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 1,027 records · Page 57Linked to original sources
PubMed2005

Human transthyretin in complex with iododiflunisal: structural features associated with a potent amyloid inhibitor.

Ex vivo and in vitro studies have revealed the remarkable amyloid inhibitory potency and specificity of iododiflunisal in relation to transthyretin [Almeida, Macedo, Cardoso, Alves, Valencia, Arsequell, Planas and Saraiva (2004) Biochem. J. 381, 351-356], a protein implicated in familial amyloidotic polyneuropathy. In the present paper, the crystal structure of transthyretin complexed with this diflunisal derivative is reported, which enables a detailed analysis of the protein-ligand interactions. Iododiflunisal binds very deep in the hormone-binding channel. The iodine substituent is tightly anchored into a pocket of the binding site and the fluorine atoms provide extra hydrophobic contacts with the protein. The carboxylate substituent is involved in an electrostatic interaction with the N(zeta) of a lysine residue. Moreover, ligand-induced conformational alterations in the side chain of some residues result in the formation of new intersubunit hydrogen bonds. All these new interactions, induced by iododiflunisal, increase the stability of the tetramer impairing the formation of amyloid fibrils. The crystal structure of this complex opens perspectives for the design of more specific and effective drugs for familial amyloidotic polyneuropathy patients.

Amyloid↗
PubMed1986

The sucrase-isomaltase complex: primary structure, membrane-orientation, and evolution of a stalked, intrinsic brush border protein.

The complete primary structure (1827 amino acids) of rabbit intestinal pro-sucrase-isomaltase (pro-SI) was deduced from the sequence of a nearly full-length cDNA. Pro-SI is anchored in the membrane by a single 20 amino acid segment spanning the bilayer only once. The amino-terminal, cytoplasmic domain consists of 12 amino acids and is not preceded by a cleaved leader sequence. This suggests a dual role for the membrane-spanning segment as an uncleaved signal for membrane insertion. This is followed by a 22 residue serine/threonine-rich, probably glycosylated, stretch, presumably forming the stalk on which the globular, catalytic domains are directed into the intestinal lumen. Following this is a high degree of homology between the isomaltase and sucrase portions (41% amino acid identity), indicating that pro-SI evolved by partial gene duplication.

Amino Acid Sequence↗
PubMed2006

The impact of exploiting grazers (Scaridae) on the dynamics of Caribbean coral reefs.

Coral reefs provide a number of ecosystem services including coastal defense from storms, the generation of building materials, and fisheries. It is increasingly clear that the management of reef resources requires an ecosystem approach in which extractive activities are weighed against the needs of the ecosystem and its functions rather than solely those of the fishery. Here, I use a spatially explicit simulation model of a Caribbean coral reef to examine the ecosystem requirements for grazing which is primarily conducted by parrotfishes (Scaridae). The model allows the impact of fishing grazers to be assessed in the wider context of other ecosystem processes including coral-algal competition, hurricanes, and mass extinction of the herbivorous urchin Diadema antillarum. Using a new analytical model of scarid grazing, it is estimated that parrotfishes can only maintain between 10% and 30% of a structurally complex forereef in a grazed state. Predictions from this grazing model were then incorporated into a broader simulation model of the ecosystem. Simulations predict that scarid grazing is unable to maintain high levels of coral cover (> or = 30%) when severe hurricanes occur on a decadal basis, such as occurs in parts of the northern Caribbean. However, reefs can withstand such intense disturbance when grazing is undertaken by both scarids and the urchin Diadema. Scarid grazing is predicted to allow recovery from hurricanes when their incidence falls to 20 years or less (e.g., most of Central and South America). Sensitivity analyses revealed that scarid grazing had the most acute impact on model behavior, and depletion led to the emergence of a stable, algal-dominated community state. Under conditions of heavy grazer depletion, coral cover was predicted to decline rapidly from an initial level of 30% to less than 1% within 40 years, even when hurricane frequency was low at 60 years. Depleted grazers caused a population bottleneck in juvenile corals in which algal overgrowth caused elevated levels of postsettlement mortality and resulted in a bimodal distribution of coral sizes. Several new hypotheses were generated including a region-wide change in the spatial heterogeneity of coral reefs following extinction of Diadema. The management of parrotfishes on Caribbean reefs is usually approached implicitly through no-take marine reserves. The model predicts that depletion of grazers in nonreserve areas can severely limit coral accretion. Other studies have shown that low coral accretion can reduce the structural complexity and therefore quality of the reef habitat for many organisms. A speculative yet rational inference from the model is that failure to manage scarid populations outside reserves will have a profoundly negative impact on the functioning of the reserve system and status of non-reserve reefs.

Animals↗
PubMed2003

Complex haplotypic structure of the central MHC region flanking TNF in a West African population.

TNF polymorphisms have been associated with susceptibility to malaria and other infectious and inflammatory conditions. We investigated a sample of 150 West African chromosomes to determine linkage disequilibrium (LD) between 25 SNP markers located in an 80 kb segment of the MHC Class III region encompassing TNF and eight neighbouring genes. We observed 45 haplotypes, and 22 of them comprise 80% of the sample. The pattern of LD is remarkably patchy, such that many markers show no LD with adjacent markers but high LD with markers that are much further away. We introduce a method of examining the implications of LD data for disease association studies based on sample size considerations: this shows that certain TNF polymorphisms would be likely to yield positive associations if the true disease allele resided in LTA or BAT1. We conclude that detailed marker maps are needed to resolve the causal origin of disease associations observed at the TNF locus.

Adult↗
PubMed2006

4-arylazo-3,5-diamino-1H-pyrazole CDK inhibitors: SAR study, crystal structure in complex with CDK2, selectivity, and cellular effects.

In a routine screening of our small-molecule compound collection we recently identified 4-arylazo-3,5-diamino-1H-pyrazoles as a novel group of ATP antagonists with moderate potency against CDK2-cyclin E. A preliminary SAR study based on 35 analogues suggests ways in which the pharmacophore could be further optimized, for example, via substitutions in the 4-aryl ring. Enzyme kinetics studies with the lead compound and X-ray crystallography of an inhibitor-CDK2 complex demonstrated that its mode of inhibition is competitive. Functional kinase assays confirmed the selectivity toward CDKs, with a preference for CDK9-cyclin T1. The most potent inhibitor, 4-[(3,5-diamino-1H-pyrazol-4-yl)diazenyl]phenol 31b (CAN508), reduced the frequency of S-phase cells of the cancer cell line HT-29 in antiproliferation assays. Further observed cellular effects included decreased phosphorylation of the retinoblastoma protein and the C-terminal domain of RNA polymerase II, inhibition of mRNA synthesis, and induction of the tumor suppressor protein p53, all of which are consistent with inhibition of CDK9.

Antimetabolites↗
PubMed1996

Affinity and structure of complexes of tropomyosin and caldesmon domains.

The interaction of caldesmon domains with tropomyosin has been studied using x-ray crystallography and an optical biosensor. Only whole caldesmon and the carboxyl-terminal domain of caldesmon (CaD-4, chicken gizzard residues 597-756) bound to tropomyosin with greater than millimolar affinity at 100 and 150 microM salt. Under these conditions the affinities of whole caldesmon and CaD-4 were both in the micromolar range. Data from the x-ray studies showed that whole caldesmon bound to tropomyosin in several places, with the region of tightest interaction being at tropomyosin residues 70-100 and/or 230-260. Studies with CaD-4 revealed that this region corresponded to the strong binding site seen with whole caldesmon. Weaker association of other regions of caldesmon to tropomyosin residues 180-210 and 5-50 was also observed. The results suggest that the carboxyl-terminus of caldesmon binds tightly to tropomyosin and that other regions of caldesmon may interact with tropomyosin tightly only when they are held close to tropomyosin by the carboxyl-terminal domain. Four models are presented to show the possible interactions of caldesmon with tropomyosin.

Animals↗
PubMed1991

Characterization of the memory gene dunce of Drosophila melanogaster.

The dunce (dnc) gene of Drosophila melanogaster encodes cAMP phosphodiesterase (PDEase) and is required for learning/memory and female fertility. The gene is structurally complex, demonstrated in part by Northern blotting experiments which detected multiple RNAs ranging in size from 4.2 to 9.6 kb (1 kb = 10(3) bases or base-pairs). To characterize these RNAs and to understand their sequence heterogeneity, we isolated and analyzed 29 new and independent cDNA clones representing the dnc RNAs. Restriction mapping, hybridization analysis and sequence determination of these cDNA clones and the corresponding genomic exons resolved these into six different classes. Exons defined by the cDNA clones are distributed over more than 148 kb of genomic DNA, with some exons being used alternatively among the RNAs. The RNAs are transcribed from at least three initiation sites: two of these were mapped by parallel S1-nuclease and primer extension experiments. In addition, some of the heterogeneity is generated by using varying lengths of a 3'-untranslated trailer sequence. Altogether, the results indicate that the size and sequence heterogeneity of dnc transcripts results from transcription initiation at multiple sites, alternative splicing, and processes which generate different 3' ends. The existence of multiple protein products is suggested by the alternative use of exons which code for portions of the open reading frame. The protein variation potentially includes N-terminal differences coded for by transcript-specific 5' exons and internal differences arising from the optional inclusion of a 39 base-pair exon and from the alternative use of two 3' splice sites separated by six base-pairs. Expression of a cDNA clone in yeast containing a large portion of the open reading frame produced cAMP PDEase activity identical in properties to the Drosophila enzyme affected by the dnc mutation. The results suggest that the remarkable structural complexity of dnc may reflect an intricate control of the spatial and/or temporal expression of various isoforms of cAMP PDEase.

3',5'-Cyclic-AMP Phosphodiesterases↗
PubMed2003

Computational study of the halogen atom-benzene complexes.

The structures of halogen atom-benzene complexes were investigated by modern DFT and ab initio computational methods. The spectroscopic properties of the complexes are also predicted and are in good agreement with experiment where such data have been reported. The fluorine atom-benzene complex is predicted to be a sigma complex due to the strength of a C-F bond. The chlorine atom-benzene complex is predicted to have an eta(1) pi complex structure, which is only slightly more favorable (1.1 kcal/mol with the BH&HLYP/6-311++G method including the ZPE correction) than a sigma complex but is significantly more stable (4.4 kcal/mol with the BH&HLYP/6-311++G method including the ZPE correction) than the eta(6) pi complex. The bromine and iodine benzene complexes are also predicted to prefer an eta(1) pi complex structure.

Journal Article↗
PubMed1984

HLA-A2 antigen phosphorylation in vitro by cyclic AMP-dependent protein kinase. Sites of phosphorylation and segmentation in class i major histocompatibility complex gene structure.

The heavy chain of the HLA-A2 antigen is phosphorylated by cyclic AMP-dependent protein kinase at two serine residues of the intracellular region. Limited proteolysis was performed on purified [32P]HLA-A2 antigens in order to define the sites of phosphorylation. Both of the phosphorylated serine residues are located in the carboxyl terminus of the heavy chain; one is encoded by exon 5, while the other is encoded by exon 6. The phosphoserine encoded by exon 5 is part of the conserved sequence Arg-Arg-Lys-Ser-Ser. This protein sequence contains the proper arrangement of amino acids for recognition and phosphorylation by the catalytic subunit of cyclic AMP-dependent protein kinase. In the murine class I antigens (H-2), exon 5 encodes a similar sequence of basic residues followed by one intervening residue and a threonine rather than a serine residue in the last amino acid position. A composite figure is presented that compares the carboxyl-terminal sequences of human and murine class I antigens and illustrates the known sites of phosphorylation recognized by various kinases. Each site of phosphorylation in the carboxyl terminus is contained within a conserved protein sequence encoded by one of the three exons. A separation and preservation of unique sites of phosphorylation could explain why there is segmentation in the genomic arrangement of class I molecules.

Amino Acid Sequence↗
PubMedDate not supplied

Imaging of complex NMR spectra.

The Point Spread Function (PSF) in NMR imaging is the result of both the line broadening due to magnet field inhomogeneity and the intrinsic spectrum of the nucleus at resonance. In the case of proton imaging, the line broadening dominates the small chemical shifts and the spectral lines are not resolved. This is not generally the case with other nuclei having strong chemical shifts and the PSF then has a complex structure. During imaging, the complex PSF is convolved with the spatial distribution of the nucleus at resonance and this leads to halo artifacts which are dependent on the imaging technique employed. The images due to the ensemble of spectral lines can be separated in principle by deconvolution of the data with the PSF before reconstruction. In the special case where the complex PSF is spatially independent, it can be obtained from the Free Induction Decay (FID) data produced in the absence of a spatially encoding gradient field. This technique has been successfully applied to in-vivo imaging of exogenous perfluorocarbon material.

Animals↗
PubMed2005

Synthesis, crystal structure and nuclease activity of a Schiff base copper(II) complex.

A new Schiff base copper(II) complex, Cu(o-VANAHE)(2) (o-VANAHE = 2-(o-vanillinamino)-1-hydroxyethane), has been synthesized and characterized. Single crystal X-ray diffraction results suggest that this complex structure belongs to triclinic crystal system, space group P1 with the following crystallographic parameters: a = 8.819(4) angstroms, b = 10.794(5) angstroms, c = 11.350(5) angstroms, alpha = 70.262(6) degrees, beta = 70.816(6) degrees, gamma = 78.360(6) degrees, V = 955.4(7) angstroms3, Z = 2, D(c) = 1.571 Mg x m(-3), and the final R1 = 0.0393, wR2 = 0.0994 for the observed reflections 2620(I > 2sigma(I)). The molecular geometry is almost coplanar. Viscosity, fluorescence spectroscopy and cyclic voltammetry have been conducted to assess their interaction between this complex and DNA. Results showed that the copper(II) complex can increase DNA's relative viscosity and quench the fluorescence intensity of EB bound to DNA. The adding of DNA to the solution of Cu(o-VANAHE)2 causes a slight decrease in the voltammetric current, as well as a slight shift in the E(1/2) to less negative potential. The interaction between the complex and DNA has also been investigated by submarine gel electrophoresis, interestingly, we found that the copper(II) complex can cleave circular plasmid pBR322 DNA to nicked and linear forms.

Copper↗
PubMed1992

Drug binding to higher ordered DNA structures: netropsin complexation with a nucleic acid triple helix.

We have used a combination of spectroscopic and calorimetric techniques to characterize how netropsin, a ligand that binds in the minor groove of DNA, influences the properties of a DNA triple helix. Specifically, our data allow us to reach the following conclusions: (i) netropsin binds to the triplex without displacing the major-groove-bound third strand; (ii) netropsin binding to the triplex exhibits a lower saturation binding density (7.0 base triplets per netropsin bound) than netropsin binding to the corresponding duplex (5.5 base pairs per netropsin bound); (iii) the netropsin-free and the netropsin-bound triplexes each melt in two well-resolved transitions, initial conversion of the triplex to the duplex state followed by duplex melting to the component single-stranded states; (iv) netropsin remains bound to DNA as the triplex melts to the duplex state; (v) netropsin binding thermally destabilizes the triplex in equilibrium with duplex equilibrium dramatically, while thermally stabilizing the duplex to single-strand equilibrium; (vi) netropsin binding to the triplex is enthalpically 4 times more favorable (more exothermic) than netropsin binding to the corresponding duplex; (vii) netropsin binding to the triplex decreases the cooperativity of the triplex----duplex melting event. These results demonstrate that occupancy of the minor groove of a triplex by a ligand such as netropsin can exert a profound impact on the properties of the host triplex, particularly with regard to the equilibrium in which the third strand is expelled from the major groove. Thus, our results reveal considerable major groove/minor groove crosstalk. Such knowledge may prove of practical importance by providing an approach for modulating the affinity and specificity of major-groove-binding third strands in triplex-forming protocols designed to target specific duplex domains. Fundamentally, our results provide insights into the crosstalk that can result when ligands bind to the two major receptor sites of duplex DNA--namely, the major and minor grooves.

Calorimetry, Differential Scanning↗
PubMed1983

Solution conformation of asparagine-linked oligosaccharides: alpha(1-6)-linked moiety.

The solution conformation is presented for representatives of each of the major classes of asparaginyl oligosaccharides. In this report the conformation of the alpha(1-6)-linked moiety is described. The conformational properties of these glycopeptides were determined by high-resolution 1H nuclear magnetic resonance in conjunction with potential energy calculations. The NMR parameters that were used in this analysis were chemical shifts and nuclear Overhauser enhancements. Potential energy calculations were used to evaluate the preferred conformers available for the different linkages in glycopeptides and to draw conclusions and to draw conclusions about the behavior in solution of these molecules. For all classes, identical conformations were found for the 6-arm except for the torsional angle, omega, about the C5-C6 bond of the alpha 1-6 linkage. For high mannose and hybrid structures omega was found to be -60 degrees, for bisected biantennary complex structures omega was 180 degrees, and for complex biantennary structures averaging between -60 degrees and 180 degrees occurs.

Asparagine↗
PubMed1997

T-cell receptor structure and TCR complexes.

The first crystal structures of intact T-cell receptors (TCRs) and their complexes with MHC peptide antigens (pMHC) were reported during the past year, along with those of a single-chain TCR Fv fragment and a beta-chain complexed with two different bacterial superantigens. These structures have shown the similarities and differences in the architecture of the antigen-binding regions of TCRs and antibodies, and how the TCR interacts with pMHC ligands as well as with superantigens.

Animals↗
PubMed1979

Complex factorial structure of Ellis' Irrational Beliefs.

Previous research with a newly developed children's scale for measuring Ellis' constructs with regard to irrational beliefs showed that while the scale clearly reflected theoretically predicted developmental trends, the internal consistency reliability of the overall 11-item scale was relatively low (.56). This low internal consistency suggested that the 11 items were in fact heterogeneous and were not measuring a single, univocal, construct. An exploratory factor analysis was performed on the responses of 788 fifth-through thirteenth-grade students. Results of the Alpha factor and analysis clearly indicate that the scale is multifaceted, i.e., comprised of four orthogonal, interpretable factors. Estimates of internal consistency reliabilities for the separate factors, when corrected for length, revealed that each of the new factors was more reliable than the full scale score in this sample. Potential revisions of the scale, as well as cautions for its use in clinical applications on its present form are discussed.

Adolescent↗