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DNA damage by copper(II) complexes: coordination-structural dependence of reactivities.

A variety of copper complexes with different structural features have been shown to bind double-helical DNA with binding constants of 10(4)-10(7) M-1 and to promote double-strand DNA damage upon reductant/H2O2 activation. The interaction of the Cu complex with DNA results in hyperchromism and shifts to longer wavelengths of the strongest transitions in the Cu complexes, as well as striking hypochromism or hyperchromism of DNA absorption at 260 nm. In the presence of DMPO as the spin trap, the solution of each copper complex exhibits typical four-line ESR spectra of the hydroxyl radical by adding 2-mercaptoethanol and H2O2 to the solution. Quantitation by 2-deoxy-D-ribose shows that the competence of hydroxyl radical generation by the copper complexes upon reductant and H2O2 activation decreases in order, that is, Cu(HTCD)(2+)-Cu(Im)4Cl2-Cu(IDB) (NO3)2 > Cu(IDB)Cl2 > Cu(IDBt)Cl2. The copper complex-mediated hydroxyl radical, a powerful oxidant that attacks the adjacent DNA, is responsible for the DNA oxidative damage. The lambda DNA damage chemistry illustrates that the competence and selectivity of double-strand lambda DNA damage by the copper complexes are dependent on their geometric structures and types of ligands. The decreasing order of the DNA damage capacity by the present complexes is Cu(Im)4Cl2-Cu(IDB)-(NO3)2 > Cu(HTCD)2+ > Cu(IDBt)Cl2 > Cu(IDB)Cl2.

Animals↗

Crystal structures of the vitamin D-binding protein and its complex with actin: structural basis of the actin-scavenger system.

Actin is the most abundant protein in eukaryotic cells, but its release from cells into blood vessels can be lethal, being associated with clinical situations including hepatic necrosis and septic shock. A homeostatic mechanism, termed the actin-scavenger system, is responsible for the depolymerization and removal of actin from the circulation. During the first phase of this mechanism, gelsolin severs the actin filaments. In the second phase, the vitamin D-binding protein (DBP) traps the actin monomers, which accelerates their clearance. We have determined the crystal structures of DBP by itself and complexed with actin to 2.1 A resolution. Similar to its homologue serum albumin, DBP consists of three related domains. Yet, in DBP a strikingly different organization of the domains gives rise to a large actin-binding cavity. After complex formation the three domains of DBP move slightly to "clamp" onto actin subdomain 3 and to a lesser extent subdomain 1. Contacts between actin and DBP throughout their extensive 3,454-A(2) intermolecular interface involve a mixture of hydrophobic, electrostatic, and solvent-mediated interactions. The area of actin covered by DBP within the complex approximately equals the sum of those covered by gelsolin and profilin. Moreover, certain interactions of DBP with actin mirror those observed in the actin-gelsolin complex, which may explain how DBP can compete effectively with gelsolin for actin binding. Formation of the strong actin-DBP complex proceeds with limited conformational changes to both proteins, demonstrating how DBP has evolved to become an effective actin-scavenger protein.

Actins↗

Beta-catenin-mediated cell-adhesion is vital for embryonic forebrain development.

Forming a complex structure such as the mammalian brain requires a complex interplay between cells and different signalling cascades during embryonic development. beta-catenin plays pivotal roles in these processes by mediating cadherin-based cell adhesion and Wnt signalling. We show for the first time that beta-catenin functions predominantly as a mediator of cell adhesion during early development of the mammalian telencephalon. Immunohistochemical analysis demonstrates that beta-catenin is localized, together with N-cadherin, to adhesion junctions at the apical lining of the neuroepithelium. The ablation of beta-catenin specifically from the forebrain leads to a disruption of apical adherens junctions and a breakdown of neuroepithelial structures. We show that beta-catenin-deficient neuroepithelial cells delaminate and undergo apoptosis. Newborn beta-catenin mutants lack the entire forebrain and anterior facial structures. Our data also indicate a lack of TCF/LEF-beta-catenin-dependent transcriptional activity in the telencephalon of Wnt reporter embryos. Together with the absence of nuclear beta-catenin, this finding suggests that canonical Wnt signalling is not active during early telencephalic development. In summary, we demonstrate that beta-catenin mediates cell-cell adhesion in the early telencephalon and is vital for maintaining the structural integrity of the neuroepithelium.

Adherens Junctions↗

Synthesis of [Ag(NH=CMe(2))(2)]ClO(4) and its use as a source of acetimine. 1. Synthesis of the first acetimine rhodium complexes and the first crystal structure of a diacetonamine complex.

The reaction of AgClO(4) and NH(3) in acetone gave [Ag(NH=CMe(2))(2)]ClO(4) (1). The reactions of 1 with [RhCl(diolefin)](2) or [RhCl(CO)(2)](2) (2:1) gave the bis(acetimine) complexes [Rh(diolefin)(NH=CMe(2))(2)]ClO(4) [diolefin = 1,5 cyclooctadiene = cod (2), norbornadiene = nbd (3)] or [Rh(CO)(2)(NH=CMe(2))(2)]ClO(4) (4), respectively. Mono(acetimine) complexes [Rh(diolefin)(NH=CMe(2))(PPh(3))]ClO(4) [diolefin = cod (5), nbd (6)] or [RhCl(diolefin)(NH=CMe(2))] [diolefin = cod (7), nbd (8)] were obtained by reacting 2 or 3 with PPh(3) (1:1) or with Me(4)NCl (1:1.1), respectively. The reaction of 4 with PR(3) (R = Ph, To, molar ratio 1:2) led to [Rh(CO)(NH=CMe(2))(PR(3))(2)]ClO(4) [R = Ph (9), C(6)H(4)Me-4 = To (10)] while cis-[Rh(CO)(NH=CMe(2))(2)(PPh(3))]ClO(4) (11) was isolated from the reaction of 1 with [RhCl(CO)(PPh(3))](2) (1:1). The crystal structures of 5 and [Ag[H(2)NC(Me)(2)CH(2)C(O)Me](PTo(3))]ClO(4) (A), a product obtained in a reaction between NH(3), AgClO(4), and PTo(3), have been determined.

Journal Article↗

Glycomics: a pathway to a class of new and improved therapeutics.

Complex glycans that are located at the surface of cells, deposited in the extracellular matrix and attached to soluble signalling molecules have a crucial role in the phenotypic expression of cellular genotypes. However, owing to their structural complexity and some redundancy in terms of structures that elicit a function, the therapeutic potential of complex glycans has not been well exploited, with a few notable exceptions. This review outlines recent advances that promise to increase our ability to use complex glycans as therapeutics. Opportunities for the development of further structure-function relationships for these complex molecules are also discussed.

Animals↗

Temporal patterns of neurogenesis in avian cranial sensory and autonomic ganglia.

Avian cranial sensory ganglia are embryonically derived from neural crest and epidermal placodes. Cells from these two populations interact with each other and with other components of their environment to influence the complex structural and functional organization of the ganglia. To help understand these processes, the times of terminal mitosis of cranial sensory neuroblasts were established. Birthdate patterns within each ganglion are described with particular attention given to the structural organization of the VII-VIII ganglionic complex. Birthdate information on cranial autonomic ganglia is also included. Chick embryos ranging in age from 1 to 8 days of incubation were treated with 3H-thymidine and sacrificed on embryonic day 8, 10, or 18. Large, placode-derived neurons are generated between days 2 and 5 of incubation. Embryonically smaller, neural crest-derived cells leave the proliferative pool between days 4 and 7. Neurons of the acoustic ganglion cease their mitotic activity in an apical to basal fashion and are the only placodal neurons to form later than day 5. Of the cranial autonomic ganglia, the period of neuron production is best defined for the ciliary ganglion, where it is 2.5-5.5 days of incubation. Most later-dividing neuroblasts in the ciliary ganglion belong to the choroid cell population. Temporal patterns of neurogenesis are discussed in relationship to other aspects of sensory gangliogenesis including embryonic origin of neurons, condensation of ganglionic anlagen, cell degeneration, and cytological characteristics of mature ganglia.

Animals↗

Determination of extracellular/intracellular fluid ratios from magnetic resonance images: accuracy, feasibility, and implementation.

This study determines the accuracy and feasibility of using localized spin-lattice (T1) relaxation time measurements from magnetic resonance (MR) images to follow changes in extracellular/intracellular fluid ratios in defined subvolumes of living tissue. A red blood cell suspension was used as a test system and a simple two-compartment model incorporating fast exchange was found to suffice for the conversion of T1 values to volume ratios. The technique requires the addition of gadolinium-DTPA to the model system to selectively enhance relaxation in the extracellular fluid space. No detectable amount of gadolinium-DTPA was found to enter the intracellular fluid space, and all magnetization decay plots obtained from both intracellular constituents and complete RBC suspensions consisted of a single exponential. Both of these results are compatible with assumptions underlying our physical model. The NMR-determined fluid ratio values were compared to those measured via the microhematocrit technique. Partial saturation image-mode determinations are strongly correlated to microhematocrit data (R2 = 0.945) and indicate that localized cell volume changes may be followed with a sensitivity of +/- 2.2%. These values compare favorably with those produced when nonimaging inversion-recovery techniques are used to determine the MR hematocrit (R2 = 0.962, sensitivity = +/- 1.1%). This technique, with modification, should be applicable to the comparison of ratios of extracellular/intracellular fluid volumes in structurally complex tissues where small subvolumes of homogeneous cell structure could be examined.

Body Fluids↗

[Agrarian overpopulation and household structure in Saguenay (1881-1931)].

"Our paper investigates the effect of land shortage in the Saguenay region [of Quebec, Canada,] upon the household structures, more precisely on the frequency of a) complex structures, b) celibacy, c) cohabitation with strangers (non-relatives). The data come from 28 parish censuses of the period 1881-1931. For each of these three indicators, findings show that the saturation of arable land did not entail significant changes." (SUMMARY IN ENG)

Agriculture↗

Lipid polymorphism as observed by cryo-electron microscopy.

Lipid polymorphism was studied with the aim to gain more insight in bilayer to non-bilayer phase transitions, with particular emphasis on the development of cubic structures on one hand and inverted hexagonal structures on the other hand. Thin vitrified films prepared from aqueous lipid suspensions were used in this study. The entire hydrated contents of these films can be visualized in their two-dimensional projection by cryo-electron microscopy. As the starting material, unilamellar vesicles were prepared from mixtures of dioleoylphosphatidylethanolamine, dioleoylphosphatidylcholine and cholesterol. By heating of the suspension, vesicle fusion (Frederik et al. (1989) Biochim. Biophys. Acta 979, 275-278) and lipid polymorphism was induced. From these suspensions thin films were prepared at various temperatures, and vitrified for low temperature observation. In a parallel series of experiments samples were fast-frozen for freeze-fracture analysis. In vitrified thin films bilayer structures were often observed in coexistence with an inverted hexagonal structure. The bilayer areas were frequently of a complex structure because multiple contacts between stacked membranes were found. These contact points were variable in size and shape and usually had the form of a diabolo (when viewed side-on) giving the impression of a bilayer contact with an aqueous channel. This structure is compatible with the interlamellar attachment site (ILA) proposed by Siegel ((1986) Biophys. J. 49, 1155-1170). In some specimens ILA's seemed to merge into arrays. After thermal cycling of the suspension, arrays of packed globules were observed, which are likely the result of close packing of ILA's. The arrays probably represent a cubic structure. A comparison of freeze-fracture replicas and vitrified thin films indicated that both techniques may provide valuable structural information on lipid polymorphism. Most of the lipidic particles observed by freeze-fracturing probably correspond to the ILA's (fractured around their waist region) as observed in vitrified thin films. The results obtained with vitrified thin films were interpreted in relation to the principles of thin-film formation. Finally, we speculate that lipid structures occurring close to each other in space may represent a developmental series of structures occurring successively in time.

Cholesterol↗

Non-random structural chromosomal changes in ovarian cancer: i(5p) a novel recurrent abnormality.

Ovarian cancer represents the leading cause of death among patients with gynecological cancer. The genetic changes underlying the initiation and progression of ovarian cancer have not been well defined. However, non-random structural chromosomal changes have been identified with common chromosomal breakpoints. We have studied cytogenetically 15 cases of ovarian adenocarcinomas by a direct culture of cancer cells and a G-banding technique investigating the presence of recurrent structural aberrations with common chromosomal breakpoints. Among very complex structural rearrangements found, we could recognize recurrent structural aberrations involving according to frequency chromosomal regions 3p13-14, 11p15, 19q13, 3q21, 11q23, 11q10, 1p13, 1p36, and 17q24-25. Isochromosomes i(5p), i(17q), i(8q) and i(11q) were also observed. Isochromosome i(5p), rarely reported in ovarian cancer was found in seven cases suggesting that it may be a novel recurrent abnormality. Translocations t(1;11), t(3;19), t(3;17), t(7;11) and t(11;17) were also identified. Conventional cytogenetics continues to be valuable detecting the presence of non-random chromosomal breakpoints and facilitating the identification of genes implicated in tumorigenesis.

Adenocarcinoma↗

Recursive self-organizing network models.

Self-organizing models constitute valuable tools for data visualization, clustering, and data mining. Here, we focus on extensions of basic vector-based models by recursive computation in such a way that sequential and tree-structured data can be processed directly. The aim of this article is to give a unified review of important models recently proposed in literature, to investigate fundamental mathematical properties of these models, and to compare the approaches by experiments. We first review several models proposed in literature from a unifying perspective, thereby making use of an underlying general framework which also includes supervised recurrent and recursive models as special cases. We shortly discuss how the models can be related to different neuron lattices. Then, we investigate theoretical properties of the models in detail: we explicitly formalize how structures are internally stored in different context models and which similarity measures are induced by the recursive mapping onto the structures. We assess the representational capabilities of the models, and we shortly discuss the issues of topology preservation and noise tolerance. The models are compared in an experiment with time series data. Finally, we add an experiment for one context model for tree-structured data to demonstrate the capability to process complex structures.

Artifacts↗

Structural basis of ubiquitin recognition by the deubiquitinating protease USP2.

Deubiquitinating proteases reverse protein ubiquitination and rescue their target proteins from destruction by the proteasome. USP2, a cysteine protease and a member of the ubiquitin specific protease family, is overexpressed in prostate cancer and stabilizes fatty acid synthase, which has been associated with the malignancy of some aggressive prostate cancers. Here, we report the structure of the human USP2 catalytic domain in complex with ubiquitin. Ubiquitin uses two major sites for the interaction with the protease. Both sites are required simultaneously, as shown by USP2 inhibition assays with peptides and ubiquitin mutants. In addition, a layer of ordered water molecules mediates key interactions between ubiquitin and USP2. As several of those molecules are found at identical positions in the previously solved USP7/ubiquitin-aldehyde complex structure, we suggest a general mechanism of water-mediated ubiquitin recognition by USPs.

Amino Acid Sequence↗

X-ray structure of 12-oxophytodienoate reductase 1 provides structural insight into substrate binding and specificity within the family of OYE.

BACKGROUND: 12-Oxophytodienoate reductase (OPR) is a flavin mononucleotide (FMN)-dependent oxidoreductase in plants that belongs to the family of Old Yellow Enzyme (OYE). It was initially characterized as an enzyme involved in the biosynthesis of the plant hormone jasmonic acid, where it catalyzes the reduction of the cyclic fatty acid derivative 9S,13S-12-oxophytodienoate (9S,13S-OPDA) to 1S,2S-3-oxo-2(2'[Z]-pentenyl)-cyclopentane-1-octanoate. Several isozymes of OPR are now known that show different stereoselectivities with regard to the four stereoisomers of OPDA. RESULTS: Here, we report the high-resolution crystal structure of OPR1 from Lycopersicon esculentum and its complex structures with the substrate 9R,13R-OPDA and with polyethylene glycol 400. OPR1 crystallizes as a monomer and folds into a (betaalpha)(8) barrel with an overall structure similar to OYE. The cyclopentenone ring of 9R,13R-OPDA is stacked above the flavin and activated by two hydrogen bonds to His187 and His190. The olefinic bond is properly positioned for hydride transfer from the FMN N(5) and proton transfer from Tyr192 to Cbeta and Calpha, respectively. Comparison of the OPR1 and OYE structures reveals striking differences in the loops responsible for binding 9R,13R-OPDA in OPR1. CONCLUSIONS: Despite extensive biochemical characterization, the physiological function of OYE still remains unknown. The similar catalytic cavity structures and the substrate binding mode in OPR1 strongly support the assumption that alpha,beta-unsaturated carbonyl compounds are physiological substrates of the OYE family. The specific binding of 9R,13R-OPDA by OPR1 explains the experimentally observed stereoselectivity and argues in favor of 9R,13R-OPDA or a structurally related oxylipin as natural substrate of OPR1.

Binding Sites↗

Structure determination of a membrane protein with two trans-membrane helices in aligned phospholipid bicelles by solid-state NMR spectroscopy.

The structure of the membrane protein MerFt was determined in magnetically aligned phospholipid bicelles by solid-state NMR spectroscopy. With two trans-membrane helices and a 10-residue inter-helical loop, this truncated construct of the mercury transport membrane protein MerF has sufficient structural complexity to demonstrate the feasibility of determining the structures of polytopic membrane proteins in their native phospholipid bilayer environment under physiological conditions. PISEMA, SAMMY, and other double-resonance experiments were applied to uniformly and selectively (15)N-labeled samples to resolve and assign the backbone amide resonances and to measure the associated (15)N chemical shift and (1)H-(15)N heteronuclear dipolar coupling frequencies as orientation constraints for structure calculations. (1)H/(13)C/(15)N triple-resonance experiments were applied to selectively (13)C'- and (15)N-labeled samples to complete the resonance assignments, especially for residues in the nonhelical regions of the protein. A single resonance is observed for each labeled site in one- and two-dimensional spectra. Therefore, each residue has a unique conformation, and all protein molecules in the sample have the same three-dimensional structure and are oriented identically in planar phospholipid bilayers. Combined with the absence of significant intensity near the isotropic resonance frequency, this demonstrates that the entire protein, including the loop and terminal regions, has a well-defined, stable structure in phospholipid bilayers.

Amino Acid Sequence↗

Clarifying boundary issues in psychopathology: the role of taxometrics in a comprehensive program of structural research.

Despite decades of debate, important questions about the boundaries that separate psychological disorder from normality and that distinguish 1 disorder from another remain largely unanswered. These issues pose empirical questions that may be addressed by assessing the latent structure of psychopathological constructs. Because these constructs are likely to be structurally complex, and no single statistical tool addresses all structural questions, it is proposed in this article that boundary issues be examined through programmatic research grounded in the taxometric method and elaborated by complementary analyses. The authors describe how such a program could delimit the structure of disorders and test competing explanations of diagnostic co-occurrence, emphasizing the potential to enhance the reliability and validity of assessment, maximize the power of research designs, and improve diagnostic classification.

Classification↗

The crystal and molecular structure of an intermolecular complex between riboflavin and an adenosine derivative.

Riboflavin and the adenosine derivative 5'-bromo-5'-deoxyadenosine form a crystalline 1:1 intermolecular complex, the structure of which has been solved by x-ray diffraction analysis. The adenine ring is found to be joined by two hydrogen bonds to the uracillike end of the riboflavin isoalloxazine ring. In addition, the riboflavin and the adenosine molecules associate through the formation of stacks of alternating parallel adenine and isoalloxazine rings. These intermolecular associations are considered to be models for intramolecular association in the coenzyme flavin adenine dinucleotide (FAD), which contains both adenosine and riboflavin.

Adenosine↗

Seismology and geodesy of the sun: Low-frequency oscillations.

The hourly averages of the solar ellipticity measured from June 13 to Sept. 17, 1966, are analyzed for indications of solar oscillations with periods in excess of 2 hr nu < 0.5 hr(-1). Nothing significant is found for frequencies nu > 0.1 hr(-1) but for lower frequencies the power spectrum shows a very complex structure containing about 20 strong narrow peaks. The complexity is illusionary. The signal apparently consists of only two frequencies. The complexity is due to aliasing by the window function with its basic 24-hr period, with many observational days missing, and with different numbers of hourly averages for the various observational days. Both signal frequencies are apparently due to odd-degree spherical harmonic oscillations of the sun.

Journal Article↗

Prediction of consensus structural motifs in a family of coregulated RNA sequences.

Given a set of homologous or functionally related RNA sequences, the consensus motifs may represent the binding sites of RNA regulatory proteins. Unlike DNA motifs, RNA motifs are more conserved in structures than in sequences. Knowing the structural motifs can help us gain a deeper insight of the regulation activities. There have been various studies of RNA secondary structure prediction, but most of them are not focused on finding motifs from sets of functionally related sequences. Although recent research shows some new approaches to RNA motif finding, they are limited to finding relatively simple structures, e.g. stem-loops. In this paper, we propose a novel genetic programming approach to RNA secondary structure prediction. It is capable of finding more complex structures than stem-loops. To demonstrate the performance of our new approach as well as to keep the consistency of our comparative study, we first tested it on the same data sets previously used to verify the current prediction systems. To show the flexibility of our new approach, we also tested it on a data set that contains pseudoknot motifs which most current systems cannot identify. A web-based user interface of the prediction system is set up at http://bioinfo. cis.nctu.edu.tw/service/gprm/.

Algorithms↗