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 523 records · Page 29Linked to original sources

Metastructures: homeomorphisms between complex inorganic structures and three-dimensional nets.

We propose a general approach to nets and structures in which vertices represent stereochemically significant groups or clusters of atoms, and edges represent the linkage between these groups. Vertices may be single atoms, dimers, coordination polyhedra, clusters of atoms or clusters of coordination polyhedra; edges may be single chemical bonds or sets of several chemical bonds. Thus, a single net may be the basis for a family of structures that are homeomorphic to that net. The coordination of polyhedra or units around a vertex is visualized by connecting the centres of the atoms or groups at the vertices connected with the central vertex. Thus, the concept of coordination number is extended to include coordinating groups. We name a net after a homeomorphic simple structure-type for which there is a one-to-one correspondence between the vertices of the net and specific atoms of the structure, and between the edges of the net and the chemical bonds. We term the resulting more complex structures metastructures in order to distinguish them from their corresponding simple structure-types. Individual metastructures are referred to as alpha structures similar to a particular simple type. Thus, the open complex framework of [V(5)O(9)(PO(4))(2)] composition in microporous Na(v)[((V(4+)(4-w)V(5+)(1+w))O(9))(PO(4))(2)].(PO(4))(x).(OH)(y).zH(2)O is an alpha-NbO structure based on the simple net that is homeomorphic to NbO. This approach is effective in hierarchically classifying both simple close-packed structures and very complicated microporous structures.

Journal Article↗

Lewis acid properties of zinc(II) in Its cyclen complex. The structure of [Zn(cyclen)(S=C(NH2)2](ClO4)2 and the bonding of thiourea to metal ions. Some implications for zinc metalloenzymes.

The structure of the complex [Zn(cyclen)Tu](NO(3))(2) (1) is reported (cyclen = 1,4,7,10-tetraazacyclododecane; Tu = thiourea): orthorhombic, space group P2(1)2(1)2(1), a = 11.4170(11) A, b = 12.1995(11) A, c = 12.5299(12) A, Z = 4, R = 0.0504. The coordination of the cyclen is the same as that found for other similar Zn(II) complexes, with square pyramidal coordination around the Zn(II) and mean Zn-N bond lengths of 2.16 A. The coordinated Tu occupies the axial coordination site, with Zn-S = 2.31 A. The Zn-S-C-N torsion angle, involving the coordinated Tu, of 75.4 degrees is unusually large, because such torsion angles involving coordinated Tu are normally closer to 0 degrees. The bonding between Zn and S is discussed in terms of overlap with the p orbitals on S, which favors the eclipsed (Zn-S-C-N torsion = 0 degrees) mode of coordination of Tu. The energies of eclipsed and staggered modes (Zn-S-C-N = 90 degrees) of coordination of Tu to metal ions are examined by means of ab initio calculations, using the STO-3G basis set. It is concluded that the rather low formation constant for the Tu complex with Zn(II)/cyclen reported in this work was due to steric effects in 1, which prevent the adoption of the lower energy eclipsed conformation. These steric effects, because of clashes that would occur between Tu in the eclipsed conformation and the cyclen ring, cause the coordination of Tu with a higher energy conformation, with Zn-S-C-N = 75.4 degrees. The latter approaches the high energy staggered conformation that has Zn-S-C-N = 90 degrees. log K(1) values for Cl(-), Br(-), I(-), and CN(-) are reported and shown to be consistent with the binding site on the Zn(II) in the Zn(II)/cyclen complex being softer in the hard and soft acids and bases (HSAB, Pearson 1997) sense than the Zn(II) aqua ion, but not as soft as Zn(II) in triaza macrocycles that promote tetrahedral coordination. The change in HSAB character from intermediate in the Zn(II) aqua ion to softer in the cyclen complex, and softer still in tridentate N-donor ligands in model complexes, and in the Zn(II) active site of carbonic anhydrase as representative of Zn(II) metalloenzymes in general, is discussed in terms of the role of such effects in the functioning of metalloenzymes.

Binding Sites↗

Complex terminal structure of a linear mitochondrial plasmid from Physarum polycephalum: three terminal inverted repeats and an ORF encoding DNA polymerase.

The mitochondria of Physarum polycephalum have a linear plasmid (mF) which promotes mitochondrial fusion. To determine the terminal structure of the mF plasmid, restriction fragments derived from its ends were cloned and sequenced. The sequences showed that the mF plasmid has three kinds of terminal inverted repeats (TIRs). The most characteristic feature is a 144-bp repeating unit which exists between a 205-bp TIR at the extreme ends of the plasmid and another 591-bp TIR. All of the clones showed at least one of these 144-bp repeating units. The GC content of the 205-bp TIR (49%) was higher than those of the other TIRs and of another sequenced region (23%). This TIR can form three thermodynamically-stable hairpin structures based on complex internal palindromic components. Moreover, in the right terminal region of the mF plasmid, there is an open reading frame (ORF) which covers the entire 591-bp TIR and most of one of the 144-bp repeating units. This ORF encodes a 547-amino-acid polypeptide, ORF-547, and shows extensive homology with the polymerization domain of the putative DNA polymerases of linear mitochondrial plasmids from other sources.

Amino Acid Sequence↗

A comparison between the binding modes of a substrate and inhibitor to papain as observed in complex crystal structures.

On the basis of the crystal structures of papain complexed with the substrate analogue benzyloxycarbonyl-L-phenylalanyl-L-alanine chloromethyl-ketone (Drenth, J., Kalk, K.H., and Swen, H.M. (1976) Biochemistry 15, 3731-3738) and with the inhibitor E-64-c, the binding modes were compared at the atomic level to clarify the functional difference between the substrate and inhibitor. Irrespective of the reverse chemical bonding in the peptide bonds, both the molecules are located at the S subsites of papain with similar interactions. However, the inhibitory activity of E-64-c is characterized by the stereochemical function of a carboxyoxirane ring and the tight binding of the isopentylaminoleucyl side chain to the S subsites.

Amino Acid Chloromethyl Ketones↗

New oxamidato-bridged Cu(II)-Ni(II) complexes: supramolecular structures with thiocyanate ligands and hydrogen bonds. Magnetostructural studies: DFT calculations.

Four new supramolecular compounds of Cu(II)-Ni(II) have been synthesized and characterized: [Cu(Me(2)oxpn)Ni(mu-NCS)(H(2)O)(tmen)](2)(ClO(4))(2) (1), [Cu(Me(2)oxpn)Ni(mu-NCS)(H(2)O)(tmen)](2)(PF(6))(2) (2), [Cu(oxpn)Ni(mu-NCS)(NCS) (tmen)](n) (3), and [Cu(Me(2)oxpn)Ni(mu-NCS)(NCS)(tmen)](n) (4), where oxpn = N,N'-bis(3-aminopropyl)oxamidate, Me(2)oxpn = N,N'-bis(3-amino-2,2'-dimethylpropyl)oxamidate, and tmen = N,N,N',N'-tetramethylethylenediamine. Their crystal structures were solved. Complexes 1 and 2 have the same tetranuclear cationic part but a different counteranion. The cationic part consists of two [Cu(Me(2)oxpn)Ni] moieties linked by SCN(-) bridged ligands and intra-tetranuclear hydrogen bonds. In the case of complex 3, a two-dimensional system was built, the thiocyanate ligand linking the dinuclear units gives a chain, and the chains are linked together by hydrogen bonds; intrachain hydrogen bonds are also present. For complex 4, the thiocyanate ligands produce intermolecular linkages between the dinuclear entities, giving a one-dimensional system; intrachain hydrogen bonds are also present. The magnetic properties of the four complexes were studied by susceptibility measurements vs temperature. DFT calculations were made to study the contribution of the SCN(-) and hydrogen bond bridges in the magnetic coupling.

Journal Article↗

Hexameric and pentameric slipped-cofacial dimers: toward an artificial light-harvesting complex.

[structure: see text] We prepared a zinc complex of bis(1-methylimidazolyl)-m-gable porphyrin. The automatically assembled coordinate species showed a complex mixture of wide molecular weight distributions accompanied with assemblies of specific assembly numbers. When this zinc complex was once dissociated by the addition of methanol and reorganized again by elimination of the methanol under high-dilution conditions in chloroform to facilitate intramolecular coordinate structure formation, two convergent assemblies were obtained through analysis by gel permeation chromatography. These assemblies gave round-shaped particles on solid substrates by probe microscopies (atomic force and scanning tunneling microscopies). These two components were separated by GPC and evidence from small-angle X-ray scattering measurements in solution with synchrotron radiation was consistent with hexameric and pentameric macrorings of the gable porphyrin. The porphyrin macrorings did not show any fluorescence quenching by assembly formation, and we anticipate that the macrorings of gable porphyrins represent a good model for an artificial light-harvesting complex.

Journal Article↗

How H-bonding modifies molecular structure and pi-electron delocalization in the ring of pyridine/pyridinium derivatives involved in H-bond complexation.

[structure: see text] Analysis of the experimental geometry of 397 variously substituted pyridine and pyridinium derivatives has shown very little variation of all bond lengths in the ring and substantial changes in the values of alpha and beta angles, being in line with theoretically modeled data (at the B3LYP/6-311+G level of theory). No dependence of bond lengths and pi-electron delocalization in the ring measured by HOMA index on the changes in bond angle at the N-atom is observed. This is at variance with the patterns observed in substituted phenolate/phenol systems involved in H-bonding. Due to significant differences in magnitude of the ipso angle at the nitrogen atom that depend on the location of hydrogen atom in pyridine/pyridinium systems (N, N...H, and N-H), this angle may be used as a valuable indicator of N...H interactions since the X-ray structural analysis does not give a reliable position for the proton.

Journal Article↗

Mitochondrial Complex I: structural and functional aspects.

This review examines two aspects of the structure and function of mitochondrial Complex I (NADH Coenzyme Q oxidoreductase) that have become matter of recent debate. The supramolecular organization of Complex I and its structural relation with the remainder of the respiratory chain are uncertain. Although the random diffusion model [C.R. Hackenbrock, B. Chazotte, S.S. Gupte, The random collision model and a critical assessment of diffusion and collision in mitochondrial electron transport, J. Bioenerg. Biomembranes 18 (1986) 331-368] has been widely accepted, recent evidence suggests the presence of supramolecular aggregates. In particular, evidence for a Complex I-Complex III supercomplex stems from both structural and kinetic studies. Electron transfer in the supercomplex may occur by electron channelling through bound Coenzyme Q in equilibrium with the pool in the membrane lipids. The amount and nature of the lipids modify the aggregation state and there is evidence that lipid peroxidation induces supercomplex disaggregation. Another important aspect in Complex I is its capacity to reduce oxygen with formation of superoxide anion. The site of escape of the single electron is debated and either FMN, iron-sulphur clusters, and ubisemiquinone have been suggested. The finding in our laboratory that two classes of hydrophobic inhibitors have opposite effects on superoxide production favours an iron-sulphur cluster (presumably N2) is the direct oxygen reductant. The implications in human pathology of better knowledge on these aspects of Complex I structure and function are briefly discussed.

Animals↗

Residue conservation information for generating near-native structures in protein-protein docking.

MOTIVATION: Protein-protein docking algorithms typically generate large numbers of possible complex structures with only a few of them resembling the native structure. Recently (Duan et al., Protein Sci, 14:316-218, 2005), it was observed that the surface density of conserved residue positions is high at the interface regions of interacting protein surfaces, except for antibody-antigen complexes, where a lesser number of conserved positions than average is observed at the interface regions. Using this observation, we identified putative interacting regions on the surface of interacting partners and significantly improved docking results by assigning top ranks to near-native complex structures. In this paper, we combine the residue conservation information with a widely used shape complementarity algorithm to generate candidate complex structures with a higher percentage of near-native structures (hits). What is new in this work is that the conservation information is used early in the generation stage and not only in the ranking stage of the docking algorithm. This results in a significantly larger number of generated hits and an improved predictive ability in identifying the native structure of protein-protein complexes. RESULTS: We report on results from 48 well-characterized protein complexes, which have enough residue conservation information from the same 59 benchmark complexes used in our previous work. We compute conservation indices of residue positions on the surfaces of interacting proteins using available homologous sequences from UNIPROT and calculate the solvent accessible surface area. We combine this information with shape-complementarity scores to generate candidate protein-protein complex structures. When compared with pure shape-complementarity algorithms, performed by FTDock, our method results in significantly more hits, with the improvement being over 100% in many instances. We demonstrate that residue conservation information is useful not only in refinement and scoring of docking solutions, but also helpful in enrichment of near-native-structures during the generation of candidate geometries of complex structures.

Amino Acid Sequence↗

Versatile photosensitization system for 1O2-mediated oxidation of alkenes based on nafion-supported platinum(II) terpyridyl acetylide complex.

[structure: see text] Platinum(II) terpyridyl acetylide complex (1) was incorporated into Nafion membranes as a photosensitizer, and the Nafion was immersed in an aqueous or organic solution of 7-dehydrocholesterol, alpha-pinene, or cyclopentadiene. This photosensitizer system can generate singlet oxygen ((1)O(2)) in high quantum yield to oxidize the alkenes in the solution outside the Nafion and can be easily removed from the reaction vessel at the end of the photooxidation.

Journal Article↗

Cellular automata model simulating complex spatiotemporal structure of wide jams.

According to the empirical observation of highway traffic, inside wide moving jams there is a complex spatiotemporal structure: jam is not compact and relatively large values of the time and the distance headway are visible. We present a cellular automata model by introducing "jam headway" and "jammed status" to simulate that complex structure. Using computer simulations, the fundamental diagram, the space-time plots, the time series of the density in the jams, and the 1-min average data of this model are analyzed. It is shown that compared to other existing models, this model can display the experimental characteristics of the wide moving jams.

Journal Article↗

Polysomatic series in the structures of complex cuprates.

The modular approach was applied to analyse the structure of complex cuprates. The modular series of various types were distinguished in the family of layered cuprates making use of the classification scheme in a fragment approximation developed earlier. The poly-somatic series were revealed in the groups of cuprates which were expected to possess the properties of both salt and oxide. The structure of the ladder-type cuprates was analysed in more detail. The present study has shown that the polysomatic model can be efficiently applied to the structural analysis of complex cuprates.

Journal Article↗

Evidence for electron equilibrium between the two hemes bL in the dimeric cytochrome bc1 complex.

Structural analysis of the dimeric mitochondrial cytochrome bc1 complex suggests that electron transfer between inter-monomer hemes bL-bL may occur during bc1 catalysis. Such electron transfer may be facilitated by the aromatic pairs present between the two bL hemes in the two symmetry-related monomers. To test this hypothesis, R. sphaeroides mutants expressing His6-tagged bc1 complexes with mutations at three aromatic residues (Phe-195, Tyr-199, and Phe-203), located between two bL hemes, were generated and characterized. All three mutants grew photosynthetically at a rate comparable to that of wild-type cells. The bc1 complexes prepared from mutants F195A, Y199A, and F203A have, respectively, 78%, 100%, and 100% of ubiquinol-cytochrome c reductase activity found in the wild-type complex. Replacing the Phe-195 of cytochrome b with Tyr, His, or Trp results in mutant complexes (F195Y, F195H, or F195W) having the same ubiquinol-cytochrome c reductase activity as the wild-type. These results indicate that the aromatic group at position195 of cytochrome b is involved in electron transfer reactions of the bc1 complex. The rate of superoxide anion (O2*) generation, measured by the chemiluminescence of 2-methyl-6-(p-methoxyphenyl)-3,7-dihydroimidazo[1,2-alpha]pyrazin-3-one hydrochloride-O2* adduct during oxidation of ubiquinol, is 3 times higher in the F195A complex than in the wild-type or mutant complexes Y199A or F203A. This supports the idea that the interruption of electron transfer between the two bL hemes enhances electron leakage to oxygen and thus decreases the ubiquinol-cytochrome c reductase activity.

Amino Acid Substitution↗

Structurally distinct T cell receptor complexes on developmentally distinct T cell populations in severe combined immunodeficiency mice expressing a TCR beta transgene.

T cell differentiation and TCR expression were assessed in severe combined immunodeficiency (SCID) mice possessing an already rearranged TCRV beta 8 transgene. Unlike nontransgenic SCID mice, TCRV beta 8-transgenic SCID mice contained a broad spectrum of T cell populations, including both immature thymocytes and mature T cells. In TCRV beta 8-transgenic SCID mice, immature CD4-CD8- and CD4+CD8+ thymocytes expressed surface TCR complexes structurally distinct from those expressed by mature single-positive T cells. Immature CD4+CD8+ thymocytes expressed surface TCR beta chains without a clonotypic TCR partner chain and largely without associated CD3 components. In contrast, mature single-positive T cells expressed fully assembled surface TCR complexes containing disulfide-linked heterodimers consisting of transgenic TCR beta chains and endogenous TCR alpha chains. The surface TCR complexes on mature T cells were associated with CD3 components and were competent to transduce TCR-mediated proliferative signals. Thus, T cells at different stages of development in TCRV beta 8-transgenic SCID mice express structurally distinct surface TCR complexes, demonstrating that the developmental stage achieved by T cells in these mice is related to the structure of the surface TCR complexes they express. Indeed, the present results indicate that successful differentiation into single-positive T cells requires surface expression of fully assembled TCR complexes.

Animals↗

Variation in mandible shape in Thrichomys apereoides (Mammalia: Rodentia): geometric analysis of a complex morphological structure.

The model of development and evolution of complex morphological structures conceived by Atchley and Hall in 1991 (Biol. Rev. 66:101-157), which establishes that changes at the macroscopic, morphogenetic level can be statistically detected as variation in skeletal units at distinct scales, was applied in combination with the formalism of geometric morphometrics to study variation in mandible shape among populations of the rodent species Thrichomys apereoides. The thin-plate spline technique produced geometric descriptors of shape derived from anatomical landmarks in the mandible, which we used with graphical and inferential approaches to partition the contribution of global and localized components to the observed differentiation in mandible shape. A major pattern of morphological differentiation in T. apereoides is attributable to localized components of shape at smaller geometric scales associated with specific morphogenetic units of the mandible. On the other hand, a clinical trend of variation is associated primarily with localized components of shape at larger geometric scales. Morphogenetic mechanisms assumed to be operating to produce the observed differentiation in the specific units of the mandible include mesenchymal condensation differentiation, muscle hypertrophy, and tooth growth. Perspectives for the application of models of morphological evolution and geometric morphometrics to morphologically based systematic biology are considered.

Animals↗

Solution and gelling properties of polysaccharide polyelectrolytes.

Attention is focussed on the special class of polysaccharide polyelectrolytes belonging to the family of the microbial polysaccharides. But a few exceptions, these are high molecular weight water- soluble polycarboxylates with complex, regular structures. Complexity and regularity in primary structure--two features normally not shared by other polysaccharides of either vegetal or animal origin--quite naturally entail unique conformational propensities, special physico-chemical properties in bulk and in solution and, as a consequence, make these biopolymers of particular interest from both a basic research and an industrial standpoint. What is outlined in this presentation should demonstrate that for many exocellular microbial polycarboxylates the solution properties are, as expected, dictated by the conformation assumed by the polyelectrolytic chains which, in turn, are governed by several free energy terms in particular stemming from specific solvent-chain interactions, among which the coulombic contribution may play a minor role.

Circular Dichroism↗

Structure elucidation of the tetrahydrocannabinol complex with randomly methylated beta-cyclodextrin.

The low aqueous solubility of the bioactive cannabinoid tetrahydrocannabinol (THC) is a serious obstacle for the development of more efficient administration forms. In this study the aqueous solubility of THC was tested in the presence of alpha-, beta- and gamma-CD, and randomly methylated beta-CD (RAMEB). It was found that only RAMEB was able to increase the aqueous solubility of THC to a significant level. A THC concentration of about 14 mg/ml was reached by using a 24% (187 mM) RAMEB solution, which means an increase in solubility of four orders of magnitude. The resulting THC/RAMEB complex was investigated through phase-solubility analysis, complemented by (1)H NMR, NOESY- and UV-studies in order to obtain details on the stoichiometry, geometry and thermodynamics of the complexation. The binding ratio of THC to CD was found to be 2:1, with the second THC molecule bound by non-inclusion interactions. Based on the obtained results a model for the complex structure is presented. Stability of the complex under laboratory room conditions was tested up to 8 weeks. Results show that complexation with RAMEB seems to be promising for the development of water-based THC formulations.

Dronabinol↗

Oxidative DNA cleavage mediated by a new copper (II) terpyridine complex: crystal structure and DNA binding studies.

The copper (II) complex [Cu(Itpy)(2)](ClO(4))(2) (1), (Itpy=imidazole terpyridine) has been synthesized and structurally characterized. Crystal structure of the complex shows the complex to be a monomeric copper (II) species with two Itpy ligands coordinated to the metal ion to give a six coordinate complex. The complex has a distorted octahedral geometry with axial elongation. Variable temperature crystal structure data shows dynamic nature of the Jahn-Teller distortion. The complex is an avid DNA binder with a binding constant of 4.26+/-0.20x10(3)M(-1). Observed changes in the viscosity and circular dichroic spectrum of calf thymus DNA solution in the presence of complex 1 suggests intercalative binding of complex 1 to DNA. The complex cleaves supercoiled pBR322 DNA oxidatively in the presence of hydrogen peroxide.

Animals↗