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At least 217 records · Page 12Linked to original sources

PubMed1989

Crystal and molecular structures of carbon-bridged pyrimidine cyclonucleosides. Substrate analogs of ribonuclease A.

The crystal and molecular structures of carbon-bridged 6,5'-cyclo-5'-deoxy-4-thiouridine (6,5'-Cs4U), 6,5'-cyclo-5'-deoxy-2',3'-O-isopropylideneuridine (6,5'-CiU) and 6,6'-cyclo-5',6'-dideoxy-allofuranosyluracil (6,6'-CU) have been determined by X-ray diffraction. The molecular conformations of 6,5'-Cs4U and 6,5'-CiU are very similar; the conformation about the glycosidic bond is anti (low region), the torsion angle O(4')-C(1')-N(1)-C(2) being -150.0 degrees for 6,5'-Cs4U and -145.5 degrees for 6,5'-CiU, and the sugar puckering being both O(4')-exo. On the other hand, 6,6'-CU takes the glycosidic torsion angle of -116.9(4) degrees (middle anti region) and the sugar conformation of C(4')-endo. The cyclization causes little alteration in the geometry of the base moiety. 6,5'-Cs4U and 6,5'-CiU exhibit the similar base-base interactions between adjacent molecules, although their molecular packings are quite different; the 4-thiouracil or uracil moiety interacts with adjacent base moieties through hydrogen bonding and stacking interactions. In 6,6'-CU, cyclonucleosides were connected by hydrogen bondings between the hydroxyl and sugar ring oxygen atoms and between the hydroxyl groups and the base nitrogen and oxygen atoms. As the 2',3'-cyclic phosphates of these carbon-bridged cyclonucleosides are hydrolyzed by ribonuclease A, it is suggested that the conformers found in these cyclonucleosides are recognized by the enzyme.

Chemical Phenomena↗

PubMed1992

[Function, molecular structure and gene expression of insulin-like growth factors ].

In this short review, gene structure, transcriptional pattern, biological activity, specific receptors and binding proteins for insulin-like growth factors (IGF: IGF I and IGF II) are explained. In spite of their close similarity in both gene and peptide structures, their receptors are completely distinct from each other in molecular structure and in signal transduction. Expression of IGF function in vivo is strongly restricted by plasma binding proteins.

Carrier Proteins↗

PubMed1996

Pulsed electromagnetic fields influence hyaline cartilage extracellular matrix composition without affecting molecular structure.

Pulsed electromagnetic fields (PEMF) influence the extracellular matrix metabolism of a diverse range of skeletal tissues. This study focuses upon the effect of PEMF on the composition and molecular structure of cartilage proteoglycans. Sixteen-day-old embryonic chick sterna were explanted to culture and exposed to a PEMF for 3 h/day for 48 h. PEMF treatment did not affect the DNA content of explants but stimulated elevation of glycosaminoglycan content in the explant and conserved the tissue's histological integrity. The glycosaminoglycans in sterna exposed to PEMF were indistinguishable from those in controls in their composition of chondroitin sulfate resulting from chondroitinase ABC digestion. Specific examination with [35S]-sulfate labels showed that PEMF treatment significantly suppressed both the degradation of pre-existing glycosaminoglycans biosynthetically labeled in ovo and the synthesis of new [35S]-sulfated glycosaminoglycans. The average size and aggregating ability of pre-existing and newly synthesized [35S]-sulfated proteoglycans extracted with 4 M guanidinium chloride from PEMF-treated cartilage explants were identical to controls. The chain length and degree of sulfation of [35S]-sulfated glycosaminoglycans also were identical in control and PEMF-treated cultures. PEMF treatment also reduced the amount of both unlabeled glycosaminoglycans and labeled pre-existing and newly synthesized [35S]-sulfated glycosaminoglycans recovered from the nutrient media. [35S]-Sulfated proteoglycans released to the media of both control and PEMF-treated cultures were mostly degradation products although their glycosaminoglycan chain size was unchanged. These results demonstrate that exposure of embryonic chick cartilage explants to PEMF for 3 h/day maintains a balanced proteoglycan composition by down-regulating its turnover without affecting either molecular structure or function.

Animals↗

PubMed1996

Molecular structure, conformational analysis, and structure-activity studies of Dendrotoxin and its homologues using molecular mechanics and molecular dynamics techniques.

Three-dimensional structures of Dendrotoxin (DtX), Toxin-I (DpI), and Toxin-K (DpK) were determined using molecular mechanics and molecular dynamics techniques. The overall molecular conformation and protein folding of the three dendrotoxins are very similar to the published crystal structures of bovine pancreatic trypsin inhibitor (BPTI) and alpha-DtX. Major secondary structural regions of the dendrotoxins are stable without much fluctuation during the dynamics simulation; the regions corresponding to the turns and bends (rich in lysines and arginines) exhibit more fluctuations. The conformational angles and the C alpha...C alpha' distances of the three disulfides (in each of the dendrotoxins) are different from each other. Comparative model building studies, involving the dendrotoxins and the proteinases, reveal that the key interactions (observed in BPTI-trypsin complex) needed for anti-protease activity are absent due to structural differences between the dendrotoxins and BPTI at the anti-protease loop; this explains the inability of the dendrotoxins to inhibit proteinases. The model also suggests that the solvent-exposed beta-turn region, rich in lysines (residues 26-28), might bind directly to the extracellular anionic sites of the receptors (K+ channels) by ionic interactions. The strikingly homologous cysteine distribution (Cys-x-x-x-Cys) in DtX, DpI, and DpK, at the C-terminus, induces the occurrence of a characteristic conformational motif, consisting of an alpha-helix (in an amphiphilic environment) stabilized by two disulfides, one involving a cysteine at the beta-strand, and the other at the N-terminus. This amphiphilic secondary structural element seems to provide the rigid frame work needed for exposing the proposed active site region of the dendrotoxins to the anionic sites of the K+ channel receptors.

Amino Acid Sequence↗

PubMed1984

The molecular structure of a DNA-triostin A complex.

The molecular structure of triostin A, a cyclic octadepsipeptide antibiotic, has been solved complexed to a DNA double helical fragment with the sequence CGTACG (C, cytosine; G, guanine; T, thymine; A, adenine). The two planar quinoxaline rings of triostin A bis intercalate on the minor groove of the DNA double helix surrounding the CG base pairs at either end. The alanine residues form hydrogen bonds to the guanines. Base stacking in the DNA is perturbed, and the major binding interaction involves a large number of van der Waals contacts between the peptides and the nucleic acid. The adenine residues in the center are in the syn conformation and are paired to thymine through Hoogsteen base pairing.

Crystallization↗

PubMed1965

ALPHA-D-GLUCOSE: PRECISE DETERMINATION OF CRYSTAL AND MOLECULAR STRUCTURE BY NEUTRON-DIFFRACTION ANALYSIS.

This analysis provides the first precise crystal and molecular structural parameters for alpha-D-glucose. The C-C, C-H, and O-H bond lengths deviate only slightly from their means of 1.523 A, 1.098 A, and 0.968 A. The C(1)-O(1) bond length, 1.389 A, is significantly shorter than the mean value, 1.420 A, of the other C-O bonds. The valence angle of the ring oxygen is 113.8 degrees.

Biophysical Phenomena↗

PubMed2001

Effect of peracylation of beta-cyclodextrin on the molecular structure and on the formation of inclusion complexes: an X-ray study.

The molecular structures of peracylated beta-cyclodextrins (CDs)--heptakis(2,3,6-tri-O-acetyl)-beta-CD (TA), heptakis(2,3,6-tri-O-propanoyl)-beta-CD (TP), and heptakis(2,3,6-tri-O-butanoyl)-beta-CD (TB)--have been determined by single crystal X-ray structure analysis. Due to the lack of O2...O3' hydrogen bonds between adjacent glucose units of the peracylated CDs, the macrocycles are elliptically distorted into nonplanar boat-shaped structures. The glucose units are tilted with respect to the O4 plane to relieve steric hindrance between adjacent acyl chains. In TB, all glucose units adopt the common (4)C(1)-chair conformation and one butanoyl chain intramolecularly penetrates the cavity, whereas, in TA and TP, one glucose unit each occurs in (O)S(2)-skew-boat conformation and one acyl chain closes the O6 side like a lid. In each of the three homologous molecules the intramolecular self-inclusion and lidlike orientation of acyl chains forces the associated O5-C5-C6-O6 torsion angle into a trans-conformation never observed before for unsubstituted CD; the inclusion behavior of TA, TP, and TB in solution has been studied by circular dichroism spectroscopy with the drug molsidomine and several organic compounds. No inclusion complexes are formed, which is attributed to the intramolecular closure of the molecular cavity by one of the acyl chains.

Acetylation↗

PubMed2002

[Development of new reactions and their pharmaceutical application based on the molecular structure characteristics].

The author and his group have been developing new reactions based on molecular structure characteristics; sigma-symmetric bifunctional molecules, dipole-dipole repulsion, active amide structures, latent active species, orbital-orbital interactions, nonbonded interactions, strained structures, allenic structures, etc. Various new reactions such as asymmetric aminolyses and Dieckmann-type cyclizations of prochiral sigma-symmetric dicarboxylic diamides, asymmetric aldol-type reactions onto gamma-hydroxybutenolides and asymmetric imine alkylations onto omega-acetoxy lactams using chiral Sn(II) enolates, asymmetric Pummerer-type reactions, cascade reactions and endo-mode cyclizations exploiting alpha,beta-unsaturated allenic esters and ketones, base- and palladium-promoted ring-expansion reactions, and syntheses of alpha-substituted serines and 1-azabicyclo [1.1.0] butane have been achieved. These new reactions were applied to the synthetic development of new seed and lead compounds (SH-enzyme inhibitors, tumor inhibitors, and antibiotics) with the aim of synthesizing new drugs. Asymmetric syntheses of (+)-Prelog-Djerassi lactonic acid methyl ester, (+)-carbacyclin, ISP-I (myriocin), (+)-conagenin, Geissman-Waiss lactone, biapenem (a new carbapenem antibiotic), thienamycin-like gamma-lactam, and bicyclic alkaloids were also achieved by utilizing these reactions. Evaluation and molecular design of the seed and model compounds for angiotensin II receptor antagonists, tumor inhibitors, and antibiotics have been investigated on the basis of QRSA and/or nonbonded S...X (X=O, N, S, halogens) interaction concepts.

Chemistry, Organic↗

PubMed2004

Molecular structures of alumina nanoballs and nanotubes: a theoretical study.

Molecular structures of alumina nanoballs and nanotubes have been determined. Tetrahedral, octahedral, and icosahedral alumina nanostructures were derived from Platonic solids and Archimedean polyhedra and were optimized by quantum chemical methods. I(h)-symmetric balls, resembling their isovalence electronic analogues, fullerenes, are preferred. The nanoballs consist of adjacent Al(5)O(5) and Al(6)O(6) rings, similar to C(5)- and C(6)-rings of fullerenes. The structural characteristics of alumina nanoballs are dominated by pi-electron donation from oxygen to aluminum. Alumina nanotubes can be derived from icosahedral nanoballs. The tubes alternate between D(5d)- and D(5h)-symmetries and are capped by halves of the icosahedral balls.

Journal Article↗

PubMed2006

Molecular structure of a D-homoandrostanyl steroid derivative: single crystal and powder diffraction analyses.

The knowledge of the structure of a molecular crystal is frequently a prerequisite for the understanding of its solid state properties. Even though single-crystal diffractometry is the method of choice when it comes to crystal structure determination, methods using powder diffraction data become more and more competitive. There has been much recent interest in the development of a new generation of "direct-space" approaches that are particularly suited for molecular crystals. The crystallographic structure of a steroid derivative molecule (17,17-di-n-propyl-17a-aza-D-homo-5alpha-androstan-3beta-ol) was obtained in two independent ways: from a single crystal by laboratory X-rays and from a polycrystalline powder by high-resolution synchrotron powder diffraction. The molecule crystallizes in the orthorhombic space group P2(1)2(1)2(1) (a = 6.5346, b = 17.6006 and c = 19.6978 A). Hydrogen bonds form infinite chains of molecules parallel to the c axis.

Androstanols↗

PubMed1987

Crystal and molecular structure of the sodium salt of the dinucleotide duplex d(CpG).

The crystal and molecular structure of the sodium salt of deoxycytidylyl-(3H-5H)-deoxyguanosine has been determined from X-ray diffraction data. The crystal, obtained from an aqueous gamma-butyrolactone solution at pH = 5.3 are orthorhombic, P212121, a = 10.640(2), b = 11.184(2) and c = 44.618(4)A. The structure was refined to an R = 0.041. The d(CpG) structure is similar to the ammonium salt solved by Cruse et al.(1). Both structures form a parallel self base paired mini-double helix. In d(CpG).Na+ one of the two paired cytosines is protonated on N(3). The cytosines form 3 hydrogen bonds while the guanines form only 2. The Na+ ion is coordinated with five groups: two water molecules, O(6) of guanine A, N(7) of guanine B and 0(5') of cytosine B, forming a square pyramid. The hydration shell around the mini-helix is analysed and compared with that of the ammonium salt, d(CpG).Na+ is the second d(CpG) oligonucleotide found with a self base pairing arrangement despite of the fact that the crystallization conditions and counterion were different in both cases. The hypothesis that self base pairing is not only a crystallization artifact but may play a role under physiological conditions as a source of transversion mutations is discussed.

Base Composition↗

PubMed1991

The crystal and molecular structure of ellagic acid dihydrate: a dietary anti-cancer agent.

The crystal and molecular structure of ellagic acid dihydrate has been determined by X-ray diffraction techniques. This acid inhibits the carcinogenic properties of a variety of chemical compounds including benzo[alpha]pyrene-7,8-diol-9,10-epoxide, aflatoxin B1, N-methyl-N-nitrosourea, 3-methyl-cholanthrene and 7,12-dimethylbenz[alpha]anthracene. Ellagic acid dihydrate forms triclinic crystals with unit cell dimensions: a = 7.656(1) A, b = 9.563(1)A, c = 4.623(1) A, alpha = 97.88(1) degrees, beta = 103.2(1) degrees, gamma = 102.22(1) degrees, V = 315.9 A3, space group = P1. There is a center of symmetry in the crystal coinciding with the center of the molecule, so that there is only one molecule in the unit cell. Ellagic acid is planar and molecules are interconnected by hydrogen bonds to water, giving rise to layers of molecules throughout the crystal. Its activity and anti-cancer properties are compared with those of a similar naturally occurring compound, quercetin.

Antineoplastic Agents↗

PubMed2005

Elucidation of the molecular structure of lipid A isolated from both a rough mutant and a wild strain of Aeromonas salmonicida lipopolysaccharides using electrospray ionization quadrupole time-of-flight tandem mass spectrometry.

The chemical structure of lipid A, isolated by mild acid hydrolysis from a rough mutant and a wild strain of Aeromonas salmonicida lipopolysaccharide, was investigated using electrospray ionization quadrupole time-of-flight (QqToF) hybrid tandem mass spectrometry and showed a great degree of microheterogeneity. The chemical structure of the main constituent of this heterogeneous mixture was identified as a beta-D-(1 --> 6) linked D-glucosamine disaccharide substituted by two phosphate groups, one being bound to the non-reducing end at position O-4' and the other to the position O-1 of the reducing end of the D-glucosamine disaccharide. The location of the fatty acids linked to the disaccharide backbone was established by identifying diagnostic ions in the conventional QqToF-MS scan. Low-energy collision tandem mass spectrometry analysis of the selected precursor diagnostic ions confirmed, unambiguously, their proposed molecular structures. We have established that myristyloxylauric (C14:0(3-O(12:0))) acid residues were both N-2' and O-3' linked to the non-reducing end of the D-GlcN residue, and that two 3-hydroxymyristic (C14:0(3-OH)) acid chains acylated the remaining positions of the reducing end. The MS and MS/MS data obtained allowed us to determine the complex molecular structure of lipid A. The QqToF-MS/MS instrument has shown excellent superiority over a conventional quadrupole-hexapole-quadrupole tandem instrument which failed to fragment the selected precursor ion.

Aeromonas salmonicida↗

PubMed2002

The analysis of structure-anticancer and antiviral activity relationships for macrocyclic pyridinophanes and their analogues on the basis of 4D QSAR models (simplex representation of molecular structure).

A new 4D-QSAR approach has been considered. For all investigated molecules the 3D structural models have been created and the set of conformers (fourth dimension) have been used. Each conformer is represented as a system of different simplexes (tetratomic fragments of fixed structure, chirality and symmetry). The investigation of influence of molecular structure of macrocyclic pyridinophanes, their analogues and certain other compounds on anticancer and antiviral (anti-influenza, antiherpes and antiadenovirus) activity has been carried out by means of the 4D-QSAR. Statistic characteristics for QSAR of PLS (partial least squares) models are satisfactory (R = 0.92-0.97; CVR = 0.63-0.83). Molecular fragments increasing and decreasing biological activity were defined. This information may be useful for design, and direct synthesis of novel anticancer and antiviral agents.

Antineoplastic Agents↗

PubMed1989

Molecular structure of an A-DNA decamer d(ACCGGCCGGT).

The molecular structure of the DNA decamer d(ACCGGCCGGT) has been solved and refined by single-crystal X-ray-diffraction analysis at 0.20 nm to a final R-factor of 18.0%. The decamer crystallizes as an A-DNA double helical fragment with unit-cell dimensions of a = b = 3.923 nm and c = 7.80 nm in the space group P6(1)22. The overall conformation of this A-DNA decamer is very similar to that of the fiber model for A-DNA which has a large average base-pair tilt and hence a wide and shallow minor groove. This structure is in contrast to that of several A-DNA octamers in which the molecules all have low base-pair-tilt angles (8-12 degrees) resulting in an appearance intermediate between B-DNA and A-DNA. The average helical parameters of this decamer are typical of A-DNA with 10.9 base pairs/turn of helix, an average helical twist angle of 33.1 degrees, and a base-pair-tilt angle of 18.2 degrees. However, the CpG step in this molecule has a low local-twist angle of 24.5 degrees, similar to that seen in other A-DNA oligomers, and therefore appears to be an intrinsic stacking pattern for this step. The molecules pack in the crystal using a recurring binding motif, namely, the terminal base pair of one helix abuts the surface of the shallow minor groove of another helix. In addition, the GC base pairs have large propeller-twist angles, unlike those found most other A-DNA structures.

Base Sequence↗

PubMed1996

Imaging molecular structure of channels and receptors with an atomic force microscope.

Biological membranes contain specialized protein macromolecules such as channels, pumps and receptors. Physiologically, membranes and their constituent macromolecules are the interface surfaces toward which most of the regulatory biochemical and other signals are directed. Yet very little is known about these surfaces. The structure of biological membranes has been analyzed primarily using imaging techniques that are limited in their resolution of surface topology. An atomic force microscope (AFM) developed by Binnig, Quate and Gerber, can image molecular structures on specimen surfaces with subnanometer resolution, under diverse environmental conditions. Also, AFM can manipulate surfaces with molecular precision: it can nanodissect, translocate, and reorganize molecules on surface. The surface topology has been imaged for several hydrated channels, pumps and receptors which were a) present in isolated native membranes, b) reconstituted in artificial membrane or, c) expressed in an appropriate expression system. These images, at molecular resolution, reveal exciting new findings about their architecture. AFM induced "force dissection" reveals surfaces which are commonly inaccessible. In whole cell studies, in addition to the molecular structure of membrane receptors and channels, correlative electrical and biochemical activities have been examined. Such study suggests a "single cell" experiment where the structure-function correlation of many cloned channels and receptors can be understood.

Animals↗

PubMedDate not supplied

New insights into molecular structure and function of ectonucleotidases in the nervous system.

Nucleotides can be released as signaling substances in the nervous system from both neural and glial cells. Their function is terminated by ecto-nucleotidases and sequential extracellular metabolism to the nucleoside. Recently considerable progress has been made in unraveling the molecular structure of an ecto-ATPase and an ecto-ATP diphosphohydrolase, two closely related ectoenzymes. Molecular structure, tissue distribution and functional properties of the ecto-nucleotidases are discussed with particular emphasis on the nervous system.

5'-Nucleotidase↗

PubMed2006

Molecular structure determination in powders by NMR crystallography from proton spin diffusion.

The inability to determine molecular structures from powdered samples is a key barrier to progress in many areas of molecular and materials science. We report an approach to structure determination that combines molecular modeling with experimental spin diffusion data obtained from the high-resolution solid-state nuclear magnetic resonance of protons, and which allows the determination of the three-dimensional structure of an organic compound, in powder form and at natural isotopic abundance.

Journal Article↗