Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 955 records · Page 53Linked to original sources
PubMed2000

Structural influences of organonitrogen ligands on vanadium oxide solids. Hydrothermal syntheses and structures of the terpyridine vanadates [V2O4(terpy)2]3[V10O28], [VO2(terpy)][V4O10], and [V9O22(terpy)3].

Hydrothermal reactions of the V2O5/2,2':6':2"-terpyridine/ZnO/H2O system under a variety of conditions yielded the organic-inorganic hybrid materials [V2O4(terpy)2]3[V10O28].2H2O (VOXI-10), [VO2(terpy)][V4O10] (VOXI-11), and [V9O22(terpy)3] (VOXI-12). The structure of VOXI-10 consists of discrete binuclear cations [V2O4(terpy)2]2+ and one-dimensional chains [V10O28]6-, constructed of cyclic [V4O12]4- clusters linked through (VO4) tetrahedra. In contrast, the structure of VOXI-11 exhibits discrete mononuclear cations [VO2(terpy)]1+ and a two-dimensional vanadium oxide network, [V4O10]1-. The structure of the oxide layer is constructed from ribbons of edge-sharing square pyramids; adjacent ribbons are connected through corner-sharing interactions into the two-dimensional architecture. VOXI-12 is also a network structure; however, in this case the terpy ligand is incorporated into the two-dimensional oxide network whose unique structure is constructed from cyclic [V6O18]6- clusters and linear (V3O5(terpy)3) moieties of corner-sharing vanadium octahedra. The rings form chains through corner-sharing linkages; adjacent chains are connected through the trinuclear units. Crystal data: VOXI-10, C90H70N18O42V16, triclinic P1, a = 12.2071(7) A, b = 13.8855(8) A, 16.9832(10) A, alpha = 69.584(1) degrees, beta = 71.204(1) degrees, gamma = 84.640(1) degrees, Z = 1; VOXI-11, C15H11N3O12V5, monoclinic, P2(1)/n, a = 7.7771(1) A, b = 10.3595(2) A, c = 25.715(4) A, beta = 92.286(1) degrees, Z = 4; VOXI-12, C45H33N9O22V9, monoclinic C2/c, a = 23.774(2) A, b = 9.4309(6) A, c = 25.380(2) A, beta = 112.047(1) degrees, Z = 4.

Journal Article↗
PubMed2005

Self-assembly of diorganotin(IV) oxides (R = Me, nBu, Ph) and 2,5-pyridinedicarboxylic acid to polymeric and trinuclear macrocyclic hybrids with porous solid-state structures: influence of substituents and solvent on the supramolecular structure.

2,5-Pyridinedicarboxylic acid has been reacted with three different diorganotin(IV) oxides (R = Me, nBu, Ph) to study the molecular and supramolecular structures of the resulting diorganotin(IV) 2,5-pyridinedicarboxylates. It has been found that coordinating solvent molecules can change the supramolecular structure completely. The molecular structures found are either polymeric (zigzag) or cyclotrimeric; the supramolecular arrangements include (i) systems having only loosely bound discrete molecules (van der Waals contacts), (ii) systems having a 2D or 3D hydrogen-bonded structure, and (iii) systems having a 3D polymeric coordination structure. Channels or cavities are formed in several cases. For a particular case, evidence has been provided that molecular aggregation to capsules through hydrogen bonding interactions is possible in solution.

Journal Article↗
PubMed2006

Controlling structure from the bottom-up: structural and optical properties of layer-by-layer assembled palladium coordination-based multilayers.

Layer-by-layer assembly of two palladium coordination-based multilayers on silicon and glass substrates is presented. The new assemblies consist of rigid-rod chromophores connected by terminal pyridine moieties to palladium centers. Both colloidal palladium and PdCl2(PhCN)2 were used in order to determine the effect of the metal complex precursor on multilayer structure and optical properties. The multilayers were formed by an iterative wet-chemical deposition process at room temperature in air on a siloxane-based template layer. Twelve consecutive deposition steps have been demonstrated resulting in structurally regular assemblies with an equal amount of chromophore and palladium added in each molecular bilayer. The optical intensity characteristics of the metal-organic films are clearly a function of the palladium precursor employed. The colloid-based system has a UV-vis absorption maximum an order of magnitude stronger than that of the PdCl2-based multilayer. The absorption maximum of the PdCl2-based film exhibits a significant red shift of 23 nm with the addition of 12 layers. Remarkably, the structure and physiochemical properties of the submicron scale PdCl2-based structures are determined by the configuration of the approximately 15 angstroms thick template layer. The refractive index of the PdCl2-based film was determined by spectroscopic ellipsometry. Well-defined three-dimensional structures, with a dimension of 5 microm, were obtained using photopatterned template monolayers. The properties and microstructure of the films were studied by UV-vis spectroscopy, spectroscopic ellipsometry, atomic force microscopy (AFM), X-ray reflectivity (XRR), scanning electron microscopy (SEM), and aqueous contact angle measurements (CA).

Journal Article↗
PubMed2005

Do theories of the glass transition, in which the structural relaxation time does not define the dispersion of the structural relaxation, need revision?

Upon decreasing temperature or increasing pressure, a noncrystallizing liquid will vitrify; that is, the structural relaxation time, taualpha, becomes so long that the system cannot attain an equilibrium configuration in the available time. Theories, including the well-known free volume and configurational entropy models, explain the glass transition by invoking a single quantity that governs the structural relaxation time. The dispersion of the structural relaxation (i.e., the structural relaxation function) is either not addressed or is derived as a parallel consequence (or afterthought) and thus is independent of taualpha. In these models the time dependence of the relaxation bears no fundamental relationship to the value of taualpha or other dynamic properties. Such approaches appear to be incompatible with a general experimental fact recently discovered in glass-formers: for a given material at a fixed value of taualpha, the dispersion is constant, independent of thermodynamic conditions (T and P); that is, the shape of the alpha-relaxation function depends only on the relaxation time. If derived independently of taualpha, it is an unlikely result that the dispersion of the structural relaxation would be uniquely defined by taualpha.

Journal Article↗
PubMed2006

Structures of lithiated lysine and structural analogues in the gas phase: effects of water and proton affinity on zwitterionic stability.

The structures of lithiated lysine, ornithine, and related molecules, both with and without a water molecule, are investigated using both density functional theory and blackbody infrared radiative dissociation experiments. The lowest-energy structure of lithiated lysine without a water molecule is nonzwitterionic; the metal ion interacts with both nitrogen atoms and the carbonyl oxygen. Structures in which lysine is zwitterionic are higher in energy by more than 29 kJ/mol. In contrast, the singly hydrated clusters with the zwitterionic and nonzwitterionic forms of lysine are more similar in energy, with the nonzwitterionic form more stable by only approximately 7 kJ/mol. Thus, a single water molecule can substantially stabilize the zwitterionic form of an amino acid. Analogous molecules that have methyl groups attached to either the N-terminus (NMeLys) or the side-chain amine (Lys(Me)) have proton affinities greater than that of lysine. In the lithiated clusters with a water molecule attached, the zwitterionic forms of NMeLys and Lys(Me) are calculated to be approximately 4 and approximately 11 kJ/mol more stable than the nonzwitterionic forms, respectively. Calculations of the potential-energy pathway for interconversion between the different forms of lysine in the lithiated complex indicate multiple stable intermediates with an overall barrier height of approximately 83 kJ/mol between the lowest-energy nonzwitterionic form and the most accessible zwitterionic form. Experimentally determined binding energies of water are similar for all these complexes and range from 57 to 64 kJ/mol. These results suggest that loss of a water molecule from the lysine complexes is both energetically and entropically favored compared to interconversion between the nonzwitterionic and zwitterionic structures. Comparisons to calculated binding energies of water to the various structures show that the experimental results are most consistent with the nonzwitterionic forms.

Energy Transfer↗
PubMed1999

Influence of non-bonded parameters on the quality of NMR structures: a new force field for NMR structure calculation.

The effects of different non-bonded parameters of force fields for NMR structure calculation on the quality of the resulting NMR solution structures were investigated using Interleukin 4 as a model system. NMR structure ensembles were calculated with an ab initio protocol using torsion angle dynamics. The calculations were repeated with five different non-bonded energy functions and parameters. The resulting ensembles were compared with the available X-ray structures, and their quality was assessed with common structure validation programs. In addition, the impact of torsion angle restraints and dihedral energy terms for the sidechains and the backbone was studied. The further improvement of the quality by refinement in explicit solvent was demonstrated. The optimal parameters, including those necessary for water refinement, are available in the new version of the PARALLHDG force field.

Interleukin-4↗
PubMed1998

A model of the quaternary structure of enolases, based on structural and evolutionary analysis of the octameric enolase from Bacillus subtilis.

Purified enolase from Bacillus subtilis has a native mass of approximately 370 kDa. Since B. subtilis enolase was found to have a subunit mass of 46.58 kDa, the quaternary structure of B. subtilis is octameric. The pl for B. subtilis enolase is 6.1, the pH optimum (pHo) for activity is 8.1-8.2, and the Km for 2-PGA is approximately 0.67 mM. Using the dimeric Calpha structure of yeast dimeric enolase as a guide, these dimers were arranged as a tetramer of dimers to simulate the electron microscopy image processing obtained for the octameric enolase purified from Thermotoga maritima. This arrangement allowed identification of helix J of one dimer (residues 86-96) and the loop between helix L and strand 1 (HL-S1 loop) of another dimer as possible subunit interaction regions. Alignment of available enolase amino acid sequences revealed that in 16 there are two tandem glycines at the C-terminal end of helix L and the HL-S1 loop is truncated by 4-6 residues relative to the yeast polypeptide, two structural features absent in enolases known to be dimers. From these arrangements and alignments it is proposed that the GG tandem at the C-terminal end of helix L and truncation of the HL-S1 loop may play a critical role in octamer formation of enolases. Interestingly, the sequence features associated with dimeric quaternary structure are found in three phylogenetically disparate groups, suggesting that the ancestral enolase was an octamer and that the dimeric structure has arisen independently multiple times through evolutionary history.

Amino Acid Sequence↗
PubMed2003

Patenting nonassociated polymeric structures (NAPS): implications for structural genomic data release.

The intellectual property laws that govern patent rights should provide a reasonable balance between the competing concerns of open access and exclusivity. Open access can facilitate knowledge dissemination and collaboration in furthering science. On the other hand, exclusivity can ensure interest and financial investment in scientific research and development. In recent days, the appropriate balance between open access and exclusivity has been a focus of public debate, particularly with regard to genomic inventions and their applications. In seeking to reconcile the timing of structural genomic data release with certain efforts to secure intellectual property rights, the International Structural Genomics Organisation joins others confronting this controversy. This paper seeks to inform the discussion with an overview of the U.S. standards for patenting nonassociated polymeric structures (NAPS), which include polynucleotides or polypeptides of unknown biological significance, and their corresponding structural data. In the United States, the present ability to obtain patent rights to these discoveries appears problematic given the requirement of specific, substantial and credible utility, among other things. Without demonstrable utility, NAPS and NAPS-related data likely will not be entitled to patent protection, whether the U.S. Patent & Trademark Office rejects NAPS claims as unpatentable in the first instance, or the U.S. federal courts invalidate NAPS claims in later patent litigation. As such, the improbability of obtaining enforceable patent rights to NAPS might undermine the rationale for delaying structural genomic data release to allow for the filing of patent applications in this regard.

Expressed Sequence Tags↗
PubMed1996

Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism.

Each protein sequence generally adopts a single native fold, but the sequence features that confer structural uniqueness are not well understood. To define the basis for structural heterogeneity, we determined the high resolution X-ray crystal structures of a single GCN4 leucine-zipper mutant (Asn 16 to aminobutyric acid) in both dimeric and trimeric coiled-coil conformations. The mutant sequence is accommodated in two distinct structures by forming similarly-shaped packing surfaces with different sets of atoms. The trimer structure, in comparison to a previously-characterized trimeric mutant with substitutions in eight core residues, shows that the twist of individual helices and the helix-helix crossing angles can vary significantly to produce the most favoured packing arrangement.

Amino Acid Sequence↗
PubMed2004

Molecular structure of 1,1,2,2-tetra-tert-butyldisilane: unusual structural motifs in sterically crowded disilanes.

The molecular structure of 1,1,2,2-tetra-tert-butyldisilane has been determined by gas-phase electron diffraction supported by ab initio calculations, in the solution phase by Raman spectroscopy, and in the solid phase by Raman spectroscopy and X-ray crystallography. The gas-phase structure (C2 symmetry) was found to be almost anticlinal, a most unusual and unexpected result. In the favoured conformation, contact between tert-butyl groups at each end of the molecule is avoided by a large deviation of the angles around the silicon atoms from the parent tetrahedral angle of 109.5 degrees. In fact, the Si-Si-C angles returned from the gas electron diffraction refinement are 117.0(5) and 110.7(6) degrees, indicating the large degree of flexibility about the silicon centres. The ab initio methods and gas electron diffraction results indicate that there is only one conformer of But2HSiSiHBut2 in the gaseous mixture. Variable temperature Raman studies indicate the possibility of a further higher energy conformer existing in the liquid phase. However, this seems quite improbable from other observations made for the Raman spectra at all temperatures. The X-ray structure is close to that observed in the gas phase, with phiHSiSiH = 94.2(18) degrees. There is a large amount of disorder about one of the silicon postions and one of the tert-butyl groups within the crystal structure, which makes detailed direct comparison with the gaseous structure difficult.

Journal Article↗
PubMed2001

The histochemical structure of the deep fascia and its structural response to surgery.

The histochemical structure of the deep fascia and its interface with the underlying muscle was examined in ten pigs. This structure was also evaluated after it had been raised as a fascial flap and in another site after the underlying muscle surface had been disrupted. The deep fascial is a simple structure of densely-packed collagen bundles and elastin fibres, and has hyaluronic acid concentrated on its inner surface, which is in contact with the underlying muscle. There is no specialised lining of this surface of the fascia to account for its gliding properties. The post-surgical specimens demonstrated preservation of the structure of the interface between fascia and muscle, including the retention of the hyaluronic acid lining, if the epimysium was intact. However, if the epimysium was disrupted, the structure of the interface was obliterated.

Animals↗
PubMed1998

Oviducal structure in four species of gekkonid lizard differing in parity mode and eggshell structure.

Oviducal structure was analysed in vitellogenic females from four species of gekkonid lizard exhibiting variation in parity mode and eggshell structure: Hemidactylus turcicus (oviparous) which produces a hard, calcareous eggshell; Saltuarius wyberba (oviparous) which produces a soft, parchment-like eggshell; and Hoplodactylus maculatus and Hoplodactylus duvaucelii (both viviparous). Oviducts were analysed by light, scanning electron and transmission electron microscopy. The uterus exhibited differences among species that were directly attributable to parity mode. H. turcicus and S. wyberba (oviparous) had numerous uterine shell glands; H. maculatus and H. duvaucelii (viviparous) had very few. The uterus also exhibited differences between the two oviparous species (H. turcicus and S. wyberba) which may be related to the type of eggshell produced. Variations were noted in the staining properties of the uterine glandular and epithelial cells. The structure of the infundibulum, uterine tube, isthmus and vagina also differed among species, but differences could not be directly related to parity mode or eggshell structure. Instead, the differences may be related to how prepared the oviduct is for ovulation in individuals analysed from the different species. This study confirms, in the Gekkonidae, aspects of oviducal structure that have been associated with parity mode in other squamate taxa.

Animals↗
PubMed2004

The effects of host contact network structure on pathogen diversity and strain structure.

For many important pathogens, mechanisms promoting antigenic variation, such as mutation and recombination, facilitate immune evasion and promote strain diversity. However, mathematical models have shown that host immune responses to polymorphic antigens can structure pathogen populations into discrete strains with nonoverlapping antigenic repertoires, despite recombination. Until now, models of strain evolution incorporating host immunity have assumed a randomly mixed host population. Here, we illustrate the effects of different host contact networks on strain diversity and dynamics by using a stochastic, spatially heterogeneous analogue of this model. For randomly mixed populations, our model confirms that cross-immunity to strains sharing alleles at antigenic loci may structure the pathogen population into discrete, nonoverlapping strains. However, this structure breaks down once the assumption of random mixing is relaxed, and an increasingly diverse pathogen population emerges as contacts between hosts become more localized. These results imply that host contact network structure plays a significant role in mediating the emergence of pathogen strain structure and dynamics.

Animals↗
PubMed2005

The structural basis of myotonic dystrophy from the crystal structure of CUG repeats.

Myotonic dystrophy (DM) type 1 is associated with an expansion of (>50) CTG repeats within the 3' untranslated region (UTR) of the dystrophin myotonin protein kinase gene (dmpk). In the corresponding mRNA transcript, the CUG repeats form an extended stem-loop structure. The double-stranded RNA of the stem sequesters RNA binding proteins away from their normal cellular targets resulting in aberrant transcription, alternative splicing patterns, or both, thereby leading to DM. To better understand the structural basis of DM type 1, we determined to 1.58-A resolution the x-ray crystal structure of an 18-bp RNA containing six CUG repeats. The CUG repeats form antiparallel double-stranded helices that stack end-on-end in the crystal to form infinite, pseudocontinuous helices similar to the long CUG stem loops formed by the expanded CUG repeats in DM type 1. The CUG helix is very similar in structure to A-form RNA with the exception of the unique U-U mismatches. This structure provides a high-resolution view of a toxic, trinucleotide repeat RNA.

3' Untranslated Regions↗
PubMed2002

Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline.

Structural genomics is emerging as a principal approach to define protein structure-function relationships. To apply this approach on a genomic scale, novel methods and technologies must be developed to determine large numbers of structures. We describe the design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium Thermotoga maritima. By using this pipeline, we successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes (73%) and have identified crystallization conditions for 432 proteins, comprising 23% of the T. maritima proteome. Representative structures from TM0423 glycerol dehydrogenase and TM0449 thymidylate synthase-complementing protein are presented as examples of final outputs from the pipeline.

Cloning, Molecular↗
PubMed1983

Secondary structure of the Tetrahymena ribosomal RNA intervening sequence: structural homology with fungal mitochondrial intervening sequences.

Splicing of the ribosomal RNA precursor of Tetrahymena is an autocatalytic reaction, requiring no enzyme or other protein in vitro. The structure of the intervening sequence (IVS) appears to direct the cleavage/ligation reactions involved in pre-rRNA splicing and IVS cyclization. We have probed this structure by treating the linear excised IVS RNA under nondenaturing conditions with various single- and double-strand-specific nucleases and then mapping the cleavage sites by using sequencing gel electrophoresis. A computer program was then used to predict the lowest-free-energy secondary structure consistent with the nuclease cleavage data. The resulting structure is appealing in that the ends of the IVS are in proximity; thus, the IVS can help align the adjacent coding regions (exons) for ligation, and IVS cyclization can occur. The Tetrahymena IVS has several sequences in common with those of fungal mitochondrial mRNA and rRNA IVSs, sequences that by genetic analysis are known to be important cis-acting elements for splicing of the mitochondrial RNAs. In the predicted structure of the Tetrahymena IVS, these sequences interact in a pairwise manner similar to that postulated for the mitochondrial IVSs. These findings suggest a common origin of some nuclear and mitochondrial introns and common elements in the mechanism of their splicing.

Base Sequence↗
PubMed1985

Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase.

The structure of the intervening sequence (IVS) of the Tetrahymena rRNA precursor mediates cleavage-ligation reactions that result in pre-rRNA splicing and IVS cyclization. We have developed a method for RNA structure analysis and applied it to the circular form of the IVS RNA. The native RNA was treated with dimethyl sulfate or diethyl pyrocarbonate to modify bases not involved in secondary or tertiary interactions. The RNA was then used as a template for reverse transcription. Elongation of synthetic oligodeoxynucleotide primers was found to stop (or pause) one nucleotide prior to 1-methyladenosine, 3-methylcytidine, and 7-ethoxycarbonyladenosine residues. The detection of 1-methyladenosine is particularly useful for locating single-stranded regions. After chemical cleavage of the RNA, 7-methylguanosine also could be detected. In general, the sites of modification were consistent with a previous model of the secondary structure of the linear form of the IVS RNA, a model based on enzymatic cleavage data, free energy calculations, and phylogenetic comparison. Thus, IVS RNA autocyclization does not involve major rearrangements of the secondary structure, although there is evidence for a conformational change in one region of the molecule. The methods described here should be of general use for obtaining information about structure far from the ends of RNA molecules.

Animals↗
PubMed1989

Crystal structure of the Glu-239----Gln mutant of aspartate carbamoyltransferase at 3.1-A resolution: an intermediate quaternary structure.

The structure of the unligated Glu 239----Gln mutant of Escherichia coli aspartate carbamoyltransferase (EC 2.1.3.2) has been determined to 3.1-A resolution and refined to a crystallographic residual of 0.22 in the space group P321. The unit-cell dimensions of the unligated enzyme are a = 122.3 A, c = 147.1 A. The c axis cell length is intermediate between the c axis lengths of the T (tense)(c = 142.2 A) and R (relaxed) (c = 156.2 A) state structures. Furthermore, the quaternary structure of the mutant enzyme is intermediate between the quaternary structures of the T form and the R form. The differences between the quaternary structures of the Glu-239----Gln and T-form enzymes can be described as follows: the separation between the catalytic trimers increases by approximately 1.5 A along the threefold axis, and they each rotate in opposite directions approximately 0.5 degree around the threefold axis, whereas the regulatory dimers rotate approximately 2 degrees around the twofold axes.

Aspartate Carbamoyltransferase↗