Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “complex 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 1,441 records · Page 80Linked to original sources
PubMed1986

Diagnosis of Maroteaux-Lamy syndrome by the use of radiolabelled oligosaccharides as substrates for the determination of arylsulphatase B activity.

The kinetic parameters (Km and V) of human arylsulphatase B (4-sulpho-N-acetylgalactosamine sulphatase) activity in cultured skin fibroblasts were determined with a variety of substrates matching structural aspects of the physiological substrates in vivo chondroitin 4-sulphate and dermatan sulphate. More structurally complex substrates, in which several aspects of the aglycone structure of the natural substrate were maintained, were desulphated up to 4400 times faster than the minimum arylsulphatase-B-specific substrate, namely the monosaccharide N-acetylgalactosamine 4-sulphate. Aglycone structures that influence substrate binding and/or enzyme activity were an adjacent-residue C-6 carboxy group and a second but internal N-acetylgalactosamine 4-sulphate residue. Arylsulphatase B activity in fibroblast homogenates assayed with O-(beta-N-acetylgalactosamine 4-sulphate)-(1----4)-O-D-(beta-glucuronic acid)-(1----3)-O-D-N-acetyl[1-3H] galactosaminitol 4-sulphate derived from chondroitin 4-sulphate as substrate clearly distinguished Maroteaux-Lamy-syndrome patients from normal controls and other mucopolysaccharidosis patients. We recommend the use of the above trisaccharide substrate for both postnatal and prenatal diagnosis of Maroteaux-Lamy syndrome.

Cells, Cultured↗
PubMed1992

Human alpha-L-iduronidase. Catalytic properties and an integrated role in the lysosomal degradation of heparan sulphate.

The kinetic parameters (Km and kcat) of human liver alpha-L-iduronidase were determined with a variety of heparin-derived disaccharide and tetrasaccharide substrates. More structurally complex substrates, in which several aspects of the aglycone structure of the natural substrates heparin and heparan sulphate were maintained, were hydrolysed with catalytic efficiencies up to 255 times that observed for the simplest disaccharide substrate to be hydrolysed. The major aglycone structure that influenced both substrate binding and enzyme activity was the presence of a C-6 sulphate ester on the residue adjacent to the iduronic acid residue being hydrolysed. Sulphate ions and a number of substrate and product analogues were potent inhibitors of enzyme activity. Human liver alpha-L-iduronidase activity towards 4-methylumbelliferyl alpha-L-iduronide at pH 4.8 had two Km values of 37 microM and 1.92 mM with corresponding kcat. values of 299 and 650 mol of product formed/min per mol of enzyme respectively, which may explain the wide range of Km values previously reported for alpha-L-iduronidase activity toward its substrate. Skin fibroblast alpha-L-iduronidase activity towards the heparin-derived oligosaccharides was influenced by the same substrate aglycone structural features as was observed for the human liver enzyme. A comparison was made of the effect of substrate aglycone structure upon catalytic activities of the enzymes which act to degrade the highly sulphated regions of heparan sulphate. A model was proposed whereby the substrate is directed from alpha-L-iduronidase to subsequent enzyme activities to ensure the efficient degradation of heparan sulphate.

Carbohydrate Sequence↗
PubMed2006

Subelliptic boundary conditions for SpinC-Dirac operators, gluing, relative indices, and tame Fredholm pairs.

Let X be a Spin manifold with boundary, such that the Spin structure is defined near the boundary by an almost complex structure, which is either strictly pseudoconvex or pseudoconcave (and hence contact). Using generalized Szego projectors, we define modified partial differential-Neumann boundary conditions, Reo, for spinors, which lead to subelliptic Fredholm boundary value problems for the Spin-Dirac operator, eth(eo). To study the index of these boundary value problems we introduce a generalization of Fredholm pairs to the "tame" category. In this context, we show that the index of the graph closure of (eth(eo), Reo) equals the tame relative index, on the boundary, between Reo and the Calderon projector. Let X0 and X1 be strictly pseudoconvex, Spin manifolds, as above. Let phi : bX1 --> bX0, be a contact diffeomorphism, S0, S1 denote generalized Szego projectors on bX0, bX1, respectively, and R0(eo), R1(eo), the subelliptic boundary conditions they define. If X1 is the manifold X1 with its orientation reversed, then the glued manifold X = X0 coproduct operator(phi) X1 has a canonical Spin structure and Dirac operator, ethX(eo). Applying these results we obtain a formula for the relative index, R-Ind(S0, phi*S1), [formula: see text]. As a special case, this formula verifies a conjecture of Atiyah and Weinstein [(1997) RIMS Kokyuroku 1014:1-14] for the index of the quantization of a contact transformation between cosphere bundles.

Journal Article↗
PubMed1960

The fine structure of synapses in the ciliary ganglion of the chick.

Ciliary ganglia of chick embryos and newly hatched chicks were examined in the light and electron microscopes. Particular attention was given to the fine structure of calyciform synapses, which are characteristically found in ciliary ganglia of birds. The calyciform endings are characterized by large expansions of the presynaptic axons upon ganglion cells, and the terminal processes extend over a considerable area of the cell surface. Often, indeed they appear to envelop the cell. In the electron microscope image, the appositional membranes are separated by a space about 300 to 400 A wide; i.e., the synaptic cleft. At irregularly spaced regions, the appositional membranes show areas of increased density. The presynaptic processes contain clusters of synaptic vesicles, localized at these dense regions. Thus the fine structure complex typical of other synapses is evident. The unique structural features of this synapse are as follows: (a) The calyx or presynaptic terminal derives from a single axon, does not arborize, and terminates upon a single ganglion cell. Thus, unlike the classical bouton terminal, this represents an anatomical device for firing single cells by single axons. (b) The surface area in contiguity, i.e., the area of appositional membranes, is far more extensive than the bouton terminal. The fine structure of this synapse is compared with others, for example, the classical boutons terminaux and purely electrical synapses, in an attempt to correlate fine structure with function.

Animals↗
PubMed2003

Structure of 20K endoglucanase from Melanocarpus albomyces at 1.8 A resolution.

The crystal structure of the 20K endoglucanase from the thermophilic fungus Melanocarpus albomyces (Ma20k) has been determined. The structure was refined to 1.8 A resolution using data obtained at 120 K. Ma20k belongs to glycoside hydrolase family 45. The three-dimensional structures of endoglucanase V (EGV) from the fungus Humicola insolens and of an endoglucanase from H. grisea var. thermoidea have previously been determined. The overall structure of Ma20k consists of a six-stranded beta-barrel domain similar to that found previously in family 45 endoglucanases. The flexible loop between strands V and VI, which was disordered in the uncomplexed structures of the Humicola endoglucanases but was ordered in complexed structures of EGV, is found to be well ordered in the native structure of Ma20k. The structure of Ma20k allows comparison between thermophilic and mesophilic proteins of family 45 and different principles for thermostability are discussed.

Amino Acid Sequence↗
PubMed1989

The cyclic nucleotide phosphodiesterase gene of Dictyostelium discoideum utilizes alternate promoters and splicing for the synthesis of multiple mRNAs.

The cyclic nucleotide phosphodiesterase (phosphodiesterase) gene plays essential roles in the development of Dictyostelium discoideum during cellular aggregation and postaggregation morphogenesis. Genomic clones spanning the gene were isolated and used to determine the sequence and structure of the phosphodiesterase gene. We found an unusually complex organization for a gene of D. discoideum. Two transcripts of 2.4 and 1.9 kilobases (kb) were synthesized from start sites separated by 1.1 kb. A developmentally regulated promoter was utilized for the 2.4-kb mRNA, and a constitutive promoter regulated synthesis of the 1.9-kb transcript. The gene was found to be divided into four exons that are alternately spliced to give rise to the two mRNAs. The precursor of the 2.4-kb mRNA contained a 2.3-kb intron, whereas the precursor of the constitutive transcript was synthesized with a 1.7-kb intron. The two transcripts contained identical protein-coding regions and 400-nucleotide 3' untranslated sequences. The 2.4-kb developmentally regulated mRNA was distinguished by a long 5' untranslated leader of 666 nucleotides. The complex structure of the gene may allow multiple levels of control of the expression of the phosphodiesterase during development.

Base Sequence↗
PubMed1980

Neurophysiological correlates of depressive symptomatology.

Some evidence has been presented in previous articles supporting the hypothesis that relevant relationships may occur between clinical symptoms of depression and complex EEG features investigated by means of a systemic structural analysis (SSA). The present paper deals with a closer analysis of the clinical-neurophysiological relationships in depressive syndromes. 22 untreated depressed patients of both sexes participated in the study. The patients were rated by means of the Cronholm and Ottosson Rating Scale for Depression (CORSD) at the time of the EEG investigation. Special computer programs were used to investigate the relationships between clinical symptoms and elementary EEG characteristics. It was found that symptoms comprised in the 'anxiety-depression' subscale of the CORSD were related to fast activity in the EEG, whereas symptoms comprised in the 'retardation' subscale showed significant relationship with slow EEG activity. The implicaions of these findings are discussed in terms of excitatory and inhibitory processes in the CNS. Both these processes exhibit a high degree of structural complexity and integration.

Adult↗
PubMed2004

Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions.

We have determined the structure of a mutant (Q237W) of HhaI DNA methyltransferase, complexed with the methyl-donor product AdoHcy. The Q237W mutant proteins were crystallized in the monoclinic space group C2 with two molecules in the crystallographic asymmetric unit. Protein-protein interface calculations in the crystal lattices suggest that the dimer interface has the specific characteristics for homodimer protein-protein interactions, while the two active sites are spatially independent on the outer surface of the dimer. The solution behavior suggests the formation of HhaI dimers as well. The same HhaI dimer interface is also observed in the previously characterized binary (M.HhaI-AdoMet) and ternary (M.HhaI-DNA-AdoHcy) complex structures, crystallized in different space groups. The dimer is characterized either by a non-crystallographic two-fold symmetry or a crystallographic symmetry. The dimer interface involves three segments: the amino-terminal residues 2-8, the carboxy-terminal residues 313-327, and the linker (amino acids 179-184) between the two functional domains--the catalytic methylation domain and the DNA target recognition domain. Both the amino- and carboxy-terminal segments are part of the methylation domain. We also examined protein-protein interactions of other structurally characterized DNA MTases, which are often found as a 2-fold related 'dimer' with the largest dimer interface area for the group-beta MTases. A possible evolutionary link between the Type I and Type II restriction-modification systems is discussed.

Crystallization↗
PubMed1985

Applications of the finite-element method to ventricular mechanics.

The finite-element method of structural analysis is ideally suited for the analysis of complex structures. Applications of this method to analysis of the heart will be discussed in light of the insights that have been obtained as well as the limitations of each analysis. In analyzing the heart, one of the aspects that is particularly difficult to handle is the presumed anisotropy as well as the nonlinearity of the material properties of the wall. Currently, use of finite-element methods for stress analysis requires that one first assumes a reasonable constitutive relation and then use incremental methods to predict the stresses. Studies using this approach will be reviewed. In theory, one could invert this approach by measuring the loading and resulting deformation in an intact heart and using the finite-element method to predict the constitutive relations. In order for this to succeed requires accurate measurement of the loading and the deformations. As we gain increasing expertise in these measurement areas, the feasibility of achieving this seems more realistic. While this alternative approach should be useful, there has been only minimal attention paid to this area. I will discuss this approach from a theoretical viewpoint and review the state-of-the-art.

Biomechanical Phenomena↗
PubMed1998

Three-dimensional structures of single-chain Fv-neuraminidase complexes.

The structure of the complex between a recombinant single-chain Fv construct of antibody NC10 with a five-residue peptide linker between VH and VL (termed scFv(5)), and its antigen, tetrameric neuraminidase from influenza virus (NA), has been determined and refined at 2.5 A resolution. The antibody-antigen binding interface is very similar to that of a similar NC10 scFv-NA complex in which the scFv has a 15-residue peptide linker (scFv(15)), and the NC10 Fab-NA complex. However, scFv(5) and scFv(15) have different stoichiometries in solution. While scFv(15) is predominantly monomeric in solution, scFv(5) forms dimers exclusively, because the five-residue linker is not long enough to permit VH and VL domains from the same polypeptide associating and forming an antigen-binding site. Upon forming a complex with NA, scFv(15) forms a approximately 300 kDa complex corresponding to one NA tetramer binding four scFv(15) monomers, while scFv(5) forms a approximately 590 kDa complex, corresponding to two NA tetramers crosslinked by four bivalent scFv(5) dimers. However, the dimeric scFv(5) in the scFv(5)-NA crystals does not crosslink NA tetramers, and modelling studies indicate that it is not possible to pack four dimeric and simultaneously bivalent scFvs between the NA tetramers with only a five-residue linker between VH and VL. The inability arises from the exacting requirement to orient the two antigen-binding surfaces to bind the tetrameric NA antigen while avoiding steric clashes with NC10 scFv(5) dimers bound to other sites on the NA tetramer. The utility of bivalent or bifunctional scFvs with short linkers may therefore be restricted by the steric constraints imposed by binding multivalent antigens.

Animals↗
PubMedDate not supplied

1H NMR study of the structure of a pyridocarbazole dimer-d[CpGpCpG] complex.

The structure of the complexes formed between a 7H-pyridocarbazole dimer (ditercalinium) or the corresponding monomer and d[CpGpCpG] is analyzed in aqueous solution by 270 MHz 1H NMR. In both cases the strong upfield shifts observed on most aromatic resonances are assigned to the formation of intercalated complexes. Bisintercalation of the dimer in the tetranucleotide minihelix is then observed at pH 5.5. The observation of intermolecular negative NOEs induced to some drug resonances by irradiation of sugar protons confirms these conclusions. The orientation of the ligand in the intercalation site is discussed.

Carbazoles↗
PubMed1999

The fractal structure of glycogen: A clever solution to optimize cell metabolism.

Fractal objects are complex structures built with a simple procedure involving very little information. This has an obvious interest for living beings, because they are splendid examples of optimization to achieve the most efficient structure for a number of goals by means of the most economic way. The lung alveolar structure, the capillary network, and the structure of several parts of higher plant organization, such as ears, spikes, umbels, etc., are supposed to be fractals, and, in fact, mathematical functions based on fractal geometry algorithms can be developed to simulate them. However, the statement that a given biological structure is fractal should imply that the iterative process of its construction has a real biological meaning, i.e., that its construction in nature is achieved by means of a single genetic, enzymatic, or biophysical mechanism successively repeated; thus, such an iterative process should not be just an abstract mathematical tool to reproduce that object. This property has not been proven at present for any biological structure, because the mechanisms that build the objects mentioned above are unknown in detail. In this work, we present results that show that the glycogen molecule could be the first known real biological fractal structure.

Carbohydrate Conformation↗
PubMed2006

Neutral and cationic mononuclear copper(II) complexes with enrofloxacin: structure and biological activity.

The mononuclear copper complexes with the quinolone antibacterial drug enrofloxacin (=Herx) in the presence or not of a nitrogen donor heterocyclic ligand 1,10-phenanthroline (=phen) and 2,2'-bipyridine (=bipy) have been prepared and characterized. Interaction of copper(II) with deprotonated enrofloxacin leads to the formation of the neutral complex Cu(erx)2(H2O), 1, while the presence of phen or bipy leads to the formation of a neutral or a cationic mononuclear complex, respectively. The crystal structures of (chloro)(1,10-phenanthroline)(enrofloxacinato)copper(II), 2, and (aqua)(2,2'-bipyridine)(enrofloxacinato)copper(II) chloride, 3, have been determined with X-ray crystallography. The complexes have been studied with X-band electron paramagnetic resonance in aqueous solutions at liquid helium temperature. The study of the interaction of the complexes with calf-thymus DNA has been performed with diverse spectroscopic techniques and has showed that all complexes are bound to DNA by the intercalative mode. The antimicrobial efficiency of the complexes has been tested on three different microorganisms and the available evidence supports that the best inhibition is provided by Cu(erx)2(H2O) (minimum inhibitory concentration=0.125 microg mL(-1)) against Escherichia coli and Pseudomonas aeruginosa.

Anti-Infective Agents↗
PubMed1998

Structure of a complex between a cap analogue and mRNA guanylyl transferase demonstrates the structural chemistry of RNA capping.

Paramecium bursaria Chlorella virus PBCV-1 mRNA guanylyl transferase (capping enzyme) has been complexed with an mRNA cap analogue G[5']ppp[5']G and crystallized. The crystals belong to space group C2221 with unit cell dimensions a = 78.4 A, b = 164.1 A, c = 103.3 A, and diffraction data to 3.1 A has been collected by using synchrotron radiation. The structure has been solved by molecular replacement by using each of the two domains in the previously determined structure of the enzyme in complex with GTP. The conformation is open with respect to the active site cleft, and all contacts between enzyme and ligand are mediated by domain 1. One of the guanine bases is bound in the same pocket that is utilized by GTP. The conformation of the ligand positions the beta phosphate and the active site lysine on opposite sides of the alpha phosphate. This geometry is optimal for nucleophilic substitution reactions and has previously been found for GTP in the closed conformational form of the capping enzyme, where the lysine can be guanylylated upon treatment with excess manganese(II) ions. The remainder of the cap analogue runs along the conserved active site Lys82 Thr83 Asp84 Gly85 Ile86 Arg87 motif, and the second guanine, corresponding to the 5' RNA base, is stacked against the hydrophobic Ile86. The ligand displays approximate 2-fold symmetry with intramolecular hydrogen bonding between the 2' and 3' hydroxyls of the two ribose rings.

Binding Sites↗
PubMed2006

Simulating self-assembly of ZnS nanoparticles into mesoporous materials.

Characterization of materials is crucial for the quantification and prediction of their physical, chemical, and mechanical properties. However, as the complexity of a system increases, so do the challenges involved in elucidating its structure. While molecular simulation and modeling have proved invaluable as complements to experiment, such simulations now face serious challenges: new materials are being synthesized with ever increasing structural complexity, and it may soon prove impossible to generate models that are sufficiently realistic to describe them adequately. Perhaps, ultimately, it will only be possible to generate such models by simulating the synthetic process itself. Here, we attempt such a strategy to generate full atomistic models for mesoporous molecular sieves. As in experiment, this is done by allowing nanoparticles to self-assemble at high temperature to form an amorphous mesoporous framework. The temperature is then reduced, and the system is allowed to crystallize. Animations of atomic trajectories, available as Supporting Information, reveal the evolution of multiple seeds which propagate to form a complex framework. The products are polycrystalline mesoporous framework structures containing cavities connected by channels running along "zero", one, two, and three perpendicular directions. We suggest that it is easier to generate these model structures by attempting to simulate the synthetic process rather than by using more conventional techniques. The strategy is illustrated using ZnS as a model system. Further development of the mathematics of minimal surfaces will advance our understanding of these structures.

Journal Article↗
PubMed2006

Modeling AAA+ ring complexes from monomeric structures.

AAA+ proteins form large, ring-shaped complexes, which act as energy-dependent unfoldases of macromolecules. Many crystal structures of proteins in this superfamily have been determined, but mostly in monomeric or non-physiological oligomeric forms. The assembly of ring-shaped complexes from monomer coordinates is, therefore, of considerable interest. We have extracted structural features of complex formation relating to the distance of monomers from the central axis, their relative orientation and the molecular contacts at their interfaces from experimentally determined oligomers and have implemented a semi-automated modeling procedure based on RosettaDock into the iMolTalk server (http://protevo.eb.tuebingen.mpg.de/iMolTalk). As examples of this procedure, we present here models of Apaf-1, MalT and ClpB. We show that the recent EM-based model of the apoptosome is not compatible with the conserved structural features of AAA+ complexes and that the D1 and D2 rings of ClpB are most likely offset by one subunit, in agreement with the structure proposed for ClpA.

Adenosine Triphosphatases↗
PubMedDate not supplied

Three-dimensional structure of a complex of antibody with influenza virus neuraminidase.

The structure of a complex between influenza virus neuraminidase and an antibody displays features inconsistent with the inflexible 'lock and key' model of antigen-antibody binding. The structure of the antigen changes on binding, and that of the antibody may also change; the interaction therefore has some of the character of a handshake.

Amino Acid Sequence↗