a humic substance, such that they cannot be separated effectively by chemical or physical methods. Thus biomolecules strongly bound within humic fractions are by definition humic components, a conclusion that necessarily calls into question key biogeochemical pathways traditionally thought to be required for the formation of humic substances. Further research is needed to elucidate the intermolecular interactions that link humic components into supramolecular associations and to establish the pathways by which these associations emerge from the degradation of organic litter.

Humic Substances↗
PubMed1988

Molecular structure, conformation and interactions of antitumor antibiotic cyanonaphthridinomycin, a covalent binder of DNA.

X-ray, NMR and molecular modeling studies on cyanonaphthridinomycin (C22H26N4O5), a DNA binding antibiotic, have been carried out to study the structure, conformation and interactions with DNA. The crystals belong to the space group P21 with the cell dimensions of a = 5.934(1)b = 20.684(4), c = 16.866(3)A, gamma = 90.9 degrees and Z = 4(two molecules/asymmetric unit). The structure was solved by direct methods and difference Fourier methods and refined to an R value of 0.087 for 4061 reflections. The conformation of the molecule is compared with that of naphthridinomycin. There are differences in the orientation of the methoxyl group and the saturated oxazole ring. 1 and 2D NMR studies have been carried out and the dihedral angles obtained from coupling constants have been compared with those obtained from the crystal structure. Molecular mechanics studies were carried out to obtain the energy minimized structure and its comparison with X-ray and NMR results. Molecular modelling studies were performed to propose models for drug-DNA interactions. Both partial intercalation and groove-binding models have been proposed.

Antibiotics, Antineoplastic↗
PubMed1980

Crystal and molecular structure of nafoxidine and stereochemical features of anticancer antiestrogens.

We have determined the molecular structure of the anticancer antiestrogen nafoxidine and compared its three-dimensional structure with two other clinically useful antiestrogens in order to delineate stereochemical parameters in these compounds. Crystals of nafoxidine hydrochloride-ethanol are monoclinic with cell dimensions a = 17.040, b = 7.967, c = 25.260 A, beta = 123.7 degrees, and space group P21/c with four formula units per cell. The structure was solved by direct phasing methods and refined to a discrepancy index of 0.068. The methoxyphenyl and phenyl rings are trans to each other relative to the ethylene bond, and the substituted amine-aryl ether chain has an extended conformation. Stereoscopic superposition drawings and tabular data are given to show structural similarities and difference in nafoxidine, clomiphene, and tamoxifen, the three antiestrogens with with demonstrated clinical efficacy in the management of metastatic mammary carcinoma.

Antineoplastic Agents↗
PubMed2006

Molecular structures and vibrational frequencies of xanthine and its methyl derivatives (caffeine and theobromine) by ab initio Hartree-Fock and density functional theory calculations.

The molecular structures, vibrational frequencies and corresponding vibrational assignments of xanthine and its methyl derivatives (caffeine and theobromine) have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-31G(d, p) basis set level. The calculations were utilized to the C(S) symmetries of the molecules. The obtained vibrational frequencies and optimised geometric parameters (bond lengths and bond angles) were seen to be well agreement with the experimental data. The used scale factors which have been obtained the ratio of the frequency values of the strongest peaks in the calculated and experimental spectra seem to cause the gained vibrations well corresponding to the experimental ones. Theoretical infrared intensities and Raman activities are also reported.

Caffeine↗
PubMed1991

Molecular structure and dynamics of acetylcholine.

Molecular dynamics simulations and energy calculations based on the AMBER force field were used to examine the molecular movements and low-energy conformations of acetylcholine in vacuum and in aqueous solution. Electronic structures of acetylcholine were calculated by ab initio quantum mechanical calculations. Three conformations obtained from crystal structures and two from previous calculations were used as starting geometries in the simulations. The trans, gauche conformer had lowest energy both in vacuum and in aqueous solution. Both trans, gauche and trans, trans conformers were observed during molecular dynamics in water, which indicates that both conformations are relatively stable. The acetyl methyl group rotated more rapidly than those at the nitrogen atom during molecular dynamics simulations in water. Correlation times of both types of methyl groups were in good agreement with NMR data, which demonstrates that such simulations provide valid information about molecular movements of the neurotransmitter.

Acetylcholine↗
PubMed1976

Molecular structure of yeast RNA polymerase III: demonstration of the tripartite transcriptive system in lower eukaryotes.

Homogeneous RNA polymerase III (RNA nucleotidyltransferase III) has been obtained from yeast. The subunit composition of the enzyme was examined by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The enzyme is composed of 12 putative subunits with molecular weights 160,000, 128,000, 82,000, 41,000, 40,500, 37,000, 34,000, 28,000, 24,000, 20,000, 14,500, and 11,000. The high-molecular-weight subunits and several of the smaller subunits of yeast RNA polymerase III are clearly different from those of enzymes I and II, indicating a distinct molecular structure. However, the molecular weights of some of the small subunits (41,000, 28,000, 24,000, and 14,500) appear to be identical to those of polymerases I and II. Thus, it is possible that the three classes of enzymes in yeast have some common subunits. As in other eukaryotes, yeast polymerase II is inhibited by relatively low concentrations of alpha-amanitin; however, contrary to what has been found in higher eukaryotes, yeast polymerase III is resistant (up to 2 mg/ml) to alpha-amanitin, while yeast polymerase I is sensitive to high concentrations of the drug (50% inhibition at 0.3 mg/ml). These results establish the existence of RNA polymerase III in yeast and provide a structural basis for the discrimination of the three functional polymerases in eukaryotes.

Amanitins↗
PubMed2004

Molecular structure retention relationships in comprehensive two-dimensional gas chromatography.

Comprehensive two-dimensional gas chromatography (GC x GC) offers new opportunities to develop relationships between molecular structure and retentions in the two dimensional (2D) separation space defined by the GC x GC retention in each dimension. Whereas single dimension GC provides only one retention property for a solute, and hence the specific relationship between retention and chemical property is not readily apparent or derivable, the 2D presentation of compounds in GC x GC provides a subtle and exquisite correlation of chemical property and retention unlike any other GC experiment. The 'orthogonality' of the two separation dimensions is intimately related to the manner in which different separation mechanisms, available through use of two dissimilar phases, are accessible to the different chemical compounds or classes in a sample mixture, and indeed the specific chemical classes present in the sample. The GC x GC experiment now permits various processes such as chemical decompositions, molecular interconversions, various non-linear chromatography effects, and processes such as slow reversible interactions that may arise with stationary phases or in the injector or column couplings, to be identified and further investigated. Here, we briefly review implementation of the GC x GC method, consider the molecular selectivity of GC x GC, and highlight a selection of molecular processes that can be probed by using GC x GC.

Chromatography, Gas↗
PubMed1980

Molecular structures of 5,6- and 7,8-benzoflavones, inhibitors of aryl hydrocarbon hydroxylase.

The crystal and molecular structures of two isomeric inhibitors of carcinogenesis by certain polycyclic aromatic hydrocarbons are described. The two compounds are 7,8-benzoflavone and 5,6-benzoflavone, which are shown by X-ray crystallographic studies to differ appreciably in their three-dimensional structures. Polycyclic aromatic hydrocarbons are metabolically activated by an enzyme system that is responsibe for the detoxification of many chemicals that enter the body. The two benzoflavones described here differ in their effect towards specific enzymes in the metabolizing system. Potential energy calculations predict that a nonplanar conformation is most probable for these flavone derivatives, as a result of the presence of a biphenyl-like system. Such a conformation is found for 7,8-benzoflavone with a torsion angle of 23 degrees between the phenyl group and the rest of the molecule. The isomeric 5,6-benzoflavone is, in contrast, found to be a predominantly flat molecule. There is an interaction between O(4) and a neighboring -C-H group which may explain the planarity of 5,6-benzoflavone. A comparison is made with structures of some common carcinogenic polycyclic aromatic hydrocarbons, the activities of which these two benzoflavones inhibit.

Aryl Hydrocarbon Hydroxylases↗
PubMed1980

Molecular structure of chromatin during sperm differentiation of the dogfish Scyliorhinus caniculus (L.).

The molecular structure of chromatin during dogfish spermiogenesis was examined by electron microscopy after the dispersion of nuclei at low ionic strength. In early and late stages of differentiation (round and elongating spermatids), chromatin is globular, although basic nuclear proteins are different from those present in somatic nuclei. Three protein fractions are complexed with DNA in sperm nuclei. These fractions appear at the end of differentiation (elongated spermatids), subsequently undergoing a modification of their solubilization properties; only one protein fraction remains acid-soluble. Dispersed chromatin from sperm nuclei again shows a beads-on-a-string configuration both in the presence of the three specific sperm proteins and when the acid soluble fraction is extracted. Variations of the mean diameter of chromatin subunits during spermiogenesis appear rather limited compared to extensive modifications of chromatin superstructures.

Animals↗