Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in

2015-07-28

Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging themore » ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.« less

Structural, electronic, and optical properties of the C-C complex in bulk silicon from first principles

NASA Astrophysics Data System (ADS)

Timerkaeva, Dilyara; Attaccalite, Claudio; Brenet, Gilles; Caliste, Damien; Pochet, Pascal

2018-04-01

The structure of the CiCs complex in silicon has long been the subject of debate. Numerous theoretical and experimental studies have attempted to shed light on the properties of these defects that are at the origin of the light emitting G-center. These defects are relevant for applications in lasing, and it would be advantageous to control their formation and concentration in bulk silicon. It is therefore essential to understand their structural and electronic properties. In this paper, we present the structural, electronic, and optical properties of four possible configurations of the CiCs complex in bulk silicon, namely, the A-, B-, C-, and D-forms. The configurations were studied by density functional theory and many-body perturbation theory. Our results suggest that the C-form was misinterpreted as a B-form in some experiments. Our optical investigation also tends to exclude any contribution of A- and B-forms to light emission. Taken together, our results suggest that the C-form could play an important role in heavily carbon-doped silicon.

The structure of the yeast plasma membrane SNARE complex reveals destabilizing water-filled cavities.

PubMed

Strop, Pavel; Kaiser, Stephen E; Vrljic, Marija; Brunger, Axel T

2008-01-11

SNARE proteins form a complex that leads to membrane fusion between vesicles, organelles, and plasma membrane in all eukaryotic cells. We report the 1.7A resolution structure of the SNARE complex that mediates exocytosis at the plasma membrane in the yeast Saccharomyces cerevisiae. Similar to its neuronal and endosomal homologues, the S. cerevisiae SNARE complex forms a parallel four-helix bundle in the center of which is an ionic layer. The S. cerevisiae SNARE complex exhibits increased helix bending near the ionic layer, contains water-filled cavities in the complex core, and exhibits reduced thermal stability relative to mammalian SNARE complexes. Mutagenesis experiments suggest that the water-filled cavities contribute to the lower stability of the S. cerevisiae complex.

Fiber Diffraction of the Prion-Forming Domain HET-s(218-289) Shows Dehydration-Induced Deformation of a Complex Amyloid Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wan, William; Stubbs, Gerald

2014-05-01

Amyloids are filamentous protein aggregates that can be formed by many different proteins and are associated with both disease and biological functions. The pathogenicities or biological functions of amyloids are determined by their particular molecular structures, making accurate structural models a requirement for understanding their biological effects. One potential factor that can affect amyloid structures is hydration. Previous studies of simple stacked β-sheet amyloids have suggested that dehydration does not impact structure, but other studies indicated dehydration-related structural changes of a putative water-filled nanotube. Our results show that dehydration significantly affects the molecular structure of the fungal prion-forming domain HET-s(218–289),more » which forms a β-solenoid with no internal solvent-accessible regions. The dehydration-related structural deformation of HET-s(218–289) indicates that water can play a significant role in complex amyloid structures, even when no obvious water-accessible cavities are present.« less

Molecular architecture of the TRAPPII complex and implications for vesicle tethering.

PubMed

Yip, Calvin K; Berscheminski, Julia; Walz, Thomas

2010-11-01

Multisubunit tethering complexes participate in the process of vesicle tethering--the initial interaction between transport vesicles and their acceptor compartments. TRAPPII (named for transport protein particle II) is a highly conserved tethering complex that functions in the late Golgi apparatus and consists of all of the subunits of TRAPPI and three additional, specific subunits. We have purified native yeast TRAPPII and characterized its structure and subunit organization by single-particle EM. Our data show that the nine TRAPPII components form a core complex that dimerizes into a three-layered, diamond-shaped structure. The TRAPPI subunits assemble into TRAPPI complexes that form the outer layers. The three TRAPPII-specific subunits cap the ends of TRAPPI and form the middle layer, which is responsible for dimerization. TRAPPII binds the Ypt1 GTPase and probably uses the TRAPPI catalytic core to promote guanine nucleotide exchange. We discuss the implications of the structure of TRAPPII for coat interaction and TRAPPII-associated human pathologies.

Visual complexity: a review.

PubMed

Donderi, Don C

2006-01-01

The idea of visual complexity, the history of its measurement, and its implications for behavior are reviewed, starting with structuralism and Gestalt psychology at the beginning of the 20th century and ending with visual complexity theory, perceptual learning theory, and neural circuit theory at the beginning of the 21st. Evidence is drawn from research on single forms, form and texture arrays and visual displays. Form complexity and form probability are shown to be linked through their reciprocal relationship in complexity theory, which is in turn shown to be consistent with recent developments in perceptual learning and neural circuit theory. Directions for further research are suggested.

Supramolecular structure of glibenclamide and β-cyclodextrins complexes.

PubMed

Lucio, David; Irache, Juan Manuel; Font, María; Martínez-Ohárriz, María Cristina

2017-09-15

Glibenclamide is an antidiabetic drug showing low bioavailability as consequence of its low solubility. To solve this drawback, the interaction with cyclodextrins has been proposed. The formation of GB-βCDs inclusion complexes was carried out using different methods, βCD derivatives and drug-to-cyclodextrin ratios. The structures of the corresponding complexes have been studied by molecular modelling, X-ray diffraction and differential thermal analysis. The dissolution behavior of inclusion complexes has been compared to that of pure GB. Dimeric inclusion complexes were obtained with different CD disposals, head-to-head for βCD and head-to-tail for HPβCD and RMβCD. Amorphous inclusion complexes were obtained by employing methods of freeze-drying or coevaporation in ammonia-water. However, crystalline structures were formed by kneading and coevaporation in ethanol/water in the case of GB-βCD complexes. The arrangement of these structures depended on the GB:βCD ratio, yielding cage type structures for 1:3 and 1:5 ratios and channel-type structures for higher GB contents. The amount of GB released and its dissolution rate was considerably increased by the use of amorphous inclusion complexes; whereas, slower GB release rates were found from crystalline inclusion complexes formed by kneading or coevaporation in ethanol/water. In addition, it was found that the porous structure strongly conditioned the GB dissolution rate from crystalline products. Copyright © 2017 Elsevier B.V. All rights reserved.

Identification of Complex Carbon Nanotube Structures

NASA Technical Reports Server (NTRS)

Han, Jie; Saini, Subhash (Technical Monitor)

1998-01-01

A variety of complex carbon nanotube (CNT) structures have been observed experimentally. These include sharp bends, branches, tori, and helices. They are believed to be formed by using topological defects such as pentagons and heptagons to connect different CNT. The effects of type, number, and arrangement (separation and orientation) of defects on atomic structures and energetics of complex CNT are investigated using topology, quantum mechanics and molecular mechanics calculations. Energetically stable models are derived for identification of observed complex CNT structures.

Crystal structure and solution species of Ce(III) and Ce(IV) formates: from mononuclear to hexanuclear complexes.

PubMed

Hennig, Christoph; Ikeda-Ohno, Atsushi; Kraus, Werner; Weiss, Stephan; Pattison, Philip; Emerich, Hermann; Abdala, Paula M; Scheinost, Andreas C

2013-10-21

Cerium(III) and cerium(IV) both form formate complexes. However, their species in aqueous solution and the solid-state structures are surprisingly different. The species in aqueous solutions were investigated with Ce K-edge EXAFS spectroscopy. Ce(III) formate shows only mononuclear complexes, which is in agreement with the predicted mononuclear species of Ce(HCOO)(2+) and Ce(HCOO)2(+). In contrast, Ce(IV) formate forms in aqueous solution a stable hexanuclear complex of [Ce6(μ3-O)4(μ3-OH)4(HCOO)x(NO3)y](12-x-y). The structural differences reflect the different influence of hydrolysis, which is weak for Ce(III) and strong for Ce(IV). Hydrolysis of Ce(IV) ions causes initial polymerization while complexation through HCOO(-) results in 12 chelate rings stabilizing the hexanuclear Ce(IV) complex. Crystals were grown from the above-mentioned solutions. Two crystal structures of Ce(IV) formate were determined. Both form a hexanuclear complex with a [Ce6(μ3-O)4(μ3-OH)4](12+) core in aqueous HNO3/HCOOH solution. The pH titration with NaOH resulted in a structure with the composition [Ce6(μ3-O)4(μ3-OH)4(HCOO)10(NO3)2(H2O)3]·(H2O)9.5, while the pH adjustment with NH3 resulted in [Ce6(μ3-O)4(μ3-OH)4(HCOO)10(NO3)4]·(NO3)3(NH4)5(H2O)5. Furthermore, the crystal structure of Ce(III) formate, Ce(HCOO)3, was determined. The coordination polyhedron is a tricapped trigonal prism which is formed exclusively by nine HCOO(-) ligands. The hexanuclear Ce(IV) formate species from aqueous solution is widely preserved in the crystal structure, whereas the mononuclear solution species of Ce(III) formate undergoes a polymerization during the crystallization process.

Assembly and stoichiometry of the core structure of the bacterial flagellar type III export gate complex.

PubMed

Fukumura, Takuma; Makino, Fumiaki; Dietsche, Tobias; Kinoshita, Miki; Kato, Takayuki; Wagner, Samuel; Namba, Keiichi; Imada, Katsumi; Minamino, Tohru

2017-08-01

The bacterial flagellar type III export apparatus, which is required for flagellar assembly beyond the cell membranes, consists of a transmembrane export gate complex and a cytoplasmic ATPase complex. FlhA, FlhB, FliP, FliQ, and FliR form the gate complex inside the basal body MS ring, although FliO is required for efficient export gate formation in Salmonella enterica. However, it remains unknown how they form the gate complex. Here we report that FliP forms a homohexameric ring with a diameter of 10 nm. Alanine substitutions of conserved Phe-137, Phe-150, and Glu-178 residues in the periplasmic domain of FliP (FliPP) inhibited FliP6 ring formation, suppressing flagellar protein export. FliO formed a 5-nm ring structure with 3 clamp-like structures that bind to the FliP6 ring. The crystal structure of FliPP derived from Thermotoga maritia, and structure-based photo-crosslinking experiments revealed that Phe-150 and Ser-156 of FliPP are involved in the FliP-FliP interactions and that Phe-150, Arg-152, Ser-156, and Pro-158 are responsible for the FliP-FliO interactions. Overexpression of FliP restored motility of a ∆fliO mutant to the wild-type level, suggesting that the FliP6 ring is a functional unit in the export gate complex and that FliO is not part of the final gate structure. Copurification assays revealed that FlhA, FlhB, FliQ, and FliR are associated with the FliO/FliP complex. We propose that the assembly of the export gate complex begins with FliP6 ring formation with the help of the FliO scaffold, followed by FliQ, FliR, and FlhB and finally FlhA during MS ring formation.

Assembly and stoichiometry of the core structure of the bacterial flagellar type III export gate complex

PubMed Central

Fukumura, Takuma; Makino, Fumiaki; Dietsche, Tobias; Kinoshita, Miki; Kato, Takayuki; Wagner, Samuel; Namba, Keiichi; Imada, Katsumi

2017-01-01

The bacterial flagellar type III export apparatus, which is required for flagellar assembly beyond the cell membranes, consists of a transmembrane export gate complex and a cytoplasmic ATPase complex. FlhA, FlhB, FliP, FliQ, and FliR form the gate complex inside the basal body MS ring, although FliO is required for efficient export gate formation in Salmonella enterica. However, it remains unknown how they form the gate complex. Here we report that FliP forms a homohexameric ring with a diameter of 10 nm. Alanine substitutions of conserved Phe-137, Phe-150, and Glu-178 residues in the periplasmic domain of FliP (FliPP) inhibited FliP6 ring formation, suppressing flagellar protein export. FliO formed a 5-nm ring structure with 3 clamp-like structures that bind to the FliP6 ring. The crystal structure of FliPP derived from Thermotoga maritia, and structure-based photo-crosslinking experiments revealed that Phe-150 and Ser-156 of FliPP are involved in the FliP–FliP interactions and that Phe-150, Arg-152, Ser-156, and Pro-158 are responsible for the FliP–FliO interactions. Overexpression of FliP restored motility of a ∆fliO mutant to the wild-type level, suggesting that the FliP6 ring is a functional unit in the export gate complex and that FliO is not part of the final gate structure. Copurification assays revealed that FlhA, FlhB, FliQ, and FliR are associated with the FliO/FliP complex. We propose that the assembly of the export gate complex begins with FliP6 ring formation with the help of the FliO scaffold, followed by FliQ, FliR, and FlhB and finally FlhA during MS ring formation. PMID:28771466

Structural, luminescence, thermodynamic and theoretical studies on mononuclear complexes of Eu(III) with pyridine monocarboxylate-N-oxides in aqueous solution

NASA Astrophysics Data System (ADS)

Dumpala, Rama Mohana Rao; Rawat, Neetika; Boda, Anil; Ali, Sk. Musharaf; Tomar, B. S.

2018-02-01

The mononuclear complexes formed by Eu(III) with three isomeric pyridine monocarboxylate-N-oxides namely picolinic acid-N-oxide (PANO), nicotinic acid-N-oxide (NANO) and isonicotinic acid-N-oxide (IANO) in aqueous solutions were studied by potentiometry, luminescence spectroscopy and isothermal titration calorimetry (ITC) to determine the speciation, coordination, luminescence properties and thermodynamic parameters of the complexes formed during the course of the reaction. More stable six membered chelate complexes with stoichiometry (MLi, i = 1-4) are formed by Eu(III) with PANO while non chelating ML and ML2 complexes are formed by NANO and IANO. The stability of Eu(III) complexes follow the order PANO > IANO > NANO. The ITC studies inferred an endothermic and innersphere complex formation of Eu(III)-PANO and Eu(III)-IANO whereas an exothermic and outer-sphere complex formation for Eu(III)-NANO. The luminescence life time data further supported the ITC results. Density functional theoretical calculations were carried out to optimize geometries of the complexes and to estimate the energies, structural parameters (bond distances, bond angles) and charges on individual atoms of the same. Theoretical approximations are found to be in good agreement with the experimental observations.

The Structure of Lombricine Kinase

PubMed Central

Bush, D. Jeffrey; Kirillova, Olga; Clark, Shawn A.; Davulcu, Omar; Fabiola, Felcy; Xie, Qing; Somasundaram, Thayumanasamy; Ellington, W. Ross; Chapman, Michael S.

2011-01-01

Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309–317, which is disordered in substrate-free structures of homologs and is known from the NMR of arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His178. Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates. PMID:21212263

Structure of complexes between aluminum chloride and other chlorides, 2: Alkali-(chloroaluminates). Gaseous complexes

NASA Technical Reports Server (NTRS)

Hargittai, M.

1980-01-01

The structural chemistry of complexes between aluminum chloride and other metal chlorides is important both for practice and theory. Condensed-phase as well as vapor-phase complexes are of interest. Structural information on such complexes is reviewed. The first emphasis is given to the molten state because of its practical importance. Aluminum chloride forms volatile complexes with other metal chlorides and these vapor-phase complexes are dealt with in the second part. Finally, the variations in molecular shape and geometrical parameters are summarized.

High Molecular Weight Forms of Mammalian Respiratory Chain Complex II

PubMed Central

Nůsková, Hana; Holzerová, Eliška; Vrbacký, Marek; Pecina, Petr; Hejzlarová, Kateřina; Kľučková, Katarína; Rohlena, Jakub; Neuzil, Jiri; Houštěk, Josef

2013-01-01

Mitochondrial respiratory chain is organised into supramolecular structures that can be preserved in mild detergent solubilisates and resolved by native electrophoretic systems. Supercomplexes of respiratory complexes I, III and IV as well as multimeric forms of ATP synthase are well established. However, the involvement of complex II, linking respiratory chain with tricarboxylic acid cycle, in mitochondrial supercomplexes is questionable. Here we show that digitonin-solubilised complex II quantitatively forms high molecular weight structures (CIIhmw) that can be resolved by clear native electrophoresis. CIIhmw structures are enzymatically active and differ in electrophoretic mobility between tissues (500 – over 1000 kDa) and cultured cells (400–670 kDa). While their formation is unaffected by isolated defects in other respiratory chain complexes, they are destabilised in mtDNA-depleted, rho0 cells. Molecular interactions responsible for the assembly of CIIhmw are rather weak with the complexes being more stable in tissues than in cultured cells. While electrophoretic studies and immunoprecipitation experiments of CIIhmw do not indicate specific interactions with the respiratory chain complexes I, III or IV or enzymes of the tricarboxylic acid cycle, they point out to a specific interaction between CII and ATP synthase. PMID:23967256

Structural characterization of metal complexes in aqueous solutions: a XAS study of stannous fluoride

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alsina, Marco A.; Gaillard, Jean-François

The identity and structure of tin(ii)-fluoride complexes formed in aqueous solutions are determined by combining X-ray absorption spectroscopy, thermodynamic modeling and quantum mechanical calculations.

Jealousy Graphs: Structure and Complexity of Decentralized Stable Matching

DTIC Science & Technology

2013-01-01

REPORT Jealousy Graphs: Structure and Complexity of Decentralized Stable Matching 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: The stable matching...Franceschetti 858-822-2284 3. DATES COVERED (From - To) Standard Form 298 (Rev 8/98) Prescribed by ANSI Std. Z39.18 - Jealousy Graphs: Structure and...market. Using this structure, we are able to provide a ner analysis of the complexity of a subclass of decentralized matching markets. Jealousy

Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity

PubMed Central

Sayer, Christopher; Isupov, Michail N.; Westlake, Aaron; Littlechild, Jennifer A.

2013-01-01

The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes show activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-­aminotransferases. PMID:23519665

Solution-state structure and affinities of cyclodextrin: Fentanyl complexes by nuclear magnetic resonance spectroscopy and molecular dynamics simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mayer, Brian P.; Kennedy, Daniel J.; Lau, Edmond Y.

Cyclodextrins (CDs) are investigated for their ability to form inclusion complexes with the analgesic fentanyl and three similar molecules: acetylfentanyl, thiofentanyl, and acetylthiofentanyl. Stoichiometry, binding strength, and complex structure are revealed through nuclear magnetic resonance (NMR) techniques and discussed in terms of molecular dynamics (MD) simulations. It was found that β-cyclodextrin is generally capable of forming the strongest complexes with the fentanyl panel. Two-dimensional NMR data and computational chemical calculations are used to derive solution-state structures of the complexes. Binding of the fentanyls to the CDs occurs at the amide phenyl ring, leaving the majority of the molecule solvated bymore » water, an observation common to all four fentanyls. This finding suggests a universal binding behavior, as the vast majority of previously synthesized fentanyl analogues contain this structural moiety. Furthermore, this baseline study serves as the most complete work on CD:fentanyl complexes to date and provides the insights into strategies for producing future generations of designer cyclodextrins capable of stronger and more selective complexation of fentanyl and its analogues.« less

Solution-state structure and affinities of cyclodextrin: Fentanyl complexes by nuclear magnetic resonance spectroscopy and molecular dynamics simulation

DOE PAGES

Mayer, Brian P.; Kennedy, Daniel J.; Lau, Edmond Y.; ...

2016-02-04

Cyclodextrins (CDs) are investigated for their ability to form inclusion complexes with the analgesic fentanyl and three similar molecules: acetylfentanyl, thiofentanyl, and acetylthiofentanyl. Stoichiometry, binding strength, and complex structure are revealed through nuclear magnetic resonance (NMR) techniques and discussed in terms of molecular dynamics (MD) simulations. It was found that β-cyclodextrin is generally capable of forming the strongest complexes with the fentanyl panel. Two-dimensional NMR data and computational chemical calculations are used to derive solution-state structures of the complexes. Binding of the fentanyls to the CDs occurs at the amide phenyl ring, leaving the majority of the molecule solvated bymore » water, an observation common to all four fentanyls. This finding suggests a universal binding behavior, as the vast majority of previously synthesized fentanyl analogues contain this structural moiety. Furthermore, this baseline study serves as the most complete work on CD:fentanyl complexes to date and provides the insights into strategies for producing future generations of designer cyclodextrins capable of stronger and more selective complexation of fentanyl and its analogues.« less

A model of the complex between human {beta}-microseminoprotein and CRISP-3 based on NMR data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghasriani, Houman; Fernlund, Per; Udby, Lene

2009-01-09

{beta}-Microseminoprotein (MSP), a 10 kDa seminal plasma protein, forms a tight complex with cysteine-rich secretory protein 3 (CRISP-3) from granulocytes. The 3D structure of human MSP has been determined but there is as yet no 3D structure for CRISP-3. We have now studied the complex between human MSP and CRISP-3 with multidimensional NMR. {sup 15}N-HSQC spectra show substantial differences between free and complexed hMSP. Using several 3D-NMR spectra of triply labeled hMSP in complex with a recombinant N-terminal domain of CRISP-3, most of the backbone of hMSP could be assigned. The data show that only one side of hMSP, comprisingmore » {beta}-strands 1, 4, 5, and 8 are affected by the complex formation, indicating that {beta}-strands 1 and 8 form the main binding surface. Based on this we present a tentative structure for the hMSP-CRISP-3 complex using the known crystal structure of triflin as a model of CRISP-3.« less

Solution structure of the His12 --> Cys mutant of the N-terminal zinc binding domain of HIV-1 integrase complexed to cadmium.

PubMed Central

Cai, M.; Huang, Y.; Caffrey, M.; Zheng, R.; Craigie, R.; Clore, G. M.; Gronenborn, A. M.

1998-01-01

The solution structure of His12 --> Cys mutant of the N-terminal zinc binding domain (residues 1-55; IN(1-55)) of HIV-1 integrase complexed to cadmium has been solved by multidimensional heteronuclear NMR spectroscopy. The overall structure is very similar to that of the wild-type N-terminal domain complexed to zinc. In contrast to the wild-type domain, however, which exists in two interconverting conformational states arising from different modes of coordination of the two histidine side chains to the metal, the cadmium complex of the His12 --> Cys mutant exists in only a single form at low pH. The conformation of the polypeptide chain encompassing residues 10-18 is intermediate between the two forms of the wild-type complex. PMID:9865962

Spectroscopic and first-principles calculation studies of the chemical forms of palladium ion in nitric acid solution for development of disposal of high-level radioactive nuclear wastes

NASA Astrophysics Data System (ADS)

Watanabe, Shinta; Sato, Toshikazu; Yoshida, Tomoko; Nakaya, Masato; Yoshino, Masahito; Nagasaki, Takanori; Inaba, Yusuke; Takeshita, Kenji; Onoe, Jun

2018-04-01

We have investigated the chemical forms of palladium (Pd) ion in nitric acid solution, using XAFS/UV-vis spectroscopic and first-principles methods in order to develop the disposal of high-level radioactive nuclear liquid wastes (HLLW: radioactive metal ions in 2 M nitric acid solution). The results of theoretical calculations and XAFS/UV-vis spectroscopy indicate that Pd is a divalent ion and forms a square-planar complex structure coordinated with four nitrate ions, [Pd(NO3)4]2-, in nitric acid solution. This complex structure is also thermodynamically predicted to be most stable among complexes [Pd(H2O)x(NO3)4-x]x-2 (x = 0-4). Since the overall feature of UV-vis spectra of the Pd complex was independent of nitric acid concentration in the range 1-6 M, the structure of the Pd complex remains unchanged in this range. Furthermore, we examined the influence of γ-ray radiation on the [Pd(NO3)4]2- complex, using UV-vis spectroscopy, and found that UV-vis spectra seemed not to be changed even after 1.0 MGy irradiation. This implies that the Pd complex structure will be still stable in actual HLLW. These findings obtained above are useful information to develop the vitrification processes for disposal of HLLW.

Adsorption mechanisms of selenium oxyanions at the aluminum oxide/water interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peak, Derek

2008-06-09

Sorption processes at the mineral/water interface typically control the mobility and bioaccessibility of many inorganic contaminants such as oxyanions. Selenium is an important micronutrient for human and animal health, but at elevated concentrations selenium toxicity is a concern. The objective of this study was to determine the bonding mechanisms of selenate (SeO{sub 4}{sup 2-}) and selenite (SeO{sub 3}{sup 2-}) on hydrous aluminum oxide (HAO) over a wide range of reaction pH using extended X-ray absorption fine structure (EXAFS) spectroscopy. Additionally, selenate adsorption on corundum ({alpha}-Al{sub 2}O{sub 3}) was studied to determine if adsorption mechanisms change as the aluminum oxide surfacemore » structure changes. The overall findings were that selenite forms a mixture of outer-sphere and inner-sphere bidentate-binuclear (corner-sharing) surface complexes on HAO, selenate forms primarily outer-sphere surface complexes on HAO, and on corundum selenate forms outer-sphere surface complexes at pH 3.5 but inner-sphere monodentate surface complexes at pH 4.5 and above. It is possible that the lack of inner-sphere complex formation at pH 3.5 is caused by changes in the corundum surface at low pH or secondary precipitate formation. The results are consistent with a structure-based reactivity for metal oxides, wherein hydrous metal oxides form outer-sphere complexes with sulfate and selenate, but inner-sphere monodentate surface complexes are formed between sulfate and selenate and {alpha}-Me{sub 2}O{sub 3}.« less

Structure of 1:1 complex of 1-naphthylmethyl ester of monensin A with sodium perchlorate studied by X-ray, FT-IR and ab initio methods

NASA Astrophysics Data System (ADS)

Huczyński, Adam; Janczak, Jan; Brzezinski, Bogumil

2012-12-01

A new crystalline complex formed between 1-naphthylmethyl ester of the naturally occurring antibiotic - monensin A (MON8) with sodium perchlorate has been obtained and studied using X-ray crystallography and FT-IR spectroscopy. The X-ray data of the complex show that MON8 forms a pseudo-cyclic structure stabilised by one weak intramolecular hydrogen bond and the sodium cation co-ordinated by two oxygen atoms of hydroxyl groups and four etheric oxygen atoms in the hydrophilic sphere. Within this structure the oxygen atoms of the ester groups are not involved in the coordination of sodium cation. In contrast to the solid state structure of the complex, in acetonitrile solution an equilibrium between two structures, in which the oxygen atom of the carbonyl ester group is either involved or not involved in the complexation of the sodium cation, is found. In acetonitrile this equilibrium is shifted towards the latter structure i.e. the structure existing in the solid state. The gas-phase structure of [MON8sbnd Na]+ cation as shown the ab initio MO calculations is comparable with the crystal one. Three-dimensional molecular electrostatic potential calculated for the neutral MON8 and [MON8sbnd Na]+ molecules is helpful for understanding the structural aspects of the sodium complex formation.

Fabrication of meso- and nano-scale structures on surfaces of chalcogenide semiconductors by surface hydrodynamic interference patterning

NASA Astrophysics Data System (ADS)

Bilanych, V.; Komanicky, V.; Lacková, M.; Feher, A.; Kuzma, V.; Rizak, V.

2015-10-01

We observe the change of surface relief on amorphous Ge-As-Se thin films after irradiation with an electron beam. The beam softens the glass and induces various topological surface changes in the irradiated area. The film relief change depends on the film thickness, deposited charge, and film composition. Various structures are formed: Gausian-like cones, extremely sharp Taylor cones, deep craters, and craters with large spires grown on the side. Our investigation shows that these effects can be at least partially a result of electro-hydrodynamic material flow, but the observed phenomena are likely more complex. When we irradiated structural patterns formed by the electron beam with a red laser beam, we could not only fully relax the produced patterns, but also form very complex and intricate superstructures. These organized meso- and nano-scale structures are formed by a combination of photo-induced structural relaxation, light interference on structures fabricated by the e-beam, and photo-induced material flow.

Structural study of Cu(II) complexes with benzo[b]furancarboxylic acids

NASA Astrophysics Data System (ADS)

Kalinowska, Diana; Klepka, Marcin T.; Wolska, Anna; Drzewiecka-Antonik, Aleksandra; Ostrowska, Kinga; Struga, Marta

2017-11-01

Four Cu(II) complexes with 2- and 3-benzo[b]furancarboxylic acids have been synthesized and characterized using combination of two spectroscopic techniques. These techniques were: (i) FTIR and (ii) XAFS. FTIR analysis confirmed that complexes were formed and gave insight into identification of possible coordinating groups to the metallic center. XANES analysis indicated that the oxidation state of Cu is +2. EXAFS analysis allowed to identify that the first coordination sphere is formed by 4-5 oxygen atoms with the Cu-O distances around 2 Å. Combining these techniques it was possible to structurally describe novel Cu(II) complexes with benzo[b]furancarboxylic acids.

The Structure of Lombricine Kinase: Implications for Phosphagen Conformational Changes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bush, D. Jeffrey; Kirillova, Olga; Clark, Shawn A.

2012-05-29

Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309-317, which is disordered in substrate-free structures of homologs and is known from the NMR ofmore » arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His{sup 178}. Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates.« less

Structures of the Substrate-free and Product-bound Forms of HmuO, a Heme Oxygenase from Corynebacterium diphtheriae

PubMed Central

Unno, Masaki; Ardèvol, Albert; Rovira, Carme; Ikeda-Saito, Masao

2013-01-01

Heme oxygenase catalyzes the degradation of heme to biliverdin, iron, and carbon monoxide. Here, we present crystal structures of the substrate-free, Fe3+-biliverdin-bound, and biliverdin-bound forms of HmuO, a heme oxygenase from Corynebacterium diphtheriae, refined to 1.80, 1.90, and 1.85 Å resolution, respectively. In the substrate-free structure, the proximal and distal helices, which tightly bracket the substrate heme in the substrate-bound heme complex, move apart, and the proximal helix is partially unwound. These features are supported by the molecular dynamic simulations. The structure implies that the heme binding fixes the enzyme active site structure, including the water hydrogen bond network critical for heme degradation. The biliverdin groups assume the helical conformation and are located in the heme pocket in the crystal structures of the Fe3+-biliverdin-bound and the biliverdin-bound HmuO, prepared by in situ heme oxygenase reaction from the heme complex crystals. The proximal His serves as the Fe3+-biliverdin axial ligand in the former complex and forms a hydrogen bond through a bridging water molecule with the biliverdin pyrrole nitrogen atoms in the latter complex. In both structures, salt bridges between one of the biliverdin propionate groups and the Arg and Lys residues further stabilize biliverdin at the HmuO heme pocket. Additionally, the crystal structure of a mixture of two intermediates between the Fe3+-biliverdin and biliverdin complexes has been determined at 1.70 Å resolution, implying a possible route for iron exit. PMID:24106279

Complex DNA Brick Assembly.

PubMed

Ong, Luvena L; Ke, Yonggang

2017-01-01

DNA nanostructures are a useful technology for precisely organizing and manipulating nanomaterials. The DNA bricks method is a modular and versatile platform for applications requiring discrete or periodic structures with complex three-dimensional features. Here, we describe how structures are designed from the fundamental strand architecture through assembly and characterization of the formed structures.

Structural study of surfactant-dependent interaction with protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mehan, Sumit; Aswal, Vinod K., E-mail: vkaswal@barc.gov.in; Kohlbrecher, Joachim

2015-06-24

Small-angle neutron scattering (SANS) has been used to study the complex structure of anionic BSA protein with three different (cationic DTAB, anionic SDS and non-ionic C12E10) surfactants. These systems form very different surfactant-dependent complexes. We show that the structure of protein-surfactant complex is initiated by the site-specific electrostatic interaction between the components, followed by the hydrophobic interaction at high surfactant concentrations. It is also found that hydrophobic interaction is preferred over the electrostatic interaction in deciding the resultant structure of protein-surfactant complexes.

Structural study of surfactant-dependent interaction with protein

NASA Astrophysics Data System (ADS)

Mehan, Sumit; Aswal, Vinod K.; Kohlbrecher, Joachim

2015-06-01

Small-angle neutron scattering (SANS) has been used to study the complex structure of anionic BSA protein with three different (cationic DTAB, anionic SDS and non-ionic C12E10) surfactants. These systems form very different surfactant-dependent complexes. We show that the structure of protein-surfactant complex is initiated by the site-specific electrostatic interaction between the components, followed by the hydrophobic interaction at high surfactant concentrations. It is also found that hydrophobic interaction is preferred over the electrostatic interaction in deciding the resultant structure of protein-surfactant complexes.

Structure of human Fe-S assembly subcomplex reveals unexpected cysteine desulfurase architecture and acyl-ACP-ISD11 interactions.

PubMed

Cory, Seth A; Van Vranken, Jonathan G; Brignole, Edward J; Patra, Shachin; Winge, Dennis R; Drennan, Catherine L; Rutter, Jared; Barondeau, David P

2017-07-03

In eukaryotes, sulfur is mobilized for incorporation into multiple biosynthetic pathways by a cysteine desulfurase complex that consists of a catalytic subunit (NFS1), LYR protein (ISD11), and acyl carrier protein (ACP). This NFS1-ISD11-ACP (SDA) complex forms the core of the iron-sulfur (Fe-S) assembly complex and associates with assembly proteins ISCU2, frataxin (FXN), and ferredoxin to synthesize Fe-S clusters. Here we present crystallographic and electron microscopic structures of the SDA complex coupled to enzyme kinetic and cell-based studies to provide structure-function properties of a mitochondrial cysteine desulfurase. Unlike prokaryotic cysteine desulfurases, the SDA structure adopts an unexpected architecture in which a pair of ISD11 subunits form the dimeric core of the SDA complex, which clarifies the critical role of ISD11 in eukaryotic assemblies. The different quaternary structure results in an incompletely formed substrate channel and solvent-exposed pyridoxal 5'-phosphate cofactor and provides a rationale for the allosteric activator function of FXN in eukaryotic systems. The structure also reveals the 4'-phosphopantetheine-conjugated acyl-group of ACP occupies the hydrophobic core of ISD11, explaining the basis of ACP stabilization. The unexpected architecture for the SDA complex provides a framework for understanding interactions with acceptor proteins for sulfur-containing biosynthetic pathways, elucidating mechanistic details of eukaryotic Fe-S cluster biosynthesis, and clarifying how defects in Fe-S cluster assembly lead to diseases such as Friedreich's ataxia. Moreover, our results support a lock-and-key model in which LYR proteins associate with acyl-ACP as a mechanism for fatty acid biosynthesis to coordinate the expression, Fe-S cofactor maturation, and activity of the respiratory complexes.

Development of explosive welding procedures to fabricate channeled nozzle structures

NASA Technical Reports Server (NTRS)

Pattee, H. E.; Linse, V. D.

1976-01-01

Research was conducted to demonstrate the feasibility of fabricating a large contoured structure with complex internal channeling by explosive welding procedures. Structures or nozzles of this nature for wind tunnel applications were designed. Such nozzles vary widely in their complexity. However, in their simplest form, they consist of a grooved base section to which a cover sheet is attached to form a series of internal cooling passages. The cover sheet attachment can be accomplished in various ways: fusion welding, brazing, and diffusion welding. The cover sheet has also been electroformed in place. Of these fabrication methods, brazing has proved most successful in producing nozzles with complex contoured surfaces and a multiplicity of internal channels.

Native structure of a type IV secretion system core complex essential for Legionella pathogenesis.

PubMed

Kubori, Tomoko; Koike, Masafumi; Bui, Xuan Thanh; Higaki, Saori; Aizawa, Shin-Ichi; Nagai, Hiroki

2014-08-12

Bacterial type IV secretion systems are evolutionarily related to conjugation systems and play a pivotal role in infection by delivering numerous virulence factors into host cells. Using transmission electron microscopy, we report the native molecular structure of the core complex of the Dot/Icm type IV secretion system encoded by Legionella pneumophila, an intracellular human pathogen. The biochemically isolated core complex, composed of at least five proteins--DotC, DotD, DotF, DotG, and DotH--has a ring-shaped structure. Intriguingly, morphologically distinct premature complexes are formed in the absence of DotG or DotF. Our data suggest that DotG forms a central channel spanning inner and outer membranes. DotF, a component dispensable for type IV secretion, plays a role in efficient embedment of DotG into the functional core complex. These results highlight a common scheme for the biogenesis of transport machinery.

LINC Complexes Form by Binding of Three KASH Peptides to Domain Interfaces of Trimeric SUN Proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sosa, Brian A.; Rothballer, Andrea; Kutay, Ulrike

Linker of nucleoskeleton and cytoskeleton (LINC) complexes span the nuclear envelope and are composed of KASH and SUN proteins residing in the outer and inner nuclear membrane, respectively. LINC formation relies on direct binding of KASH and SUN in the perinuclear space. Thereby, molecular tethers are formed that can transmit forces for chromosome movements, nuclear migration, and anchorage. We present crystal structures of the human SUN2-KASH1/2 complex, the core of the LINC complex. The SUN2 domain is rigidly attached to a trimeric coiled coil that prepositions it to bind three KASH peptides. The peptides bind in three deep and expansivemore » grooves formed between adjacent SUN domains, effectively acting as molecular glue. In addition, a disulfide between conserved cysteines on SUN and KASH covalently links both proteins. The structure provides the basis of LINC complex formation and suggests a model for how LINC complexes might arrange into higher-order clusters to enhance force-coupling.« less

Crystal structure of the Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex.

PubMed

Numata, Tomoyuki; Inanaga, Hideko; Sato, Chikara; Osawa, Takuo

2015-01-30

Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA. Here, we show that the Csm1, Csm3, and Csm4 proteins from Methanocaldococcus jannaschii form a stable subcomplex. We also report the crystal structure of the M. jannaschii Csm3-Csm4 subcomplex at 3.1Å resolution. The complex structure revealed the presence of a basic concave surface around their interface, suggesting the RNA and/or DNA binding ability of the complex. A gel retardation analysis showed that the Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Based on bioinformatics, we constructed a model structure of the Csm1-Csm4-Csm3 ternary complex, which provides insights into its role in the Csm interference complex. Copyright © 2014 Elsevier Ltd. All rights reserved.

Structure of a group II intron in complex with its reverse transcriptase.

PubMed

Qu, Guosheng; Kaushal, Prem Singh; Wang, Jia; Shigematsu, Hideki; Piazza, Carol Lyn; Agrawal, Rajendra Kumar; Belfort, Marlene; Wang, Hong-Wei

2016-06-01

Bacterial group II introns are large catalytic RNAs related to nuclear spliceosomal introns and eukaryotic retrotransposons. They self-splice, yielding mature RNA, and integrate into DNA as retroelements. A fully active group II intron forms a ribonucleoprotein complex comprising the intron ribozyme and an intron-encoded protein that performs multiple activities including reverse transcription, in which intron RNA is copied into the DNA target. Here we report cryo-EM structures of an endogenously spliced Lactococcus lactis group IIA intron in its ribonucleoprotein complex form at 3.8-Å resolution and in its protein-depleted form at 4.5-Å resolution, revealing functional coordination of the intron RNA with the protein. Remarkably, the protein structure reveals a close relationship between the reverse transcriptase catalytic domain and telomerase, whereas the active splicing center resembles the spliceosomal Prp8 protein. These extraordinary similarities hint at intricate ancestral relationships and provide new insights into splicing and retromobility.

A conserved αβ transmembrane interface forms the core of a compact T-cell receptor–CD3 structure within the membrane

PubMed Central

Krshnan, Logesvaran; Park, Soohyung; Im, Wonpil; Call, Melissa J.; Call, Matthew E.

2016-01-01

The T-cell antigen receptor (TCR) is an assembly of eight type I single-pass membrane proteins that occupies a central position in adaptive immunity. Many TCR-triggering models invoke an alteration in receptor complex structure as the initiating event, but both the precise subunit organization and the pathway by which ligand-induced alterations are transferred to the cytoplasmic signaling domains are unknown. Here, we show that the receptor complex transmembrane (TM) domains form an intimately associated eight-helix bundle organized by a specific interhelical TCR TM interface. The salient features of this core structure are absolutely conserved between αβ and γδ TCR sequences and throughout vertebrate evolution, and mutations at key interface residues caused defects in the formation of stable TCRαβ:CD3δε:CD3γε:ζζ complexes. These findings demonstrate that the eight TCR–CD3 subunits form a compact and precisely organized structure within the membrane and provide a structural basis for further investigation of conformationally regulated models of transbilayer TCR signaling. PMID:27791034

A conserved αβ transmembrane interface forms the core of a compact T-cell receptor-CD3 structure within the membrane.

PubMed

Krshnan, Logesvaran; Park, Soohyung; Im, Wonpil; Call, Melissa J; Call, Matthew E

2016-10-25

The T-cell antigen receptor (TCR) is an assembly of eight type I single-pass membrane proteins that occupies a central position in adaptive immunity. Many TCR-triggering models invoke an alteration in receptor complex structure as the initiating event, but both the precise subunit organization and the pathway by which ligand-induced alterations are transferred to the cytoplasmic signaling domains are unknown. Here, we show that the receptor complex transmembrane (TM) domains form an intimately associated eight-helix bundle organized by a specific interhelical TCR TM interface. The salient features of this core structure are absolutely conserved between αβ and γδ TCR sequences and throughout vertebrate evolution, and mutations at key interface residues caused defects in the formation of stable TCRαβ:CD3δε:CD3γε:ζζ complexes. These findings demonstrate that the eight TCR-CD3 subunits form a compact and precisely organized structure within the membrane and provide a structural basis for further investigation of conformationally regulated models of transbilayer TCR signaling.

Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights.

PubMed

Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji

2016-12-13

Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.

A density functional study of silicon fullerene endohedral X@Si20F20 and exohedral X-Si20F20 (X=O2-, S2-, Se2-) complexes

NASA Astrophysics Data System (ADS)

Behzadi, Hadi; Esrafili, Mehdi D.; Manzetti, Sergio; Roonasi, Payman

2014-02-01

This study reports the structure and electronic properties of three stable endohedral X@Si20F20 and exohedral X-Si20F20 (X=O2-, S2-, Se2-) complexes. The study revealed that the endohedral complexes with S2- and Se2- result as energy minimum structures, with the guest anion located in the cage center. In the case of endohedral O2--complexes, the pattern is quite different whereas the O2- complexes dramatically deviated from the architecture of S2- and Se2-, by having O2- located toward one of silicon atoms in the cage. With respect to the exohedral form, the energy minimized structure is obtained by positioning the anion between two silicon atoms and forming two Si-X bonds. For both cases, the strength of the interactions is calculated to increase accordingly to the pattern: Se2-@Si20F20 (Se2--Si20F20)

Leaching behavior and chemical stability of copper butyl xanthate complex under acidic conditions.

PubMed

Chang, Yi Kuo; Chang, Juu En; Chiang, Li Choung

2003-08-01

Although xanthate addition can be used for treating copper-containing wastewater, a better understanding of the leaching toxicity and the stability characteristics of the copper xanthate complexes formed is essential. This work was undertaken to evaluate the leaching behavior of copper xanthate complex precipitates by means of toxicity characteristics leaching procedure (TCLP) and semi-dynamic leaching test (SDLT) using 1 N acetic acid solution as the leachant. Also, the chemical stability of the copper xanthate complex during extraction has been examined with the studying of variation of chemical structure using UV-vis, Fourier transform infrared and X-ray photoelectron spectroscopies (XPS). Both TCLP and SDLT results showed that a negligible amount of copper ion was leached out from the copper xanthate complex precipitate, indicating that the complex exhibited a high degree of copper leaching stability under acidic conditions. Nevertheless, chemical structure of the copper xanthate complex precipitate varied during the leaching tests. XPS data suggested that the copper xanthate complex initially contained both cupric and cuprous xanthate, but the unstable cupric xanthate change to the cuprous form after acid extraction, indicating the cuprous xanthate to be the final stabilizing structure. Despite that, the changes of chemical structure did not induce the rapid leaching of copper from the copper xanthate complex.

Development of nanoscale structure in LAT-based signaling complexes

PubMed Central

2016-01-01

ABSTRACT The adapter molecule linker for activation of T cells (LAT) plays a crucial role in forming signaling complexes induced by stimulation of the T cell receptor (TCR). These multi-molecular complexes are dynamic structures that activate highly regulated signaling pathways. Previously, we have demonstrated nanoscale structure in LAT-based complexes where the adapter SLP-76 (also known as LCP2) localizes to the periphery of LAT clusters. In this study, we show that initially LAT and SLP-76 are randomly dispersed throughout the clusters that form upon TCR engagement. The segregation of LAT and SLP-76 develops near the end of the spreading process. The local concentration of LAT also increases at the same time. Both changes require TCR activation and an intact actin cytoskeleton. These results demonstrate that the nanoscale organization of LAT-based signaling complexes is dynamic and indicates that different kinds of LAT-based complexes appear at different times during T cell activation. PMID:27875277

Ordovician volcanic and plutonic complexes of the Sakmara allochthon in the southern Urals

NASA Astrophysics Data System (ADS)

Ryazantsev, A. V.; Tolmacheva, T. Yu.

2016-11-01

The Ordovician terrigenous, volcanic-sedimentary and volcanic sequences that formed in rifts of the active continental margin and igneous complexes of intraoceanic suprasubduction settings structurally related to ophiolites are closely spaced in allochthons of the Sakmara Zone in the southern Urals. The stratigraphic relationships of the Ordovician sequences have been established. Their age and facies features have been specified on the basis of biostratigraphic and geochronological data. The gabbro-tonalite-trondhjemite complex and the basalt-andesite-rhyolite sequence with massive sulfide mineralization make up a volcanic-plutonic association. These rock complexes vary in age from Late Ordovician to Early Silurian in certain structural units of the Sakmara Allochthon and to the east in the southern Urals. The proposed geodynamic model for the Ordovician in Paleozoides of the southern Urals reconstructs the active continental margin, whose complexes formed under extension settings, and the intraoceanic suprasubduction structures. The intraoceanic complexes display the evolution of a volcanic arc, back-, or interarc trough.

Spectroscopic and structural studies of the first complex formed between salinomycin and organic amine

NASA Astrophysics Data System (ADS)

Antoszczak, Michał; Janczak, Jan; Brzezinski, Bogumił; Huczyński, Adam

2017-02-01

For the first time, the crystalline complex of salinomycin with benzylamine was obtained and its molecular structure was studied using single crystal X-ray diffraction, FT-IR, 1H NMR, 13C NMR, 2D NMR and ESI MS methods. These studies provided evidence that the proton from the carboxylic group of salinomycin (SAL) is transferred to the amine group of benzylamine (BnA) forming the host-guest complex (SAL-BnA). It was shown that the SAL-BnA complex both in solid state and in chloroform solution is stabilized by the intramolecular O-H⋯O hydrogen bonds and also by the intermolecular hydrogen bonding interactions of the carboxylate, ketone and/or hydroxyl groups of SAL with water molecules present in the investigated system. The solvated acetonitrile molecules are additionally located in the voids between the SAL-BnA complex molecules in the crystal structure, while water molecules involved in the dihydrated crystalline SAL-BnA complex partially move into the solvent upon dissolution in chloroform.

The structure of the core NuRD repression complex provides insights into its interaction with chromatin

PubMed Central

Millard, Christopher J; Varma, Niranjan; Saleh, Almutasem; Morris, Kyle; Watson, Peter J; Bottrill, Andrew R; Fairall, Louise; Smith, Corinne J; Schwabe, John WR

2016-01-01

The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure of chromatin, and has important roles in the regulation of gene expression, DNA damage repair and cell differentiation. HDACs 1 and 2 are recruited by the MTA1 corepressor to form the catalytic core of the complex. The histone chaperone protein RBBP4, has previously been shown to bind to the carboxy-terminal tail of MTA1. We show that MTA1 recruits a second copy of RBBP4. The crystal structure reveals an extensive interface between MTA1 and RBBP4. An EM structure, supported by SAXS and crosslinking, reveals the architecture of the dimeric HDAC1:MTA1:RBBP4 assembly which forms the core of the NuRD complex. We find evidence that in this complex RBBP4 mediates interaction with histone H3 tails, but not histone H4, suggesting a mechanism for recruitment of the NuRD complex to chromatin. DOI: http://dx.doi.org/10.7554/eLife.13941.001 PMID:27098840

Structural basis of the pH-dependent assembly of a botulinum neurotoxin complex.

PubMed

Matsui, Tsutomu; Gu, Shenyan; Lam, Kwok-Ho; Carter, Lester G; Rummel, Andreas; Mathews, Irimpan I; Jin, Rongsheng

2014-11-11

Botulinum neurotoxins (BoNTs) are among the most poisonous biological substances known. They assemble with non-toxic non-hemagglutinin (NTNHA) protein to form the minimally functional progenitor toxin complexes (M-PTC), which protects BoNT in the gastrointestinal tract and releases it upon entry into the circulation. Here we provide molecular insight into the assembly between BoNT/A and NTNHA-A using small-angle X-ray scattering. We found that the free form BoNT/A maintains a pH-independent conformation with limited domain flexibility. Intriguingly, the free form NTNHA-A adopts pH-dependent conformational changes due to a torsional motion of its C-terminal domain. Once forming a complex at acidic pH, they each adopt a stable conformation that is similar to that observed in the crystal structure of the M-PTC. Our results suggest that assembly of the M-PTC depends on the environmental pH and that the complex form of BoNT/A is induced by interacting with NTNHA-A at acidic pH. Copyright © 2014 Elsevier Ltd. All rights reserved.

Microwave-assisted synthesis and crystal structure of oxo(diperoxo)(4,4'-di-tert-butyl-2,2'-bipyridine)-molybdenum(VI).

PubMed

Amarante, Tatiana R; Almeida Paz, Filipe A; Gago, Sandra; Gonçalves, Isabel S; Pillinger, Martyn; Rodrigues, Alírio E; Abrantes, Marta

2009-09-16

The oxodiperoxo complex MoO(O2)(2)(tbbpy) (tbbpy = 4,4'-di-tert-butyl-2,2'- bipyridine) was isolated from the reaction of MoO2Cl(2)(tbbpy) in water under microwaveassisted heating at 120 masculineC for 4 h. The structure of the oxodiperoxo complex was determined by single crystal X-ray diffraction. The Mo(VI) centre is seven-coordinated with a geometry which strongly resembles a highly distorted bipyramid. Individual MoO(O2)(2)(tbbpy) complexes are interdigitated along the [010] direction to form a column. The crystal structure is formed by the close packing of the columnar-stacked complexes. Interactions between neighbouring columns are essentially of van der Waals type mediated by the need to effectively fill the available space.

[Creation of expert centers on endometriosis].

PubMed

Daraï, Emile; Bendifallah, Sofiane; Chabbert-Buffet, Nathalie; Golfier, François

2017-12-01

Endometriosis is a frequent pathology with a high incidence of deep infiltrating endometriosis and complex forms that can affect 20% of patients with endometriosis. The incidence of infertility associated with endometriosis can reach 50%. The complexity of care requires the creation of expert centers working in networks with general practitioners. Criteria for defining these expert centers are being drawn up, based on structural criteria (multidisciplinary consultation meeting), links with medical assistance structures for procreation and activity criteria for severe and complex forms (number of interventions per center and per surgeon). Copyright © 2017. Published by Elsevier Masson SAS.

Molecular dynamics simulations show altered secondary structure of clawless in binary complex with DNA providing insights into aristaless-clawless-DNA ternary complex formation.

PubMed

Kachhap, Sangita; Priyadarshini, Pragya; Singh, Balvinder

2017-05-01

Aristaless (Al) and clawless (Cll) homeodomains that are involved in leg development in Drosophila melanogaster are known to bind cooperatively to 5'-(T/C)TAATTAA(T/A)(T/A)G-3' DNA sequence, but the mechanism of their binding to DNA is unknown. Molecular dynamics (MD) studies have been carried out on binary, ternary, and reconstructed protein-DNA complexes involving Al, Cll, and DNA along with binding free energy analysis of these complexes. Analysis of MD trajectories of Cll-3A01, binary complex reveals that C-terminal end of helixIII of Cll, unwind in the absence of Al and remains so in reconstructed ternary complex, Cll-3A01-Al. In addition, this change in secondary structure of Cll does not allow it to form protein-protein interactions with Al in the ternary reconstructed complex. However, secondary structure of Cll and its interactions are maintained in other reconstructed ternary complex, Al-3A01-Cll where Cll binds to Al-3A01, binary complex to form ternary complex. These interactions as observed during MD simulations compare well with those observed in ternary crystal structure. Thus, this study highlights the role of helixIII of Cll and protein-protein interactions while proposing likely mechanism of recognition in ternary complex, Al-Cll-DNA.

Structure of the Apo Form of Bacillus stearothermophilus Phosphofructokinase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mosser, Rockann; Reddy, Manchi C.M.; Bruning, John B.

2012-02-08

The crystal structure of the unliganded form of Bacillus stearothermophilus phosphofructokinase (BsPFK) was determined using molecular replacement to 2.8 {angstrom} resolution (Protein Data Bank entry 3U39). The apo BsPFK structure serves as the basis for the interpretation of any structural changes seen in the binary or ternary complexes. When the apo BsPFK structure is compared with the previously published liganded structures of BsPFK, the structural impact that the binding of the ligands produces is revealed. This comparison shows that the apo form of BsPFK resembles the substrate-bound form of BsPFK, a finding that differs from previous predictions.

DNA-lipid complexes: stability of honeycomb-like and spaghetti-like structures.

PubMed Central

May, S; Ben-Shaul, A

1997-01-01

A molecular level theory is presented for the thermodynamic stability of two (similar) types of structural complexes formed by (either single strand or supercoiled) DNA and cationic liposomes, both involving a monolayer-coated DNA as the central structural unit. In the "spaghetti" complex the central unit is surrounded by another, oppositely curved, monolayer, thus forming a bilayer mantle. The "honeycomb" complex is a bundle of hexagonally packed DNA-monolayer units. The formation free energy of these complexes, starting from a planar cationic/neutral lipid bilayer and bare DNA, is expressed as a sum of electrostatic, bending, mixing, and (for the honeycomb) chain frustration contributions. The electrostatic free energy is calculated using the Poisson-Boltzmann equation. The bending energy of the mixed lipid layers is treated in the quadratic curvature approximation with composition-dependent bending rigidity and spontaneous curvature. Ideal lipid mixing is assumed within each lipid monolayer. We found that the most stable monolayer-coated DNA units are formed when the charged/neutral lipid composition corresponds (nearly) to charge neutralization; the optimal monolayer radius corresponds to close DNA-monolayer contact. These conclusions are also valid for the honeycomb complex, as the chain frustration energy is found to be negligible. Typically, the stabilization energies for these structures are on the order of 1 k(B)T/A of DNA length, reflecting mainly the balance between the electrostatic and bending energies. The spaghetti complexes are less stable due to the additional bending energy of the external monolayer. A thermodynamic analysis is presented for calculating the equilibrium lipid compositions when the complexes coexist with excess bilayer. PMID:9370436

Crystal Structure of an L-Carnitine Complex with Pyrogallol[4]arene

NASA Astrophysics Data System (ADS)

Fujisawa, I.; Takeuchi, D.; Kitamura, Y.; Okamoto, R.; Aoki, K.

2012-03-01

L-Carnitine is essential for the transport of long-chain fatty acids from cytosol into mitochondria for generating metabolic energy. The survey of crystal structures of carnitine-containing proteins in the Protein Data Bank reveals that carnitine can take several conformations with the quarternary trimethylammonium terminal being always bound to aromatic residues through cation-π interactions in acyltransferases or carnitine-binding proteins. In order to demonstrate the importance of cation-π interaction as a carnitine recognition mechanism in the artificial receptor-ligand system that mimics the carnitine-binding sites, we have determined the crystal structure of a complex formed between L-carnitine and pyrogallol[4]arene (pyrogallol cyclic tetramer: PCT) as a carnitine receptor, 2PCT·2(L-carnitine)·4EtOH. There form two crystallographically independent monomeric [PCT·L-carnitine] substructures, which further form an obliquely arranged capsule-like dimeric [PCT·L-carnitine]2 structure through a pair of O-H (PCT)···O (L-carnitine) hydrogen bonds. This is the first report of PCT complex with chiral molecules. In each of the two monomeric [PCT·L-carnitine] substructures, the L-carnitine molecule takes the elongated form with an intramolecular hydrogen bond between the hydroxyl group and the carboxylate oxygen, and the cationic trimethylammonium moiety is incorporated into the cavity of the bowl-shaped PCT molecule through cation-π interactions. These features are similar to those at the D-carnitine-binding site in the crystal structure of the glycine betaine/carnitine/choline-binding protein complex.

Electron transfer and conformational change in complexes of trimethylamine dehydrogenase and electron transferring flavoprotein.

PubMed

Jones, Matthew; Talfournier, Francois; Bobrov, Anton; Grossmann, J Günter; Vekshin, Nikolai; Sutcliffe, Michael J; Scrutton, Nigel S

2002-03-08

The trimethylamine dehydrogenase-electron transferring flavoprotein (TMADH.ETF) electron transfer complex has been studied by fluorescence and absorption spectroscopies. These studies indicate that a series of conformational changes occur during the assembly of the TMADH.ETF electron transfer complex and that the kinetics of assembly observed with mutant TMADH (Y442F/L/G) or ETF (alpha R237A) complexes are much slower than are the corresponding rates of electron transfer in these complexes. This suggests that electron transfer does not occur in the thermodynamically most favorable state (which takes too long to form), but that one or more metastable states (which are formed more rapidly) are competent in transferring electrons from TMADH to ETF. Additionally, fluorescence spectroscopy studies of the TMADH.ETF complex indicate that ETF undergoes a stable conformational change (termed structural imprinting) when it interacts transiently with TMADH to form a second, distinct, structural form. The mutant complexes compromise imprinting of ETF, indicating a dependence on the native interactions present in the wild-type complex. The imprinted form of semiquinone ETF exhibits an enhanced rate of electron transfer to the artificial electron acceptor, ferricenium. Overall molecular conformations as probed by small-angle x-ray scattering studies are indistinguishable for imprinted and non-imprinted ETF, suggesting that changes in structure likely involve confined reorganizations within the vicinity of the FAD. Our results indicate a series of conformational events occur during the assembly of the TMADH.ETF electron transfer complex, and that the properties of electron transfer proteins can be affected lastingly by transient interaction with their physiological redox partners. This may have significant implications for our understanding of biological electron transfer reactions in vivo, because ETF encounters TMADH at all times in the cell. Our studies suggest that caution needs to be exercised in extrapolating the properties of in vitro interprotein electron transfer reactions to those occurring in vivo.

Causality: Physics and Philosophy

ERIC Educational Resources Information Center

Chatterjee, Atanu

2013-01-01

Nature is a complex causal network exhibiting diverse forms and species. These forms or rather systems are physically open, structurally complex and naturally adaptive. They interact with the surrounding media by operating a positive-feedback loop through which, they adapt, organize and self-organize themselves in response to the ever-changing…

Pseudo-enantiomeric chiral components and formation of the helical micro- and nanostructures in charge-transfer complexes

NASA Astrophysics Data System (ADS)

Langer, Jerzy J.; Hreczycho, Grzegorz

2018-03-01

Helical organic micro- and nanostructures are formed by a charge-transfer complex, cinchonidine-TCNQ. These unusual forms result from the chirality, the steric structure and specific interactions of cinchonidine molecules. These materials are semiconductors (10-4 S cm-1), with the typical absorption spectra in IR and UV-vis, but also have a characteristic of CD spectrum. Surprisingly, conductive micro and nano helices are not formed in pseudo-enantiomeric cinchonine, i.e. the complex of cinchonine and TCNQ.

A Dicobalt Complex with an Unsymmetrical Quinonoid Bridge Isolated in Three Units of Charge: A Combined Structural, (Spectro)electrochemical, Magnetic and Spectroscopic Study.

PubMed

van der Meer, Margarethe; Rechkemmer, Yvonne; Frank, Uta; Breitgoff, Frauke D; Hohloch, Stephan; Su, Cheng-Yong; Neugebauer, Petr; Marx, Raphael; Dörfel, María; van Slageren, Joris; Sarkar, Biprajit

2016-09-19

Quinonoid ligands are excellent bridges for generating redox-rich dinuclear assemblies. A large majority of these bridges are symmetrically substituted, with examples of unsymmetrically substituted quinonoid bridges being extremely rare. We present here a dicobalt complex in its various redox states with an unsymmetrically substituted quinonoid bridging ligand. Two homovalent forms and one mixed-valent form have been isolated and characterized by single crystal X-ray diffraction. The complex displays a large comproportionation constant for the mixed-valent state which is three orders of magnitude higher than that observed for the analogous complex with a symmetrically substituted bridge. Results from electrochemistry, UV/Vis/NIR spectroelectrochemistry, SQUID magnetometry, multi-frequency EPR spectroscopy and FIR spectroscopy are used to probe the electronic structures of these complexes. FIR provides direct evidence of exchange coupling. The results presented here display the advantages of using an unsymmetrically substituted bridge: site specific redox chemistry, high thermodynamic stabilization of the mixed-valent form, isolation and crystallization of various redox forms of the complex. This work represents an important step on the way to generating heterodinuclear complexes for use in cooperative catalysis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure of homeodomain-leucine zipper/DNA complexes studied using hydroxyl radical cleavage of DNA and methylation interference.

PubMed

Tron, Adriana E; Comelli, Raúl N; Gonzalez, Daniel H

2005-12-27

Homeodomain-leucine zipper (HD-Zip) proteins, unlike most homeodomain proteins, bind a pseudopalindromic DNA sequence as dimers. We have investigated the structure of the DNA complexes formed by two HD-Zip proteins with different nucleotide preferences at the central position of the binding site using footprinting and interference methods. The results indicate that the respective complexes are not symmetric, with the strand bearing a central purine (top strand) showing higher protection around the central region and the bottom strand protected toward the 3' end. Binding to a sequence with a nonpreferred central base pair produces a decrease in protection in either the top or the bottom strand, depending upon the protein. Modeling studies derived from the complex formed by the monomeric Antennapedia homeodomain with DNA indicate that in the HD-Zip/DNA complex the recognition helix of one of the monomers is displaced within the major groove respective to the other one. This monomer seems to lose contacts with a part of the recognition sequence upon binding to the nonpreferred site. The results show that the structure of the complex formed by HD-Zip proteins with DNA is dependent upon both protein intrinsic characteristics and the nucleotides present at the central position of the recognition sequence.

The coordination structure of the extracted copper(II) complex with a synergistic mixture containing dinonylnaphthalene sulfonic acid and n-hexyl 3-pyridinecarboxylate ester

NASA Astrophysics Data System (ADS)

Zhu, Shan; Hu, Huiping; Hu, Jiugang; Li, Jiyuan; Hu, Fang; Wang, Yongxi

2017-09-01

In continuation of our interest in the coordination structure of the nickel(II) complex with dinonylnaphthalene sulfonic acid (HDNNS) and 2-ethylhexyl 4-pyridinecarboxylate ester (4PC), it was observed that the coordination sphere was completed by the coordination of two N atoms of pyridine rings in ligands 4PC and four water molecules while no direct interaction between Ni(II) and deprotonated HDNNS was observed. To investigate whether the coordination structure of nickel(II) with the synergistic mixture containing HDNNS and 4PC predominates or not in the copper(II) complex with the synergistic mixtures containing HDNNS and pyridinecarboxylate esters, a copper(II) synergist complex with n-hexyl 3-pyridinecarboxylate ester (L) and naphthalene-2-sulfonic acid (HNS, the short chain analogue of HDNNS), was prepared and studied by X-ray single crystal diffraction, elemental analyses and thermo gravimetric analysis (TGA), respectively. It was shown that the composition of the copper(II) synergist complex was [Cu(H2O)2(L)2(NS)2] and formed a trans-form distorted octahedral coordination structure. Two oxygen atoms of the two coordinated water molecules and two N atoms of the pyridine rings in the ligands L defined the basal plane while two O atoms from two sulfonate anions of the deprotonated HNS ligands occupied the apical positions by direct coordination with Cu(II), which was distinguished from the coordination structure of the nickel(II) synergist complex as reported in our previous work. In the crystal lattice, neighboring molecules [Cu(H2O)2L2(NS)2] were linked through the intermolecular hydrogen bonds between the hydrogen atoms of the coordinated water molecules and the oxygen atoms of the sulfonate anions in the copper(II) synergist complex to form a 2D plane. In order to bridge the gap between the solid state structure of the copper(II) synergist complex and the solution structure of the extracted copper(II) complex with the actual synergistic mixture containing L and HDNNS in the non-polar organic phase, the structures of the two copper(II) complexes were further investigated by Fourier transform infrared spectroscopy (FT-IR) and electrospray ionization mass spectrometry (ESI-MS), and the results indicated that the extracted copper(II) complex in the non-polar organic phase might possess a similar coordination structure as the copper(II) synergist complex.

Structural Study of the RIPoptosome Core Reveals a Helical Assembly for Kinase Recruitment

PubMed Central

2015-01-01

Receptor interaction protein kinase 1 (RIP1) is a molecular cell-fate switch. RIP1, together with Fas-associated protein with death domain (FADD) and caspase-8, forms the RIPoptosome that activates apoptosis. RIP1 also associates with RIP3 to form the necrosome that triggers necroptosis. The RIPoptosome assembles through interactions between the death domains (DDs) of RIP1 and FADD and between death effector domains (DEDs) of FADD and caspase-8. In this study, we analyzed the overall structure of the RIP1 DD/FADD DD complex, the core of the RIPoptosome, by negative-stain electron microscopy and modeling. The results show that RIP1 DD and FADD DD form a stable complex in vitro similar to the previously described Fas DD/FADD DD complex, suggesting that the RIPoptosome and the Fas death-inducing signaling complex share a common assembly mechanism. Both complexes adopt a helical conformation that requires type I, II, and III interactions between the death domains. PMID:25119434

Local laser-strengthening: Customizing the forming behavior of car body steel sheets

NASA Astrophysics Data System (ADS)

Wagner, M.; Jahn, A.; Beyer, E.; Balzani, D.

2018-05-01

Future trends in designing lightweight components especially for automotive applications increasingly require complex and delicate structures with highest possible level of capacity [1]. The manufacturing of metallic car body components is primarily realized by deep or stretch drawing. The forming process of especially cold rolled and large-sized components is typically characterized by inhomogeneous stress and strain distributions. As a result, the avoidance of undesirable deep drawing effects like earing and local necking is among the greatest challenges in forming complex car body structures [2]. Hence, a novel local laser-treatment approach with the objective of customizing the forming behavior of car body steel sheets is currently explored.

Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex

PubMed Central

Tsurumura, Toshiharu; Tsumori, Yayoi; Qiu, Hao; Oda, Masataka; Sakurai, Jun; Nagahama, Masahiro; Tsuge, Hideaki

2013-01-01

Clostridium perfringens iota-toxin (Ia) mono-ADP ribosylates Arg177 of actin, leading to cytoskeletal disorganization and cell death. To fully understand the reaction mechanism of arginine-specific mono-ADP ribosyl transferase, the structure of the toxin-substrate protein complex must be characterized. Recently, we solved the crystal structure of Ia in complex with actin and the nonhydrolyzable NAD+ analog βTAD (thiazole-4-carboxamide adenine dinucleotide); however, the structures of the NAD+-bound form (NAD+-Ia-actin) and the ADP ribosylated form [Ia-ADP ribosylated (ADPR)-actin] remain unclear. Accidentally, we found that ethylene glycol as cryo-protectant inhibits ADP ribosylation and crystallized the NAD+-Ia-actin complex. Here we report high-resolution structures of NAD+-Ia-actin and Ia-ADPR-actin obtained by soaking apo-Ia-actin crystal with NAD+ under different conditions. The structures of NAD+-Ia-actin and Ia-ADPR-actin represent the pre- and postreaction states, respectively. By assigning the βTAD-Ia-actin structure to the transition state, the strain-alleviation model of ADP ribosylation, which we proposed previously, is experimentally confirmed and improved. Moreover, this reaction mechanism appears to be applicable not only to Ia but also to other ADP ribosyltransferases. PMID:23382240

Truncated forms of the prion protein PrP demonstrate the need for complexity in prion structure.

PubMed

Wan, William; Stöhr, Jan; Kendall, Amy; Stubbs, Gerald

2015-01-01

Self-propagation of aberrant protein folds is the defining characteristic of prions. Knowing the structural basis of self-propagation is essential to understanding prions and their related diseases. Prion rods are amyloid fibrils, but not all amyloids are prions. Prions have been remarkably intractable to structural studies, so many investigators have preferred to work with peptide fragments, particularly in the case of the mammalian prion protein PrP. We compared the structures of a number of fragments of PrP by X-ray fiber diffraction, and found that although all of the peptides adopted amyloid conformations, only the larger fragments adopted conformations that modeled the complexity of self-propagating prions, and even these fragments did not always adopt the PrP structure. It appears that the relatively complex structure of the prion form of PrP is not accessible to short model peptides, and that self-propagation may be tied to a level of structural complexity unobtainable in simple model systems. The larger fragments of PrP, however, are useful to illustrate the phenomenon of deformed templating (heterogeneous seeding), which has important biological consequences.

Truncated forms of the prion protein PrP demonstrate the need for complexity in prion structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wan, William; Stöhr, Jan; Kendall, Amy

2015-09-01

Self-propagation of aberrant protein folds is the defining characteristic of prions. Knowing the structural basis of self-propagation is essential to understanding prions and their related diseases. Prion rods are amyloid fibrils, but not all amyloids are prions. Prions have been remarkably intractable to structural studies, so many investigators have preferred to work with peptide fragments, particularly in the case of the mammalian prion protein PrP. We compared the structures of a number of fragments of PrP by X-ray fiber diffraction, and found that although all of the peptides adopted amyloid conformations, only the larger fragments adopted conformations that modeled themore » complexity of self-propagating prions, and even these fragments did not always adopt the PrP structure. It appears that the relatively complex structure of the prion form of PrP is not accessible to short model peptides, and that self-propagation may be tied to a level of structural complexity unobtainable in simple model systems. The larger fragments of PrP, however, are useful to illustrate the phenomenon of deformed templating (heterogeneous seeding), which has important biological consequences.« less

Synthesis and Elucidation Structure of Tetrakis-diphenylaminecopper(II) Chloride Hexahydrate

NASA Astrophysics Data System (ADS)

Syaima, H.; Rahardjo, S. B.; Suciningrum, E.

2017-11-01

CuCl2·2H2O with diphenylamine formed a complex compound in 1:4-mole ratio of metal to the ligand in methanol. Its structural properties were investigated by employing metal content analysis by Atomic Absorption Spectroscopy (AAS), magnetic susceptibility, UV-vis and FTIR spectroscopy. The forming of the complex was indicated by shifting of UV-Vis spectra. The result of analysis Cu(II) in the complex showed empirical formula of the complex were Cu(diphenylamine)4Cl2(H2O)6. The electrical conductivity of complex showed the charge ratio of cation and anion = 2:1. Finally, the proposed formula of the complex was [Cu(diphenylamine)4]Cl2·6H2O. Based on infrared spectra, it was revealed that diphenylamine existed as monodentate bind to copper(II) through the functional group of N-H. The electronic spectral study of the complex showed three transition peaks on 861, 592, and 419 nm corresponding to the 2B1g → 2A1g, 2B1g → 2B2g dan 2B1g → 2Eg transitions. The complex was paramagnetic and indicated that ligands form square planar geometry around the Cu(II).

Structure of β- N-dimethylamino-4-dodecyloxypropiophenone complexes with di- and polycarboxylic acids

NASA Astrophysics Data System (ADS)

Lebedeva, Tamara L.; Shandryuk, George A.; Sycheva, Tatyana I.; Bezborodov, Vladimir S.; Talroze, Raissa V.; Platé, Nicolai A.

1995-07-01

The type of bonds responsible for the complexation of di- and polyacids with the tertiary amine β- N-dimethylamino-4-dodecyloxypropiophenone is studied by means of FTIR spectroscopy. The complexes are shown to be stable due to strong H-bonding with partial charge transfer. The characteristic composition for complexes of polyacrylic, polymethacrylic and malonic acids is calculated as 2:1 (number of carboxylic groups per number of amine molecules) whereas glutaric acid forms complexes of different composition including 1:1. The characteristic composition results from the structure of the initial acid. The structures of both the characteristic complex and "excess" acid are also discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cavalier, Michael C.; Yim, Young-Sun; Asamizu, Shumpei

The pseudo-glycosyltransferase VldE catalyzes non-glycosidic C-N coupling between an unsaturated cyclitol and a saturated aminocyclitol with the conservation of the stereochemical configuration of the substrates to form validoxylamine A 7'-phosphate, the biosynthetic precursor of the antibiotic validamycin A. To study the molecular basis of its mechanism, the three-dimensional structures of VldE from Streptomyces hygroscopicus subsp. limoneus was determined in apo form, in complex with GDP, in complex with GDP and validoxylamine A 7'-phosphate, and in complex with GDP and trehalose. The structure of VldE with the catalytic site in both an “open” and “closed” conformation is also described. With thesemore » structures, the preferred binding of the guanine moiety by VldE, rather than the uracil moiety as seen in OtsA could be explained. The elucidation of the VldE structure in complex with the entirety of its products provides insight into the internal return mechanism by which catalysis occurs with a net retention of the stereochemical configuration of the donated cyclitol.« less

Fantasy Play of Preschoolers as a Function of Toy Structures.

ERIC Educational Resources Information Center

Einsiedler, Wolfgang

Two studies are presented which investigate the influence of various toy structures on the frequency of individual fantasy play forms in 3- to 6-year-old children. In the first study, the effects of high-realistic/high-complexity and low-realistic/low-complexity toy structures were compared. There were significant main effects for the factor toy…

Structure of the apo form of the catabolite control protein A (CcpA) from Bacillus megaterium with a DNA-binding domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Rajesh Kumar; Palm, Gottfried J.; Panjikar, Santosh

2007-04-01

Crystal structure analysis of the apo form of catabolite control protein A reveals the three-helix bundle of the DNA-binding domain. In the crystal packing, this domain interacts with the binding site for the corepressor protein. Crystal structure determination of catabolite control protein A (CcpA) at 2.6 Å resolution reveals for the first time the structure of a full-length apo-form LacI-GalR family repressor protein. In the crystal structures of these transcription regulators, the three-helix bundle of the DNA-binding domain has only been observed in cognate DNA complexes; it has not been observed in other crystal structures owing to its mobility. Inmore » the crystal packing of apo-CcpA, the protein–protein contacts between the N-terminal three-helix bundle and the core domain consisted of interactions between the homodimers that were similar to those between the corepressor protein HPr and the CcpA N-subdomain in the ternary DNA complex. In contrast to the DNA complex, the apo-CcpA structure reveals large subdomain movements in the core, resulting in a complete loss of contacts between the N-subdomains of the homodimer.« less

Fluoroquinolone-Gyrase-DNA Complexes

PubMed Central

Mustaev, Arkady; Malik, Muhammad; Zhao, Xilin; Kurepina, Natalia; Luan, Gan; Oppegard, Lisa M.; Hiasa, Hiroshi; Marks, Kevin R.; Kerns, Robert J.; Berger, James M.; Drlica, Karl

2014-01-01

DNA gyrase and topoisomerase IV control bacterial DNA topology by breaking DNA, passing duplex DNA through the break, and then resealing the break. This process is subject to reversible corruption by fluoroquinolones, antibacterials that form drug-enzyme-DNA complexes in which the DNA is broken. The complexes, called cleaved complexes because of the presence of DNA breaks, have been crystallized and found to have the fluoroquinolone C-7 ring system facing the GyrB/ParE subunits. As expected from x-ray crystallography, a thiol-reactive, C-7-modified chloroacetyl derivative of ciprofloxacin (Cip-AcCl) formed cross-linked cleaved complexes with mutant GyrB-Cys466 gyrase as evidenced by resistance to reversal by both EDTA and thermal treatments. Surprisingly, cross-linking was also readily seen with complexes formed by mutant GyrA-G81C gyrase, thereby revealing a novel drug-gyrase interaction not observed in crystal structures. The cross-link between fluoroquinolone and GyrA-G81C gyrase correlated with exceptional bacteriostatic activity for Cip-AcCl with a quinolone-resistant GyrA-G81C variant of Escherichia coli and its Mycobacterium smegmatis equivalent (GyrA-G89C). Cip-AcCl-mediated, irreversible inhibition of DNA replication provided further evidence for a GyrA-drug cross-link. Collectively these data establish the existence of interactions between the fluoroquinolone C-7 ring and both GyrA and GyrB. Because the GyrA-Gly81 and GyrB-Glu466 residues are far apart (17 Å) in the crystal structure of cleaved complexes, two modes of quinolone binding must exist. The presence of two binding modes raises the possibility that multiple quinolone-enzyme-DNA complexes can form, a discovery that opens new avenues for exploring and exploiting relationships between drug structure and activity with type II DNA topoisomerases. PMID:24497635

Coevolutionary constraints in the sequence-space of macromolecular complexes reflect their self-assembly pathways.

PubMed

Mallik, Saurav; Kundu, Sudip

2017-07-01

Is the order in which biomolecular subunits self-assemble into functional macromolecular complexes imprinted in their sequence-space? Here, we demonstrate that the temporal order of macromolecular complex self-assembly can be efficiently captured using the landscape of residue-level coevolutionary constraints. This predictive power of coevolutionary constraints is irrespective of the structural, functional, and phylogenetic classification of the complex and of the stoichiometry and quaternary arrangement of the constituent monomers. Combining this result with a number of structural attributes estimated from the crystal structure data, we find indications that stronger coevolutionary constraints at interfaces formed early in the assembly hierarchy probably promotes coordinated fixation of mutations that leads to high-affinity binding with higher surface area, increased surface complementarity and elevated number of molecular contacts, compared to those that form late in the assembly. Proteins 2017; 85:1183-1189. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats

PubMed Central

Pierce, Sarah E.; Wang, Junmei; Jayawickramarajah, Janarthanan; Hamilton, Andrew D.; Brodbelt, Jennifer S.

2010-01-01

Isoguanine (2-oxo-6-amino-guanine), a natural but non-standard base, exhibits unique self-association properties compared to its isomer, guanine, and results in formation of different higher order DNA structures. In this work, the higher order structures formed by oligonucleotides containing guanine repeats or isoguanine repeats after annealing in solutions containing various cations are evaluated by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. The guanine-containing strand (G9) consistently formed quadruplexes upon annealing, whereas the isoguanine strand (Ig9) formed both pentaplexes and quadruplexes depending on the annealing cation. Quadruplex formation with G9 showed some dependence on the identity of the cation present during annealing with high relative quadruplex formation detected with six of ten cations. Analogous annealing experiments with Ig9 resulted in complex formation with all ten cations, and the majority of the resulting complexes were pentaplexes. CD results indicated most of the original complexes survived the desalting process necessary for ESI-MS analysis. In addition, several complexes, especially the pentaplexes, were found to be capable of cation exchange with ammonium ions. Ab initio calculations were conducted for isoguanine tetrads and pentads coordinated with all ten cations to predict the most energetically stable structures of the complexes in the gas phase. The observed preference of forming quadruplexes versus pentaplexes as a function of the coordinated cation can be interpreted by the calculated reaction energies of both the tetrads and pentads in combination with the distortion energies of tetrads. PMID:19746468

Complex structure of the fission yeast SREBP-SCAP binding domains reveals an oligomeric organization.

PubMed

Gong, Xin; Qian, Hongwu; Shao, Wei; Li, Jingxian; Wu, Jianping; Liu, Jun-Jie; Li, Wenqi; Wang, Hong-Wei; Espenshade, Peter; Yan, Nieng

2016-11-01

Sterol regulatory element-binding protein (SREBP) transcription factors are master regulators of cellular lipid homeostasis in mammals and oxygen-responsive regulators of hypoxic adaptation in fungi. SREBP C-terminus binds to the WD40 domain of SREBP cleavage-activating protein (SCAP), which confers sterol regulation by controlling the ER-to-Golgi transport of the SREBP-SCAP complex and access to the activating proteases in the Golgi. Here, we biochemically and structurally show that the carboxyl terminal domains (CTD) of Sre1 and Scp1, the fission yeast SREBP and SCAP, form a functional 4:4 oligomer and Sre1-CTD forms a dimer of dimers. The crystal structure of Sre1-CTD at 3.5 Å and cryo-EM structure of the complex at 5.4 Å together with in vitro biochemical evidence elucidate three distinct regions in Sre1-CTD required for Scp1 binding, Sre1-CTD dimerization and tetrameric formation. Finally, these structurally identified domains are validated in a cellular context, demonstrating that the proper 4:4 oligomeric complex formation is required for Sre1 activation.

Crystal structures of the apo and ATP bound Mycobacterium tuberculosis nitrogen regulatory PII protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shetty, Nishant D.; Reddy, Manchi C.M.; Palaninathan, Satheesh K.

2010-10-11

PII constitutes a family of signal transduction proteins that act as nitrogen sensors in microorganisms and plants. Mycobacterium tuberculosis (Mtb) has a single homologue of PII whose precise role has as yet not been explored. We have solved the crystal structures of the Mtb PII protein in its apo and ATP bound forms to 1.4 and 2.4 {angstrom} resolutions, respectively. The protein forms a trimeric assembly in the crystal lattice and folds similarly to the other PII family proteins. The Mtb PII:ATP binary complex structure reveals three ATP molecules per trimer, each bound between the base of the T-loop ofmore » one subunit and the C-loop of the neighboring subunit. In contrast to the apo structure, at least one subunit of the binary complex structure contains a completely ordered T-loop indicating that ATP binding plays a role in orienting this loop region towards target proteins like the ammonium transporter, AmtB. Arg38 of the T-loop makes direct contact with the {gamma}-phosphate of the ATP molecule replacing the Mg{sup 2+} position seen in the Methanococcus jannaschii GlnK1 structure. The C-loop of a neighboring subunit encloses the other side of the ATP molecule, placing the GlnK specific C-terminal 3{sub 10} helix in the vicinity. Homology modeling studies with the E. coli GlnK:AmtB complex reveal that Mtb PII could form a complex similar to the complex in E. coli. The structural conservation and operon organization suggests that the Mtb PII gene encodes for a GlnK protein and might play a key role in the nitrogen regulatory pathway.« less

The VMC Survey. XXVII. Young Stellar Structures in the LMC’s Bar Star-forming Complex

NASA Astrophysics Data System (ADS)

Sun, Ning-Chen; de Grijs, Richard; Subramanian, Smitha; Bekki, Kenji; Bell, Cameron P. M.; Cioni, Maria-Rosa L.; Ivanov, Valentin D.; Marconi, Marcella; Oliveira, Joana M.; Piatti, Andrés E.; Ripepi, Vincenzo; Rubele, Stefano; Tatton, Ben L.; van Loon, Jacco Th.

2017-11-01

Star formation is a hierarchical process, forming young stellar structures of star clusters, associations, and complexes over a wide range of scales. The star-forming complex in the bar region of the Large Magellanic Cloud is investigated with upper main-sequence stars observed by the VISTA Survey of the Magellanic Clouds. The upper main-sequence stars exhibit highly nonuniform distributions. Young stellar structures inside the complex are identified from the stellar density map as density enhancements of different significance levels. We find that these structures are hierarchically organized such that larger, lower-density structures contain one or several smaller, higher-density ones. They follow power-law size and mass distributions, as well as a lognormal surface density distribution. All these results support a scenario of hierarchical star formation regulated by turbulence. The temporal evolution of young stellar structures is explored by using subsamples of upper main-sequence stars with different magnitude and age ranges. While the youngest subsample, with a median age of log(τ/yr) = 7.2, contains the most substructure, progressively older ones are less and less substructured. The oldest subsample, with a median age of log(τ/yr) = 8.0, is almost indistinguishable from a uniform distribution on spatial scales of 30-300 pc, suggesting that the young stellar structures are completely dispersed on a timescale of ˜100 Myr. These results are consistent with the characteristics of the 30 Doradus complex and the entire Large Magellanic Cloud, suggesting no significant environmental effects. We further point out that the fractal dimension may be method dependent for stellar samples with significant age spreads.

Structural characterization of polymorphs and molecular complexes of finasteride

NASA Astrophysics Data System (ADS)

Wawrzycka, Irena; Stȩpniak, Krystyna; Matyjaszczyk, Sławomir; Kozioł, Anna E.; Lis, Tadeusz; Abboud, Khalil A.

1999-01-01

The molecular structure of finasteride, 17 β-( N-tert-butylcarbamoyl)-4-aza-5 α-androst-1-en-3-one, and structures of three related crystalline forms have been determined by X-ray analysis. The rigid steroid skeleton of the molecule adopts a half-chair/chair/chair/half-chair conformation. Two peptide groups, one cyclic (lactam) in the ring A and a second being a part of the substituent at C17, are the main factors influencing intermolecular contacts. Different hydrogen-bond interactions of these hydrophilic groups are observed in the crystal structures. An infinite ribbon of finasteride molecules is formed between lactam groups in the orthorhombic homomolecular crystal ( 1) obtained from an ethanol solution. The linear molecular complex finasteride-acetic acid ( 1a) is connected by hydrogen bonds between the lactam of finasteride and the carboxyl group of acetic acid. The crystallization from an ethyl acetate solution gives a complex structure of bis-finasteride monohydrate ethyl acetate clathrate ( 1b) with guest molecule disordered in channels. Crystals of a second (monoclinic) finasteride polymorph ( 2) were obtained during thermal decomposition of 1a, and sublimation of 1, 1a and 1b. Two polymorphic forms show different IR spectra.

Self-organized minimum-energy structures for dielectric elastomer actuators

NASA Astrophysics Data System (ADS)

Kofod, G.; Paajanen, M.; Bauer, S.

2006-11-01

When a stretched elastomer is laminated to a flat plastic frame, a complex shape is formed, which is termed a minimum-energy structure. It is shown how self-organized structures can be applied in the development of actuators with complex, out-of-plane actuationmodes. This unusual concept is then demonstrated in the case of dielectric elastomer actuators. Among advantages of this approach are the simplicity in manufacturing, the potential complexity and sophistication of the manufactured structures, and the general benefits of the concept when applied to other electro-mechanically active materials.

Approximate analytical solutions in the analysis of elastic structures of complex geometry

NASA Astrophysics Data System (ADS)

Goloskokov, Dmitriy P.; Matrosov, Alexander V.

2018-05-01

A method of analytical decomposition for analysis plane structures of a complex configuration is presented. For each part of the structure in the form of a rectangle all the components of the stress-strain state are constructed by the superposition method. The method is based on two solutions derived in the form of trigonometric series with unknown coefficients using the method of initial functions. The coefficients are determined from the system of linear algebraic equations obtained while satisfying the boundary conditions and the conditions for joining the structure parts. The components of the stress-strain state of a bent plate with holes are calculated using the analytical decomposition method.

Heterobimetallic thiocyanato-bridged coordination polymers based on [Hg(SCN) 4] 2-: Synthesis, crystal structure, magnetic properties and ESR studies

NASA Astrophysics Data System (ADS)

Jian, Fang-Fang; Xiao, Hai-Lian; Liu, Fa Qian

2006-12-01

Three new M/Hg bimetallic thiocyanato-bridged coordination polymers; [Hg(SCN) 4Ni(Im) 3] ∞1, [Hg(SCN) 4Mn(Im) 2] ∞2, and [Hg(SCN) 4Cu(Me-Im) 2 Hg(SCN) 4Cu(Me-Im) 4] ∞3, (Im=imidazole, Me-Im= N-methyl-imidazole), have been synthesized and characterized by means of elemental analysis, ESR, and single-crystal X-ray. X-ray diffraction analysis reveals that these three complexes all form 3D network structure, and their structures all contain a thiocyanato-bridged Hg⋯M⋯Hg chain ( M=Mn, Ni, Cu) in which the metal and mercury centers exhibit different coordination environments. In complex 1, the [Hg(SCN) 4] 2- anion connects three [Ni(Im) 3] 2+ using three SCN ligands giving rise to a 3D structure, and in complex 2, four SCN ligands bridge [Hg(SCN) 4] 2- and [Mn(Im) 2] 2+ to form a 3D structure. The structure of 3 contains two copper atoms with distinct coordination environment; one is coordinated by four N-methyl-imidazole ligands and two axially elongated SCN groups, and another by four SCN groups (two elongated) and two N-methyl-imidazole ligands. The magnetic property of complex 1 has been investigated. The spin state structure in hetermetallic NiHgNi systems of complex 1 is irregular. The ESR spectra results of complex 3 demonstrate Cu 2+ ion lie on octahedral environment.

Atomic structure of the Y complex of the nuclear pore

DOE PAGES

Kelley, Kotaro; Knockenhauer, Kevin E.; Kabachinski, Greg; ...

2015-03-30

The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. In this paper, we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved coremore » of the Y complex has six rather than seven members. Finally, evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.« less

Probing the structural dynamics of the CRISPR-Cas9 RNA-guided DNA-cleavage system by coarse-grained modeling.

PubMed

Zheng, Wenjun

2017-02-01

In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism. To further probe the structural dynamics of Cas9 interacting with RNA and DNA at the amino-acid level of details, we have performed systematic coarse-grained modeling using an elastic network model and related analyses. Our normal mode analysis predicted a few key modes of collective motions that capture the observed conformational changes featuring large domain motions triggered by binding of RNA and DNA. Our flexibility analysis identified specific regions with high or low flexibility that coincide with key functional sites (such as DNA/RNA-binding sites, nuclease cleavage sites, and key hinges). We also identified a small set of hotspot residues that control the energetics of functional motions, which overlap with known functional sites and offer promising targets for future mutagenesis efforts to improve the specificity of Cas9. Finally, we modeled the conformational transitions of Cas9 from the unbound form to the binary complex and then the tertiary complex, and predicted a distinct sequence of domain motions. In sum, our findings have offered rich structural and dynamic details relevant to the Cas9 machinery, and will guide future investigation and engineering of the Cas9 systems. Proteins 2017; 85:342-353. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ.

PubMed

Dharmaiah, Srisathiyanarayanan; Bindu, Lakshman; Tran, Timothy H; Gillette, William K; Frank, Peter H; Ghirlando, Rodolfo; Nissley, Dwight V; Esposito, Dominic; McCormick, Frank; Stephen, Andrew G; Simanshu, Dhirendra K

2016-11-01

Farnesylation and carboxymethylation of KRAS4b (Kirsten rat sarcoma isoform 4b) are essential for its interaction with the plasma membrane where KRAS-mediated signaling events occur. Phosphodiesterase-δ (PDEδ) binds to KRAS4b and plays an important role in targeting it to cellular membranes. We solved structures of human farnesylated-methylated KRAS4b in complex with PDEδ in two different crystal forms. In these structures, the interaction is driven by the C-terminal amino acids together with the farnesylated and methylated C185 of KRAS4b that binds tightly in the central hydrophobic pocket present in PDEδ. In crystal form II, we see the full-length structure of farnesylated-methylated KRAS4b, including the hypervariable region. Crystal form I reveals structural details of farnesylated-methylated KRAS4b binding to PDEδ, and crystal form II suggests the potential binding mode of geranylgeranylated-methylated KRAS4b to PDEδ. We identified a 5-aa-long sequence motif (Lys-Ser-Lys-Thr-Lys) in KRAS4b that may enable PDEδ to bind both forms of prenylated KRAS4b. Structure and sequence analysis of various prenylated proteins that have been previously tested for binding to PDEδ provides a rationale for why some prenylated proteins, such as KRAS4a, RalA, RalB, and Rac1, do not bind to PDEδ. Comparison of all four available structures of PDEδ complexed with various prenylated proteins/peptides shows the presence of additional interactions due to a larger protein-protein interaction interface in KRAS4b-PDEδ complex. This interface might be exploited for designing an inhibitor with minimal off-target effects.

Structure for HTS composite conductors and the manufacture of same

DOEpatents

Cotton, J.D.; Riley, G.N. Jr.

1999-06-01

A superconducting oxide composite structure including a superconducting oxide member, a metal layer surrounding the superconducting oxide member, and an insulating layer of a complex oxide formed in situ adjacent to the superconducting oxide member and the metal layer is provided together with a method of forming such a superconducting oxide composite structure including encapsulating a superconducting oxide member or precursor within a metal matrix layer from the group of: (1) a reactive metal sheath adjacent to the superconducting oxide member or precursor, the reactive metal sheath surrounded by a second metal layer or (2) an alloy containing a reactive metal; to form an intermediate product, and, heating the intermediate product at temperatures and for time sufficient to form an insulating layer of a complex oxide in situ, the insulating layer to the superconducting oxide member or precursor and the metal matrix layer. 10 figs.

Structure for hts composite conductors and the manufacture of same

DOEpatents

Cotton, James D.; Riley, Jr., Gilbert Neal

1999-01-01

A superconducting oxide composite structure including a superconducting oxide member, a metal layer surrounding the superconducting oxide member, and an insulating layer of a complex oxide formed in situ adjacent to the superconducting oxide member and the metal layer is provided together with a method of forming such a superconducting oxide composite structure including encapsulating a superconducting oxide member or precursor within a metal matrix layer from the group of: (i) a reactive metal sheath adjacent to the superconducting oxide member or precursor, the reactive metal sheath surrounded by a second metal layer or (ii) an alloy containing a reactive metal; to form an intermediate product, and, heating the intermediate product at temperatures and for time sufficient to form an insulating layer of a complex oxide in situ, the insulating layer to the superconducting oxide member or precursor and the metal matrix layer.

Protoenzymes: the case of hyperbranched polyesters

NASA Astrophysics Data System (ADS)

Mamajanov, Irena; Cody, George D.

2017-11-01

Enzymes are biopolymeric complexes that catalyse biochemical reactions and shape metabolic pathways. Enzymes usually work with small molecule cofactors that actively participate in reaction mechanisms and complex, usually globular, polymeric structures capable of specific substrate binding, encapsulation and orientation. Moreover, the globular structures of enzymes possess cavities with modulated microenvironments, facilitating the progression of reaction(s). The globular structure is ensured by long folded protein or RNA strands. Synthesis of such elaborate complexes has proven difficult under prebiotically plausible conditions. We explore here that catalysis may have been performed by alternative polymeric structures, namely hyperbranched polymers. Hyperbranched polymers are relatively complex structures that can be synthesized under prebiotically plausible conditions; their globular structure is ensured by virtue of their architecture rather than folding. In this study, we probe the ability of tertiary amine-bearing hyperbranched polyesters to form hydrophobic pockets as a reaction-promoting medium for the Kemp elimination reaction. Our results show that polyesters formed upon reaction between glycerol, triethanolamine and organic acid containing hydrophobic groups, i.e. adipic and methylsuccinic acid, are capable of increasing the rate of Kemp elimination by a factor of up to 3 over monomeric triethanolamine. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Structural basis of intramitochondrial phosphatidic acid transport mediated by Ups1-Mdm35 complex.

PubMed

Yu, Fang; He, Fangyuan; Yao, Hongyan; Wang, Chengyuan; Wang, Jianchuan; Li, Jianxu; Qi, Xiaofeng; Xue, Hongwei; Ding, Jianping; Zhang, Peng

2015-07-01

Ups1 forms a complex with Mdm35 and is critical for the transport of phosphatidic acid (PA) from the mitochondrial outer membrane to the inner membrane. We report the crystal structure of the Ups1-Mdm35-PA complex and the functional characterization of Ups1-Mdm35 in PA binding and transfer. Ups1 features a barrel-like structure consisting of an antiparallel β-sheet and three α-helices. Mdm35 adopts a three-helical clamp-like structure to wrap around Ups1 to form a stable complex. The β-sheet and α-helices of Ups1 form a long tunnel-like pocket to accommodate the substrate PA, and a short helix α2 acts as a lid to cover the pocket. The hydrophobic residues lining the pocket and helix α2 are critical for PA binding and transfer. In addition, a hydrophilic patch on the surface of Ups1 near the PA phosphate-binding site also plays an important role in the function of Ups1-Mdm35. Our study reveals the molecular basis of the function of Ups1-Mdm35 and sheds new light on the mechanism of intramitochondrial phospholipid transport by the MSF1/PRELI family proteins. © 2015 The Authors.

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2013-10-28

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DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Dong; Chen, Mingyang; Martinez-Macias, Claudia

In this study, the adsorption of N 2 on structurally well-defined dealuminated HY zeolite-supported iridium diethylene complexes was investigated. Iridium dinitrogen complexes formed when the sample was exposed to N 2 in H 2 at 298 K, as shown by infrared spectra recorded with isotopically labeled N 2. Four supported species formed in various flowing gases: Ir(N 2), Ir(N 2)(N 2), Ir(C 2H 5)(N 2), and Ir(H)(N 2). Their interconversions are summarized in a reaction network, showing, for example, that, in the presence of N 2, Ir(N 2) was the predominant dinitrogen species at temperatures of 273-373 K. Ir(CO)(N 2)more » formed transiently in flowing CO, and in the presence of H 2, rather stable iridium hydride complexes formed. Here, four structural models of each iridium complex bonded at the acidic sites of the zeolite were employed in a computational investigation, showing that the calculated vibrational frequencies agree well with experiment when full calculations are done at the level of density functional theory, independent of the size of the model of the zeolite.« less

Tor forms a dimer through an N-terminal helical solenoid with a complex topology

NASA Astrophysics Data System (ADS)

Baretić, Domagoj; Berndt, Alex; Ohashi, Yohei; Johnson, Christopher M.; Williams, Roger L.

2016-04-01

The target of rapamycin (Tor) is a Ser/Thr protein kinase that regulates a range of anabolic and catabolic processes. Tor is present in two complexes, TORC1 and TORC2, in which the Tor-Lst8 heterodimer forms a common sub-complex. We have determined the cryo-electron microscopy (EM) structure of Tor bound to Lst8. Two Tor-Lst8 heterodimers assemble further into a dyad-symmetry dimer mediated by Tor-Tor interactions. The first 1,300 residues of Tor form a HEAT repeat-containing α-solenoid with four distinct segments: a highly curved 800-residue N-terminal 'spiral', followed by a 400-residue low-curvature 'bridge' and an extended `railing' running along the bridge leading to the 'cap' that links to FAT region. This complex topology was verified by domain insertions and offers a new interpretation of the mTORC1 structure. The spiral of one TOR interacts with the bridge of another, which together form a joint platform for the Regulatory Associated Protein of TOR (RAPTOR) regulatory subunit.

Synthesis, structures, and photophysical properties of π-expanded oligothiophene 8-mers and their Saturn-like C₆₀ complexes.

PubMed

Shimizu, Hideyuki; Cojal González, José D; Hasegawa, Masashi; Nishinaga, Tohru; Haque, Tahmina; Takase, Masayoshi; Otani, Hiroyuki; Rabe, Jürgen P; Iyoda, Masahiko

2015-03-25

Two isomers of a multifunctional π-expanded macrocyclic oligothiophene 8-mer, E,E-1 and Z,Z-1, were synthesized using a McMurry coupling of a dialdehyde composed of four 2,5-thienylene and three ethynylene units under high dilution conditions. On the other hand, cyclo[8](2,5-thienylene-ethynylene) 2 was synthesized by intramolecular Sonogashira cyclization of ethynyl bromide 5. From STM measurements, both E,E-1 and Z,Z-1 formed self-assembled monolayers at the solid-liquid interface to produce porous networks, and from X-ray analyses of E,E-1 and 2, both compounds had a round shape with a honeycomb stacked structure. E,E-1 formed various fibrous polymorphs due to nanophase separation of the macrorings. E,E-1 and Z,Z-1 in solution exhibited photochromism upon irradiation with visible and UV light, respectively, and this photoisomerization was confirmed by using STM. Furthermore, amorphous films of Z,Z-1 and E,E-1 showed photoisomerization, although single crystals, fibers, and square tubes of E,E-1 remained unchanged under similar conditions. E,E-1 with a 12.5-14.7 Å inner cavity incorporated fullerene C60 in the cavity in solution and the solid state to produce a Saturn-like complex, whose structure was determined by X-ray analysis. 2 also formed a Saturn-like complex with C60 in the solid state. These Saturn-like complexes are stabilized by van der Waals interactions between the sulfur atoms of 8-mer and C60. The complexes exhibited charge-transfer interactions in the solid state. Like E,E-1, Saturn-like complex E,E-1⊃C60 formed small cube and fiber structures depending on the solvent used, whereas those of Saturn-like complex 2⊃C60 were limited due to the rigidity of the macroring of 2.

Evidence of formation of site-selective inclusion complexation between beta-cyclodextrin and poly(ethylene oxide)-block-poly(propylene oxide)- block-poly(ethylene oxide) copolymers.

PubMed

Tsai, Chi-Chun; Zhang, Wen-Bin; Wang, Chien-Lung; Van Horn, Ryan M; Graham, Matthew J; Huang, Jing; Chen, Yongming; Guo, Mingming; Cheng, Stephen Z D

2010-05-28

A series of inclusion complexes of poly(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide) (PEO-b-PPO-b-PEO) with beta-cyclodextrin (beta-CD) was prepared. Their formation, structure, and dynamics were investigated by solution two-dimensional rotating-frame Overhauser effect spectroscopy (2D ROESY) and one-dimensional (1D) and 2D solid-state (13)C NMR. The inclusion complexes between the PEO-b-PPO-b-PEO copolymers and the beta-CDs were formed in aqueous solution and detected by 2D ROESY. The high efficiency of cross polarization and spin diffusion experiments in (13)C solid-state NMR showed that the mobility of the PPO blocks dramatically decreases after beta-CD complexation, indicating that they are selectively incorporated onto the PPO blocks. The hydrophobic cavities of beta-CD restrict the PPO block mobility, which is evidence of the formation of inclusion complexes in the solid state. The 2D wide-line separation NMR experiments suggested that beta-CDs only thread onto the PPO blocks while forming the inclusion complexes. The stoichiometry of inclusion complexes was studied using (1)H NMR, and a 3:1 (PO unit to beta-CD) was found for all inclusion complexes, which indicated that the number of threaded beta-CDs was only dependent on the molecular weight of the PPO blocks. 1D wide angle x-ray diffraction studies demonstrated that the beta-CD in the inclusion complex formed a channel-like structure that is different from the pure beta-CD crystal structure.

Evidence of formation of site-selective inclusion complexation between β-cyclodextrin and poly(ethylene oxide)-block-poly(propylene oxide)- block-poly(ethylene oxide) copolymers

NASA Astrophysics Data System (ADS)

Tsai, Chi-Chun; Zhang, Wen-Bin; Wang, Chien-Lung; Van Horn, Ryan M.; Graham, Matthew J.; Huang, Jing; Chen, Yongming; Guo, Mingming; Cheng, Stephen Z. D.

2010-05-01

A series of inclusion complexes of poly(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide) (PEO-b-PPO-b-PEO) with β-cyclodextrin (β-CD) was prepared. Their formation, structure, and dynamics were investigated by solution two-dimensional rotating-frame Overhauser effect spectroscopy (2D ROESY) and one-dimensional (1D) and 2D solid-state C13 NMR. The inclusion complexes between the PEO-b-PPO-b-PEO copolymers and the β-CDs were formed in aqueous solution and detected by 2D ROESY. The high efficiency of cross polarization and spin diffusion experiments in C13 solid-state NMR showed that the mobility of the PPO blocks dramatically decreases after β-CD complexation, indicating that they are selectively incorporated onto the PPO blocks. The hydrophobic cavities of β-CD restrict the PPO block mobility, which is evidence of the formation of inclusion complexes in the solid state. The 2D wide-line separation NMR experiments suggested that β-CDs only thread onto the PPO blocks while forming the inclusion complexes. The stoichiometry of inclusion complexes was studied using H1 NMR, and a 3:1 (PO unit to β-CD) was found for all inclusion complexes, which indicated that the number of threaded β-CDs was only dependent on the molecular weight of the PPO blocks. 1D wide angle x-ray diffraction studies demonstrated that the β-CD in the inclusion complex formed a channel-like structure that is different from the pure β-CD crystal structure.

ND3, ND1 and 39 kDa subunits are more exposed in the de-active form of bovine mitochondrial complex I

PubMed Central

Babot, Marion; Labarbuta, Paola; Birch, Amanda; Kee, Sara; Fuszard, Matthew; Botting, Catherine H.; Wittig, Ilka; Heide, Heinrich; Galkin, Alexander

2014-01-01

An intriguing feature of mitochondrial complex I from several species is the so-called A/D transition, whereby the idle enzyme spontaneously converts from the active (A) form to the de-active (D) form. The A/D transition plays an important role in tissue response to the lack of oxygen and hypoxic deactivation of the enzyme is one of the key regulatory events that occur in mitochondria during ischaemia. We demonstrate for the first time that the A/D conformational change of complex I does not affect the macromolecular organisation of supercomplexes in vitro as revealed by two types of native electrophoresis. Cysteine 39 of the mitochondrially-encoded ND3 subunit is known to become exposed upon de-activation. Here we show that even if complex I is a constituent of the I + III2 + IV (S1) supercomplex, cysteine 39 is accessible for chemical modification in only the D-form. Using lysine-specific fluorescent labelling and a DIGE-like approach we further identified two new subunits involved in structural rearrangements during the A/D transition: ND1 (MT-ND1) and 39 kDa (NDUFA9). These results clearly show that structural rearrangements during de-activation of complex I include several subunits located at the junction between hydrophilic and hydrophobic domains, in the region of the quinone binding site. De-activation of mitochondrial complex I results in concerted structural rearrangement of membrane subunits which leads to the disruption of the sealed quinone chamber required for catalytic turnover. PMID:24560811

Structure of MyTH4-FERM domains in myosin VIIa tail bound to cargo.

PubMed

Wu, Lin; Pan, Lifeng; Wei, Zhiyi; Zhang, Mingjie

2011-02-11

The unconventional myosin VIIa (MYO7A) is one of the five proteins that form a network of complexes involved in formation of stereocilia. Defects in these proteins cause syndromic deaf-blindness in humans [Usher syndrome I (USH1)]. Many disease-causing mutations occur in myosin tail homology 4-protein 4.1, ezrin, radixin, moesin (MyTH4-FERM) domains in the myosin tail that binds to another USH1 protein, Sans. We report the crystal structure of MYO7A MyTH4-FERM domains in complex with the central domain (CEN) of Sans at 2.8 angstrom resolution. The MyTH4 and FERM domains form an integral structural and functional supramodule binding to two highly conserved segments (CEN1 and 2) of Sans. The MyTH4-FERM/CEN complex structure provides mechanistic explanations for known deafness-causing mutations in MYO7A MyTH4-FERM. The structure will also facilitate mechanistic and functional studies of MyTH4-FERM domains in other myosins.

Searching for life in the Universe: unconventional methods for an unconventional problem.

PubMed

Nealson, K H; Tsapin, A; Storrie-Lombardi, M

2002-12-01

The search for life, on and off our planet, can be done by conventional methods with which we are all familiar. These methods are sensitive and specific, and are often capable of detecting even single cells. However, if the search broadens to include life that may be different (even subtly different) in composition, the methods and even the approach must be altered. Here we discuss the development of what we call non-earthcentric life detection--detecting life with methods that could detect life no matter what its form or composition. To develop these methods, we simply ask, can we define life in terms of its general properties and particularly those that can be measured and quantified? Taking such an approach we can search for life using physics and chemistry to ask questions about structure, chemical composition, thermodynamics, and kinetics. Structural complexity can be searched for using computer algorithms that recognize complex structures. Once identified, these structures can be examined for a variety of chemical traits, including elemental composition, chirality, and complex chemistry. A second approach involves defining our environment in terms of energy sources (i.e., reductants), and oxidants (e.g. what is available to eat and breathe), and then looking for areas in which such phenomena are inexplicably out of chemical equilibrium. These disequilibria, when found, can then be examined in detail for the presence of the structural and chemical complexity that presumably characterizes any living systems. By this approach, we move the search for life to one that should facilitate the detection of any earthly life it encountered, as well as any non-conventional life forms that have structure, complex chemistry, and live via some form of redox chemistry.

An asymmetric structure of the Bacillus subtilis replication terminator protein in complex with DNA.

PubMed

Vivian, J P; Porter, C J; Wilce, J A; Wilce, M C J

2007-07-13

In Bacillus subtilis, the termination of DNA replication via polar fork arrest is effected by a specific protein:DNA complex formed between the replication terminator protein (RTP) and DNA terminator sites. We report the crystal structure of a replication terminator protein homologue (RTP.C110S) of B. subtilis in complex with the high affinity component of one of its cognate DNA termination sites, known as the TerI B-site, refined at 2.5 A resolution. The 21 bp RTP:DNA complex displays marked structural asymmetry in both the homodimeric protein and the DNA. This is in contrast to the previously reported complex formed with a symmetrical TerI B-site homologue. The induced asymmetry is consistent with the complex's solution properties as determined using NMR spectroscopy. Concomitant with this asymmetry is variation in the protein:DNA binding pattern for each of the subunits of the RTP homodimer. It is proposed that the asymmetric "wing" positions, as well as other asymmetrical features of the RTP:DNA complex, are critical for the cooperative binding that underlies the mechanism of polar fork arrest at the complete terminator site.

Crystal structures of C4 form maize and quaternary complex of E. coli phosphoenolpyruvate carboxylases.

PubMed

Matsumura, Hiroyoshi; Xie, Yong; Shirakata, Shunsuke; Inoue, Tsuyoshi; Yoshinaga, Takeo; Ueno, Yoshihisa; Izui, Katsura; Kai, Yasushi

2002-12-01

Phosphoenolpyruvate carboxylase (PEPC) catalyzes the first step in the fixation of atmospheric CO(2) during C(4) photosynthesis. The crystal structure of C(4) form maize PEPC (ZmPEPC), the first structure of the plant PEPCs, has been determined at 3.0 A resolution. The structure includes a sulfate ion at the plausible binding site of an allosteric activator, glucose 6-phosphate. The crystal structure of E. coli PEPC (EcPEPC) complexed with Mn(2+), phosphoenolpyruvate analog (3,3-dichloro-2-dihydroxyphosphinoylmethyl-2-propenoate), and an allosteric inhibitor, aspartate, has also been determined at 2.35 A resolution. Dynamic movements were found in the ZmPEPC structure, compared with the EcPEPC structure, around two loops near the active site. On the basis of these molecular structures, the mechanisms for the carboxylation reaction and for the allosteric regulation of PEPC are proposed.

Hardware-Software Complex for Measurement of Energy and Angular Distributions of Charged Particles Formed in Nuclear Reactions

NASA Astrophysics Data System (ADS)

Vikhlyantsev, O. P.; Generalov, L. N.; Kuryakin, A. V.; Karpov, I. A.; Gurin, N. E.; Tumkin, A. D.; Fil'chagin, S. V.

2017-12-01

A hardware-software complex for measurement of energy and angular distributions of charged particles formed in nuclear reactions is presented. Hardware and software structures of the complex, the basic set of the modular nuclear-physical apparatus of a multichannel detecting system on the basis of Δ E- E telescopes of silicon detectors, and the hardware of experimental data collection, storage, and processing are presented and described.

Optimizing structure of complex technical system by heterogeneous vector criterion in interval form

NASA Astrophysics Data System (ADS)

Lysenko, A. V.; Kochegarov, I. I.; Yurkov, N. K.; Grishko, A. K.

2018-05-01

The article examines the methods of development and multi-criteria choice of the preferred structural variant of the complex technical system at the early stages of its life cycle in the absence of sufficient knowledge of parameters and variables for optimizing this structure. The suggested methods takes into consideration the various fuzzy input data connected with the heterogeneous quality criteria of the designed system and the parameters set by their variation range. The suggested approach is based on the complex use of methods of interval analysis, fuzzy sets theory, and the decision-making theory. As a result, the method for normalizing heterogeneous quality criteria has been developed on the basis of establishing preference relations in the interval form. The method of building preferential relations in the interval form on the basis of the vector of heterogeneous quality criteria suggest the use of membership functions instead of the coefficients considering the criteria value. The former show the degree of proximity of the realization of the designed system to the efficient or Pareto optimal variants. The study analyzes the example of choosing the optimal variant for the complex system using heterogeneous quality criteria.

Molecular dynamics simulations of DNA-polycation complexes

NASA Astrophysics Data System (ADS)

Ziebarth, Jesse; Wang, Yongmei

2008-03-01

A necessary step in the preparation of DNA for use in gene therapy is the packaging of DNA with a vector that can condense DNA and provide protection from degrading enzymes. Because of the immunoresponses caused by viral vectors, there has been interest in developing synthetic gene therapy vectors, with polycations emerging as promising candidates. Molecular dynamics simulations of the DNA duplex CGCGAATTCGCG in the presence of 20 monomer long sequences of the polycations, poly-L-lysine (PLL) and polyethyleneimine (PEI), with explicit counterions and TIP3P water, are performed to provide insight into the structure and formation of DNA polyplexes. After an initial separation of approximately 50 å, the DNA and polycation come together and form a stable complex within 10 ns. The DNA does not undergo any major structural changes upon complexation and remains in the B-form. In the formed complex, the charged amine groups of the polycation mainly interact with DNA phosphate groups, and rarely occupy electronegative sites in either the major or minor grooves. Differences between complexation with PEI and PLL will be discussed.

A probabilistic framework for identifying biosignatures using Pathway Complexity

NASA Astrophysics Data System (ADS)

Marshall, Stuart M.; Murray, Alastair R. G.; Cronin, Leroy

2017-11-01

One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random structures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can easily be distinguished from non-living material assemblies. Many complex artefacts, from ordinary bioproducts to human tools, though they are not living things, are ultimately produced by biological processes-whether those processes occur at the scale of cells or societies, they are the consequences of living systems. While these objects are not living, they cannot randomly form, as they are the product of a biological organism and hence are either technological or cultural biosignatures. A generalized approach that aims to evaluate complex objects as possible biosignatures could be useful to explore the cosmos for new life forms. However, it is not obvious how it might be possible to create such a self-contained approach. This would require us to prove rigorously that a given artefact is too complex to have formed by chance. In this paper, we present a new type of complexity measure, which we call `Pathway Complexity', that allows us not only to threshold the abiotic-biotic divide, but also to demonstrate a probabilistic approach based on object abundance and complexity which can be used to unambiguously assign complex objects as biosignatures. We hope that this approach will not only open up the search for biosignatures beyond the Earth, but also allow us to explore the Earth for new types of biology, and to determine when a complex chemical system discovered in the laboratory could be considered alive. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Bow shock formation in a complex plasma.

PubMed

Saitou, Y; Nakamura, Y; Kamimura, T; Ishihara, O

2012-02-10

A bow shock is observed in a two-dimensional supersonic flow of charged microparticles in a complex plasma. A thin conducting needle is used to make a potential barrier as an obstacle for the particle flow in the complex plasma. The flow is generated and the flow velocity is controlled by changing a tilt angle of the device under the gravitational force. A void, microparticle-free region, is formed around the potential barrier surrounding the obstacle. The flow is bent around the leading edge of the void and forms an arcuate structure when the flow is supersonic. The structure is characterized by the bow shock as confirmed by a polytropic hydrodynamic theory as well as numerical simulation.

Vibrational spectra, powder X-ray diffractions and physical properties of cyanide complexes with 1-ethylimidazole

NASA Astrophysics Data System (ADS)

Kürkçüoğlu, Güneş Süheyla; Kiraz, Fulya Çetinkaya; Sayın, Elvan

2015-10-01

The heteronuclear tetracyanonickelate(II) complexes of the type [M(etim)Ni(CN)4]n (hereafter, abbreviated as M-Ni-etim, M = Mn(II), Fe(II) or Co(II); etim = 1-ethylimidazole, C5H8N2) were prepared in powder form and characterized by FT-IR and Raman spectroscopy, powder X-ray diffraction (PXRD), thermal (TG; DTG and DTA), and elemental analysis techniques. The structures of these complexes were elucidated using vibrational spectra and powder X-ray diffraction patterns with the peak assignment to provide a better understanding of the structures. It is shown that the spectra are consistent with a proposed crystal structure for these compounds derived from powder X-ray diffraction measurements. Vibrational spectra of the complexes were presented and discussed with respect to the internal modes of both the etim and the cyanide ligands. The C, H and N analyses were carried out for all the complexes. Thermal behaviors of these complexes were followed using TG, DTG and DTA curves in the temperature range 30-700 °C in the static air atmosphere. The FT-IR, Raman spectra, thermal and powder X-ray analyses revealed no significant differences between the single crystal and powder forms. Additionally, electrical and magnetic properties of the complexes were investigated. The FT-IR and Raman spectroscopy, PXRD, thermal and elemental analyses results propose that these complexes are similar in structure to the Hofmann-type complexes.

Versatile chelating behavior of benzil bis(thiosemicarbazone) in zinc, cadmium, and nickel complexes.

PubMed

López-Torres, Elena; Mendiola, Ma Antonia; Pastor, César J; Pérez, Beatriz Souto

2004-08-23

Reactions of benzil bis(thiosemicarbazone), LH(6), with M(NO(3))(2).nH(2)O (M = Zn, Cd, and Ni), in the presence of LiOH.H(2)O, show the versatile behavior of this molecule. The structure of the ligand, with the thiosemicarbazone moieties on opposite sides of the carbon backbone, changes to form complexes by acting as a chelating molecule. Complexes of these metal ions with empirical formula [MLH(4)] were obtained, although they show different molecular structures depending on their coordinating preferences. The zinc complex is the first example of a crystalline coordination polymer in which a bis(thiosemicarbazone) acts as bridging ligand, through a nitrogen atom, giving a 1D polymeric structure. The coordination sphere is formed by the imine nitrogen and sulfur atoms, and the remaining position, in a square-based pyramid, is occupied by an amine group of another ligand. The cadmium derivative shows the same geometry around the metal ion but consists of a dinuclear structure with sulfur atoms acting as a bridge between the metal ions. However, in the nickel complex LH(6) acts as a N(2)S(2) ligand yielding a planar structure for the nickel atom. The ligand and its complexes have been characterized by X-ray crystallography, microanalysis, mass spectrometry, IR, (1)H, and (13)C NMR spectroscopies and for the cadmium complex by (113)Cd NMR in solution and in the solid state.

Observations of peculiar sporadic sodium structures and their relation with wind variations

NASA Astrophysics Data System (ADS)

Sridharan, S.; Prasanth, P. Vishnu; Kumar, Y. Bhavani; Ramkumar, Geetha; Sathishkumar, S.; Raghunath, K.

2009-04-01

Resonance lidar observations of sodium density in the upper mesosphere region over Gadanki (13.5°N, 79.2°E) rarely show complex structures with rapid enhancements of sodium density, completely different from normal sporadic sodium structures. The hourly averaged meteor radar zonal winds over Trivandrum (8.5°N, 76.5°E) show an eastward shear with altitude during the nights, when these events are formed. As suggested by Kane et al. [2001. Joint observations of sodium enhancements and field-aligned ionospheric irregularities. Geophysical Research Letters 28, 1375-1378], our observations show that the complex structures may be formed due to Kelvin-Helmholtz instability, which can occur in the region of strong wind shear.

Structure of Complex Verb Forms in Meiteilon

ERIC Educational Resources Information Center

Singh, Lourembam Surjit

2016-01-01

This piece of work proposes to descriptively investigate the structures of complex verbs in Meiteilon. The categorization of such verbs is based on the nature of semantic and syntactic functions of a lexeme or verbal lexeme. A lexeme or verbal lexeme in Meiteilon may have multifunctional properties in the nature of occurrence. Such lexical items…

Structure of a bimodular botulinum neurotoxin complex provides insights into its oral toxicity

USDA-ARS?s Scientific Manuscript database

Botulinum neurotoxins (BoNTs) are highly potent oral poisons produced by Clostridium botulinum. BoNTs are secreted along with several auxiliary proteins forming progenitor toxin complexes (PTC). Here, we report the structure of a ~760 kDa 14-subunit PTC using a combination of X-ray crystallography a...

Novel unsymmetrical P/O substituted ferrocene ligands and the first structurally characterised hydroxyferrocene derivative.

PubMed

Atkinson, Robert C J; Gibson, Vernon C; Long, Nicholas J; White, Andrew J P; Williams, David J

2004-06-21

Two new unsymmetrical 1'-substituted hydroxyferrocene ligands featuring either phosphine or phosphine oxide substituents have been synthesised and the phosphine oxide derivative has been structurally characterised. A nickel complex of the hydroxyl/phosphine ligand has been formed, along with preliminary evaluation of the complex for catalysis of ethylene polymerisation.

Probing the dynamic interface between trimethylamine dehydrogenase (TMADH) and electron transferring flavoprotein (ETF) in the TMADH-2ETF complex: role of the Arg-alpha237 (ETF) and Tyr-442 (TMADH) residue pair.

PubMed

Burgess, Selena G; Messiha, Hanan Latif; Katona, Gergely; Rigby, Stephen E J; Leys, David; Scrutton, Nigel S

2008-05-06

We have used multiple solution state techniques and crystallographic analysis to investigate the importance of a putative transient interaction formed between Arg-alpha237 in electron transferring flavoprotein (ETF) and Tyr-442 in trimethylamine dehydrogenase (TMADH) in complex assembly, electron transfer, and structural imprinting of ETF by TMADH. We have isolated four mutant forms of ETF altered in the identity of the residue at position 237 (alphaR237A, alphaR237K, alphaR237C, and alphaR237E) and with each form studied electron transfer from TMADH to ETF, investigated the reduction potentials of the bound ETF cofactor, and analyzed complex formation. We show that mutation of Arg-alpha237 substantially destabilizes the semiquinone couple of the bound FAD and impedes electron transfer from TMADH to ETF. Crystallographic structures of the mutant ETF proteins indicate that mutation does not perturb the overall structure of ETF, but leads to disruption of an electrostatic network at an ETF domain boundary that likely affects the dynamic properties of ETF in the crystal and in solution. We show that Arg-alpha237 is required for TMADH to structurally imprint the as-purified semiquinone form of wild-type ETF and that the ability of TMADH to facilitate this structural reorganization is lost following (i) redox cycling of ETF, or simple conversion to the oxidized form, and (ii) mutagenesis of Arg-alpha237. We discuss this result in light of recent apparent conflict in the literature relating to the structural imprinting of wild-type ETF. Our studies support a mechanism of electron transfer by conformational sampling as advanced from our previous analysis of the crystal structure of the TMADH-2ETF complex [Leys, D. , Basran, J. , Sutcliffe, M. J., and Scrutton, N. S. (2003) Nature Struct. Biol. 10, 219-225] and point to a key role for the Tyr-442 (TMADH) and Arg-alpha237 (ETF) residue pair in transiently stabilizing productive electron transfer configurations. Our work also points to the importance of Arg-alpha237 in controlling the thermodynamics of electron transfer, the dynamics of ETF, and the protection of reducing equivalents following disassembly of the TMADH-2ETF complex.

Structural changes induced by binding of the high-mobility group I protein to a mouse satellite DNA sequence.

PubMed Central

Slama-Schwok, A; Zakrzewska, K; Léger, G; Leroux, Y; Takahashi, M; Käs, E; Debey, P

2000-01-01

Using spectroscopic methods, we have studied the structural changes induced in both protein and DNA upon binding of the High-Mobility Group I (HMG-I) protein to a 21-bp sequence derived from mouse satellite DNA. We show that these structural changes depend on the stoichiometry of the protein/DNA complexes formed, as determined by Job plots derived from experiments using pyrene-labeled duplexes. Circular dichroism and melting temperature experiments extended in the far ultraviolet range show that while native HMG-I is mainly random coiled in solution, it adopts a beta-turn conformation upon forming a 1:1 complex in which the protein first binds to one of two dA.dT stretches present in the duplex. HMG-I structure in the 1:1 complex is dependent on the sequence of its DNA target. A 3:1 HMG-I/DNA complex can also form and is characterized by a small increase in the DNA natural bend and/or compaction coupled to a change in the protein conformation, as determined from fluorescence resonance energy transfer (FRET) experiments. In addition, a peptide corresponding to an extended DNA-binding domain of HMG-I induces an ordered condensation of DNA duplexes. Based on the constraints derived from pyrene excimer measurements, we present a model of these nucleated structures. Our results illustrate an extreme case of protein structure induced by DNA conformation that may bear on the evolutionary conservation of the DNA-binding motifs of HMG-I. We discuss the functional relevance of the structural flexibility of HMG-I associated with the nature of its DNA targets and the implications of the binding stoichiometry for several aspects of chromatin structure and gene regulation. PMID:10777751

CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin

PubMed Central

van Pee, Katharina; Neuhaus, Alexander; D'Imprima, Edoardo; Mills, Deryck J; Kühlbrandt, Werner; Yildiz, Özkan

2017-01-01

Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of Streptococcus pneumoniae, by cryoEM. The pneumolysin pore is a 400 Å ring of 42 membrane-inserted monomers. Domain 3 of the soluble toxin refolds into two ~85 Å β-hairpins that traverse the lipid bilayer and assemble into a 168-strand β-barrel. The pore complex is stabilized by salt bridges between β-hairpins of adjacent subunits and an internal α-barrel. The apolar outer barrel surface with large sidechains is immersed in the lipid bilayer, while the inner barrel surface is highly charged. Comparison of the cryoEM pore complex to the prepore structure obtained by electron cryo-tomography and the x-ray structure of the soluble form reveals the detailed mechanisms by which the toxin monomers insert into the lipid bilayer to perforate the target membrane. DOI: http://dx.doi.org/10.7554/eLife.23644.001 PMID:28323617

Melatonin charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone: Molecular structure, DFT studies, thermal analyses, evaluation of biological activity and utility for determination of melatonin in pure and dosage forms

NASA Astrophysics Data System (ADS)

Mohamed, Gehad G.; Hamed, Maher M.; Zaki, Nadia G.; Abdou, Mohamed M.; Mohamed, Marwa El-Badry; Abdallah, Abanoub Mosaad

2017-07-01

A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100 μg mL- 1 ML. The solid form of the CT complex was structurally characterized by means of different spectral methods. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out. The different quantum chemical parameters of the CT complex were calculated. Thermal properties of the CT complex and its kinetic thermodynamic parameters were studied, as well as its antimicrobial and antifungal activities were investigated. Molecular docking studies were performed to predict the binding modes of the CT complex components towards E. coli bacterial RNA and the receptor of breast cancer mutant oxidoreductase.

Melatonin charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone: Molecular structure, DFT studies, thermal analyses, evaluation of biological activity and utility for determination of melatonin in pure and dosage forms.

PubMed

Mohamed, Gehad G; Hamed, Maher M; Zaki, Nadia G; Abdou, Mohamed M; Mohamed, Marwa El-Badry; Abdallah, Abanoub Mosaad

2017-07-05

A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100μgmL -1 ML. The solid form of the CT complex was structurally characterized by means of different spectral methods. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out. The different quantum chemical parameters of the CT complex were calculated. Thermal properties of the CT complex and its kinetic thermodynamic parameters were studied, as well as its antimicrobial and antifungal activities were investigated. Molecular docking studies were performed to predict the binding modes of the CT complex components towards E. coli bacterial RNA and the receptor of breast cancer mutant oxidoreductase. Copyright © 2017 Elsevier B.V. All rights reserved.

Structures of human cytosolic NADP-dependent isocitrate dehydrogenase reveal a novel self-regulatory mechanism of activity.

PubMed

Xu, Xiang; Zhao, Jingyue; Xu, Zhen; Peng, Baozhen; Huang, Qiuhua; Arnold, Eddy; Ding, Jianping

2004-08-06

Isocitrate dehydrogenases (IDHs) catalyze the oxidative decarboxylation of isocitrate to alpha-ketoglutarate, and regulation of the enzymatic activity of IDHs is crucial for their biological functions. Bacterial IDHs are reversibly regulated by phosphorylation of a strictly conserved serine residue at the active site. Eukaryotic NADP-dependent IDHs (NADP-IDHs) have been shown to have diverse important biological functions; however, their regulatory mechanism remains unclear. Structural studies of human cytosolic NADP-IDH (HcIDH) in complex with NADP and in complex with NADP, isocitrate, and Ca2+ reveal three biologically relevant conformational states of the enzyme that differ substantially in the structure of the active site and in the overall structure. A structural segment at the active site that forms a conserved alpha-helix in all known NADP-IDH structures assumes a loop conformation in the open, inactive form of HcIDH; a partially unraveled alpha-helix in the semi-open, intermediate form; and an alpha-helix in the closed, active form. The side chain of Asp279 of this segment occupies the isocitrate-binding site and forms hydrogen bonds with Ser94 (the equivalent of the phosphorylation site in bacterial IDHs) in the inactive form and chelates the metal ion in the active form. The structural data led us to propose a novel self-regulatory mechanism for HcIDH that mimics the phosphorylation mechanism used by the bacterial homologs, consistent with biochemical and biological data. This mechanism might be applicable to other eukaryotic NADP-IDHs. The results also provide insights into the recognition and specificity of substrate and cofactor by eukaryotic NADP-IDHs.

Complexity markers in morphosyntactic productions in French-speaking children with specific language impairment (SLI).

PubMed

Prigent, Gaïd; Parisse, Christophe; Leclercq, Anne-Lise; Maillart, Christelle

2015-01-01

The usage-based theory considers that the morphosyntactic productions of children with SLI are particularly dependent on input frequency. When producing complex syntax, the language of these children is, therefore, predicted to have a lower variability and to contain fewer infrequent morphosyntactic markers than that of younger children matched on morphosyntactic abilities. Using a spontaneous language task, the current study compared the complexity of the morphological and structural productions of 20 children with SLI and 20 language-matched peers (matched on both morphosyntactic comprehension and mean length of utterance). As expected, results showed that although basic structures were produced in the same way in both groups, several complex forms (i.e. tenses such as Imperfect, Future or Conditional and Conjunctions) were less frequent in the productions of children with SLI. Finally, we attempted to highlight complex linguistic forms that could be good clinical markers for these children.

The development of episodic memory: items, contexts, and relations.

PubMed

Yim, Hyungwook; Dennis, Simon J; Sloutsky, Vladimir M

2013-11-01

Episodic memory involves the formation of relational structures that bind information about the stimuli people experience to the contexts in which they experience them. The ability to form and retain such structures may be at the core of the development of episodic memory. In the first experiment reported here, 4- and 7-year-olds were presented with paired-associate learning tasks requiring memory structures of different complexity. A multinomial-processing tree model was applied to estimate the use of different structures in the two age groups. The use of two-way list-context-to-target structures and three-way structures was found to increase between the ages of 4 and 7. Experiment 2 demonstrated that the ability to form increasingly complex relational memory structures develops between the ages of 4 and 7 years and that this development extends well into adulthood. These results have important implications for theories of memory development.

Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry

NASA Astrophysics Data System (ADS)

Zhang, Jiang; Loo, Rachel R. Ogorzalek; Loo, Joseph A.

2017-09-01

Native mass spectrometry (MS) with electrospray ionization (ESI) has evolved as an invaluable tool for the characterization of intact native proteins and non-covalently bound protein complexes. Here we report the structural characterization by high resolution native top-down MS of human thrombin and its complex with the Bock thrombin binding aptamer (TBA), a 15-nucleotide DNA with high specificity and affinity for thrombin. Accurate mass measurements revealed that the predominant form of native human α-thrombin contains a glycosylation mass of 2205 Da, corresponding to a sialylated symmetric biantennary oligosaccharide structure without fucosylation. Native MS showed that thrombin and TBA predominantly form a 1:1 complex under near physiological conditions (pH 6.8, 200 mM NH4OAc), but the binding stoichiometry is influenced by the solution ionic strength. In 20 mM ammonium acetate solution, up to two TBAs were bound to thrombin, whereas increasing the solution ionic strength destabilized the thrombin-TBA complex and 1 M NH4OAc nearly completely dissociated the complex. This observation is consistent with the mediation of thrombin-aptamer binding through electrostatic interactions and it is further consistent with the human thrombin structure that contains two anion binding sites on the surface. Electron capture dissociation (ECD) top-down MS of the thrombin-TBA complex performed with a high resolution 15 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer showed the primary binding site to be at exosite I located near the N-terminal sequence of the heavy chain, consistent with crystallographic data. High resolution native top-down MS is complementary to traditional structural biology methods for structurally characterizing native proteins and protein-DNA complexes. [Figure not available: see fulltext.

Conformation-Specific Spectroscopy of a Prototypical γ-PEPTIDE-WATER Complex: Ac-γ2-hPhe-NHMe-(H2O)1

NASA Astrophysics Data System (ADS)

Buchanan, Evan G.; James, William H., III; Zwier, Timothy S.; Guo, Li; Gellman, Samuel H.

2010-06-01

The prototypical γ-peptide, Ac-γ2-hPhe-NHMe, has been previously studied in a supersonic jet expansion, with three different conformers observed. Two of the monomers form nine atom, intramolecular hydrogen bonded rings, which differ by the position of the aromatic chromophore relative to the backbone. The third monomer conformer has no intramolecular H-bonds, but forms instead an intramolecular, amide-amide stacked structure unique to the γ-peptide backbone. This talk focuses attention on the conformation-specific IR spectra of the Ac-γ2-hPhe-NHMe-(H2O)1 complex, which is observed to form six unique conformational isomers, all of which preserve the two distinct monomer structural motifs. Three conformers are assigned to the nine atom intramolecular hydrogen bond family with the water hydrogen bonded to it as donor in different locations. The other three belong to the amide-amide stacking family with the water forming a bridge between the two amide planes. Infrared photodissocation of the water molecule from the complex to form γ-peptide monomer conformations will also be discussed.

The neural correlates of morphological complexity processing: Detecting structure in pseudowords.

PubMed

Schuster, Swetlana; Scharinger, Mathias; Brooks, Colin; Lahiri, Aditi; Hartwigsen, Gesa

2018-06-01

Morphological complexity is a highly debated issue in visual word recognition. Previous neuroimaging studies have shown that speakers are sensitive to degrees of morphological complexity. Two-step derived complex words (bridging through bridge N  > bridge V  > bridging) led to more enhanced activation in the left inferior frontal gyrus than their 1-step derived counterparts (running through run V  > running). However, it remains unclear whether sensitivity to degrees of morphological complexity extends to pseudowords. If this were the case, it would indicate that abstract knowledge of morphological structure is independent of lexicality. We addressed this question by investigating the processing of two sets of pseudowords in German. Both sets contained morphologically viable two-step derived pseudowords differing in the number of derivational steps required to access an existing lexical representation and therefore the degree of structural analysis expected during processing. Using a 2 × 2 factorial design, we found lexicality effects to be distinct from processing signatures relating to structural analysis in pseudowords. Semantically-driven processes such as lexical search showed a more frontal distribution while combinatorial processes related to structural analysis engaged more parietal parts of the network. Specifically, more complex pseudowords showed increased activation in parietal regions (right superior parietal lobe and left precuneus) relative to pseudowords that required less structural analysis to arrive at an existing lexical representation. As the two sets were matched on cohort size and surface form, these results highlight the role of internal levels of morphological structure even in forms that do not possess a lexical representation. © 2018 Wiley Periodicals, Inc.

Can misfolded proteins be beneficial? The HAMLET case.

PubMed

Pettersson-Kastberg, Jenny; Aits, Sonja; Gustafsson, Lotta; Mossberg, Anki; Storm, Petter; Trulsson, Maria; Persson, Filip; Mok, K Hun; Svanborg, Catharina

2009-01-01

By changing the three-dimensional structure, a protein can attain new functions, distinct from those of the native protein. Amyloid-forming proteins are one example, in which conformational change may lead to fibril formation and, in many cases, neurodegenerative disease. We have proposed that partial unfolding provides a mechanism to generate new and useful functional variants from a given polypeptide chain. Here we present HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) as an example where partial unfolding and the incorporation of cofactor create a complex with new, beneficial properties. Native alpha-lactalbumin functions as a substrate specifier in lactose synthesis, but when partially unfolded the protein binds oleic acid and forms the tumoricidal HAMLET complex. When the properties of HAMLET were first described they were surprising, as protein folding intermediates and especially amyloid-forming protein intermediates had been regarded as toxic conformations, but since then structural studies have supported functional diversity arising from a change in fold. The properties of HAMLET suggest a mechanism of structure-function variation, which might help the limited number of human protein genes to generate sufficient structural diversity to meet the diverse functional demands of complex organisms.

Two-dimensional infrared spectroscopy reveals the complex behaviour of an amyloid fibril inhibitor

NASA Astrophysics Data System (ADS)

Middleton, Chris T.; Marek, Peter; Cao, Ping; Chiu, Chi-Cheng; Singh, Sadanand; Woys, Ann Marie; de Pablo, Juan J.; Raleigh, Daniel P.; Zanni, Martin T.

2012-05-01

Amyloid formation has been implicated in the pathology of over 20 human diseases, but the rational design of amyloid inhibitors is hampered by a lack of structural information about amyloid-inhibitor complexes. We use isotope labelling and two-dimensional infrared spectroscopy to obtain a residue-specific structure for the complex of human amylin (the peptide responsible for islet amyloid formation in type 2 diabetes) with a known inhibitor (rat amylin). Based on its sequence, rat amylin should block formation of the C-terminal β-sheet, but at 8 h after mixing, rat amylin blocks the N-terminal β-sheet instead. At 24 h after mixing, rat amylin blocks neither β-sheet and forms its own β-sheet, most probably on the outside of the human fibrils. This is striking, because rat amylin is natively disordered and not previously known to form amyloid β-sheets. The results show that even seemingly intuitive inhibitors may function by unforeseen and complex structural processes.

First examples of ternary lanthanide 5-aminoisophthalate complexes: Hydrothermal syntheses and structures of lanthanide coordination polymers with 5-aminoisophthalate and oxalate

NASA Astrophysics Data System (ADS)

Liu, Chong-Bo; Wen, Hui-Liang; Tan, Sheng-Shui; Yi, Xiu-Guang

2008-05-01

Two new lanthanide coordination polymers with mixed-carboxylates, [Ln(OX)(HAPA)(H 2O)] n[Ln = Eu ( 1), Ho ( 2); H 2APA = 5-aminoisophthalic acid; OX = oxalate] were obtained by hydrothermal reactions, and characterized by single crystal X-ray diffraction, elemental analysis and IR spectra. Complexes 1 and 2 are both 3-D supramolecular structure, in which lanthanide ions are bridged by oxalate and 5-aminoisophthalate ligands forming 2-D metal-organic framework, and 2-D networks are further architectured to form 3-D supramolecular structures by hydrogen bonds. The two carboxylate groups of H 2APA ligand are all deprotonated and exhibit chelating and bridging bidentate coordination modes, respectively, and the amino group in HAPA presents - NH3+ in the titled complexes. The thermogravimetric analysis was carried out to examine the thermal stability of the titled complexes. And the photoluminescence property of 1 was investigated.

Nuclear Pore Complexes: Global Conservation and Local Variation.

PubMed

Holzer, Guillaume; Antonin, Wolfram

2018-06-04

Nuclear pore complexes are the transport gates to the nucleus. Most proteins forming these huge complexes are evolutionarily conserved, as is the eightfold symmetry of these complexes. A new study reporting the structure of the yeast nuclear pore complex now shows striking differences from its human counterpart. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Hexamer Structure of the Rift Valley Fever Virus Nucleoprotein Suggests a Mechanism for its Assembly into Ribonucleoprotein Complexes

PubMed Central

Ferron, François; Li, Zongli; Danek, Eric I.; Luo, Dahai; Wong, Yeehwa; Coutard, Bruno; Lantez, Violaine; Charrel, Rémi; Canard, Bruno; Walz, Thomas; Lescar, Julien

2011-01-01

Rift Valley fever virus (RVFV), a Phlebovirus with a genome consisting of three single-stranded RNA segments, is spread by infected mosquitoes and causes large viral outbreaks in Africa. RVFV encodes a nucleoprotein (N) that encapsidates the viral RNA. The N protein is the major component of the ribonucleoprotein complex and is also required for genomic RNA replication and transcription by the viral polymerase. Here we present the 1.6 Å crystal structure of the RVFV N protein in hexameric form. The ring-shaped hexamers form a functional RNA binding site, as assessed by mutagenesis experiments. Electron microscopy (EM) demonstrates that N in complex with RNA also forms rings in solution, and a single-particle EM reconstruction of a hexameric N-RNA complex is consistent with the crystallographic N hexamers. The ring-like organization of the hexamers in the crystal is stabilized by circular interactions of the N terminus of RVFV N, which forms an extended arm that binds to a hydrophobic pocket in the core domain of an adjacent subunit. The conformation of the N-terminal arm differs from that seen in a previous crystal structure of RVFV, in which it was bound to the hydrophobic pocket in its own core domain. The switch from an intra- to an inter-molecular interaction mode of the N-terminal arm may be a general principle that underlies multimerization and RNA encapsidation by N proteins from Bunyaviridae. Furthermore, slight structural adjustments of the N-terminal arm would allow RVFV N to form smaller or larger ring-shaped oligomers and potentially even a multimer with a super-helical subunit arrangement. Thus, the interaction mode between subunits seen in the crystal structure would allow the formation of filamentous ribonucleocapsids in vivo. Both the RNA binding cleft and the multimerization site of the N protein are promising targets for the development of antiviral drugs. PMID:21589902

Structural investigation of inhibitor designs targeting 3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dias, Marcio V.B.; Snee, William C.; Bromfield, Karen M.

The shikimate pathway is essential in Mycobacterium tuberculosis and its absence from humans makes the enzymes of this pathway potential drug targets. In the present paper, we provide structural insights into ligand and inhibitor binding to 3-dehydroquinate dehydratase (dehydroquinase) from M. tuberculosis (MtDHQase), the third enzyme of the shikimate pathway. The enzyme has been crystallized in complex with its reaction product, 3-dehydroshikimate, and with six different competitive inhibitors. The inhibitor 2,3-anhydroquinate mimics the flattened enol/enolate reaction intermediate and serves as an anchor molecule for four of the inhibitors investigated. MtDHQase also forms a complex with citrazinic acid, a planar analoguemore » of the reaction product. The structure of MtDHQase in complex with a 2,3-anhydroquinate moiety attached to a biaryl group shows that this group extends to an active-site subpocket inducing significant structural rearrangement. The flexible extensions of inhibitors designed to form {pi}-stacking interactions with the catalytic Tyr{sup 24} have been investigated. The high-resolution crystal structures of the MtDHQase complexes provide structural evidence for the role of the loop residues 19-24 in MtDHQase ligand binding and catalytic mechanism and provide a rationale for the design and efficacy of inhibitors.« less

Unraveling the Pore-Forming Steps of Pneumolysin from Streptococcus pneumoniae.

PubMed

van Pee, Katharina; Mulvihill, Estefania; Müller, Daniel J; Yildiz, Özkan

2016-12-14

Pneumolysin (PLY) is the main virulence factor of Streptococcus pneumoniae that causes pneumonia, meningitis, and invasive pneumococcal infection. PLY is produced as monomers, which bind to cholesterol-containing membranes, where they oligomerize into large pores. To investigate the pore-forming mechanism, we determined the crystal structure of PLY at 2.4 Å and used it to design mutants on the surface of monomers. Electron microscopy of liposomes incubated with PLY mutants revealed that several mutations interfered with ring formation. Mutants that formed incomplete rings or linear arrays had strongly reduced hemolytic activity. By high-resolution time-lapse atomic force microscopy of wild-type PLY, we observed two different ring-shaped complexes. Most of the complexes protruded ∼8 nm above the membrane surface, while a smaller number protruded ∼11 nm or more. The lower complexes were identified as pores or prepores by the presence or absence of a lipid bilayer in their center. The taller complexes were side-by-side assemblies of monomers of soluble PLY that represent an early form of the prepore. Our observations suggest a four-step mechanism of membrane attachment and pore formation by PLY, which is discussed in the context of recent structural models. The functional separation of these steps is necessary for the understanding how cholesterol-dependent cytolysins form pores and lyse cells.

Comparison of biological activities of human antithrombins with high-mannose or complex-type nonfucosylated N-linked oligosaccharides

PubMed Central

Yamada, Tsuyoshi; Kanda, Yutaka; Takayama, Makoto; Hashimoto, Akitoshi; Sugihara, Tsutomu; Satoh-Kubota, Ai; Suzuki-Takanami, Eri; Yano, Keiichi; Iida, Shigeru; Satoh, Mitsuo

2016-01-01

The structure of the N-linked oligosaccharides attached to antithrombin (AT) has been shown to affect its anticoagulant activity and pharmacokinetics. Human AT has biantennary complex-type oligosaccharides with the unique feature of lacking a core fucose, which affects its biological activities by changing its heparin-binding affinity. In human plasma, AT circulates as a mixture of the α-form bearing four oligosaccharides and the β-form lacking an oligosaccharide at Asn135. However, it remains unclear how the immature high-mannose-type oligosaccharides produced by mammalian cells affect biological activities of AT. Here, we succeeded in directly comparing the activities between the high-mannose and complex types. Interestingly, although there were no substantial differences in thrombin inhibitory activity, the high-mannose type showed higher heparin-binding affinity. The anticoagulant activities were increased by heparin and correlated with the heparin-binding affinity, resulting in the strongest anticoagulant activity being displayed in the β-form with the high-mannose type. In pharmacokinetic profiling, the high-mannose type showed a much shorter plasma half-life than the complex type. The β-form was found to have a prolonged plasma half-life compared with the α-form for the high-mannose type; conversely, the α-form showed a longer half-life than the β-form for the complex-type. The present study highlights that AT physiological activities are strictly controlled not only by a core fucose at the reducing end but also by the high-mannose-type structures at the nonreducing end. The β-form with the immature high-mannose type appears to function as a more potent anticoagulant than the AT typically found in human plasma, once it emerges in the blood. PMID:26747427

Comparison of biological activities of human antithrombins with high-mannose or complex-type nonfucosylated N-linked oligosaccharides.

PubMed

Yamada, Tsuyoshi; Kanda, Yutaka; Takayama, Makoto; Hashimoto, Akitoshi; Sugihara, Tsutomu; Satoh-Kubota, Ai; Suzuki-Takanami, Eri; Yano, Keiichi; Iida, Shigeru; Satoh, Mitsuo

2016-05-01

The structure of the N-linked oligosaccharides attached to antithrombin (AT) has been shown to affect its anticoagulant activity and pharmacokinetics. Human AT has biantennary complex-type oligosaccharides with the unique feature of lacking a core fucose, which affects its biological activities by changing its heparin-binding affinity. In human plasma, AT circulates as a mixture of the α-form bearing four oligosaccharides and the β-form lacking an oligosaccharide at Asn135. However, it remains unclear how the immature high-mannose-type oligosaccharides produced by mammalian cells affect biological activities of AT. Here, we succeeded in directly comparing the activities between the high-mannose and complex types. Interestingly, although there were no substantial differences in thrombin inhibitory activity, the high-mannose type showed higher heparin-binding affinity. The anticoagulant activities were increased by heparin and correlated with the heparin-binding affinity, resulting in the strongest anticoagulant activity being displayed in the β-form with the high-mannose type. In pharmacokinetic profiling, the high-mannose type showed a much shorter plasma half-life than the complex type. The β-form was found to have a prolonged plasma half-life compared with the α-form for the high-mannose type; conversely, the α-form showed a longer half-life than the β-form for the complex-type. The present study highlights that AT physiological activities are strictly controlled not only by a core fucose at the reducing end but also by the high-mannose-type structures at the nonreducing end. The β-form with the immature high-mannose type appears to function as a more potent anticoagulant than the AT typically found in human plasma, once it emerges in the blood. © The Author 2016. Published by Oxford University Press.

Fluoroquinolone-gyrase-DNA complexes: two modes of drug binding.

PubMed

Mustaev, Arkady; Malik, Muhammad; Zhao, Xilin; Kurepina, Natalia; Luan, Gan; Oppegard, Lisa M; Hiasa, Hiroshi; Marks, Kevin R; Kerns, Robert J; Berger, James M; Drlica, Karl

2014-05-02

DNA gyrase and topoisomerase IV control bacterial DNA topology by breaking DNA, passing duplex DNA through the break, and then resealing the break. This process is subject to reversible corruption by fluoroquinolones, antibacterials that form drug-enzyme-DNA complexes in which the DNA is broken. The complexes, called cleaved complexes because of the presence of DNA breaks, have been crystallized and found to have the fluoroquinolone C-7 ring system facing the GyrB/ParE subunits. As expected from x-ray crystallography, a thiol-reactive, C-7-modified chloroacetyl derivative of ciprofloxacin (Cip-AcCl) formed cross-linked cleaved complexes with mutant GyrB-Cys(466) gyrase as evidenced by resistance to reversal by both EDTA and thermal treatments. Surprisingly, cross-linking was also readily seen with complexes formed by mutant GyrA-G81C gyrase, thereby revealing a novel drug-gyrase interaction not observed in crystal structures. The cross-link between fluoroquinolone and GyrA-G81C gyrase correlated with exceptional bacteriostatic activity for Cip-AcCl with a quinolone-resistant GyrA-G81C variant of Escherichia coli and its Mycobacterium smegmatis equivalent (GyrA-G89C). Cip-AcCl-mediated, irreversible inhibition of DNA replication provided further evidence for a GyrA-drug cross-link. Collectively these data establish the existence of interactions between the fluoroquinolone C-7 ring and both GyrA and GyrB. Because the GyrA-Gly(81) and GyrB-Glu(466) residues are far apart (17 Å) in the crystal structure of cleaved complexes, two modes of quinolone binding must exist. The presence of two binding modes raises the possibility that multiple quinolone-enzyme-DNA complexes can form, a discovery that opens new avenues for exploring and exploiting relationships between drug structure and activity with type II DNA topoisomerases.

Structural crashworthiness

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, N.; Wierzbicki, T.

1983-01-01

Behind the quest for safety in all forms of transport lies a complex technology of which structural crashworthiness forms an important part. This volume contains the work of over twenty experts whose interests range from the fundamental principles of structural collapse to the application of those principles to the design of ships, aircraft, road vehicles, and rail vehicles. The text focuses on the application of analytical and experimental techniques to predict energy dissipation characteristics of thin-walled structures and structural members under quasi-static and dynamic loadings.

Properties of lotus seed starch-glycerin monostearin complexes formed by high pressure homogenization.

PubMed

Chen, Bingyan; Zeng, Shaoxiao; Zeng, Hongliang; Guo, Zebin; Zhang, Yi; Zheng, Baodong

2017-07-01

Starch-lipid complexes were prepared using lotus seed starch (LS) and glycerin monostearate (GMS) via a high pressure homogenization (HPH) process, and the effect of HPH on the physicochemical properties of LS-GMS complexes was investigated. The results of Fourier transform infrared spectroscopy and complex index analysis showed that LS-GMS complexes were formed at 40MPa by HPH and the complex index increased with the increase of homogenization pressure. Scanning electron microscopy displayed LS-GMS complexes present more nest-shape structure with increasing homogenization pressure. X-ray diffraction and differential scanning calorimetry results revealed that V-type crystalline polymorph was formed between LS and GMS, with higher homogenization pressure producing an increasingly stable complex. LS-GMS complex inhibited starch granules swelling, solubility and pasting development, which further reduced peak and breakdown viscosity. During storage, LS-GMS complexes prepared by 70-100MPa had higher Avrami exponent values and lower recrystallization rates compared with native starch, which suggested a lower retrogradation trendency. Copyright © 2017 Elsevier Ltd. All rights reserved.

Synthesis and structural characterization of lithium, sodium and potassium complexes supported by a tridentate amino-bisphenolate ligand

NASA Astrophysics Data System (ADS)

Durango-García, Clara J.; Rufino-Felipe, Ernesto; López-Cardoso, Marcela; Muñoz-Hernández, Miguel-Ángel; Montiel-Palma, Virginia

2018-07-01

Reactions of methylamino-N,N-bis(2-methylene-4,6-di-tert-butylphenol) (1) with one or two equivalents of bulk Li, Na or K metals in THF or DMSO render mono or dialkali metal complexes depending on the stoichiometric ratio of the reactants. The metal-methylamino-N-(2-methylene-4,6-tert-butylphenol)sbnd N-(2-methylene-4,6-tert-butylphenolate) complexes, 2Li, 2Na and 2K, are generated upon the substitution of a single phenol hydrogen of 1. In the solid state, complex 2Na is a dimer due to the establishment of two symmetric hydrogen bonds between two adjacent molecules. The Na center also engages into the formation of a ten-membered metallacycle ring with a butterfly-like structure. Due to dimerization, an intermolecular six-membered core is formed involving two sodium and four oxygen atoms. The weakly coordinated nitrogen atom from the ligand is nearly perpendicular to the hexagonal core. The dimetal-methylamino-N,N‧-bis(2-methylene-4,6-di-tert-butylphenolate) complexes, 3Li, 3Na and 3K result from metal substitution of the two phenol hydrogens from ligand 1. The SC-XRD structures of 3Li and 3Na are discreet, each incorporating two metal atoms in different coordination environments. Ten-membered rings with boat-boat conformations are also observed as are rhombic central M2O2 cores. The molecular structure of 3K in DMSO shows a higher degree of aggregation. It effectively comprises four K atoms, two ligand backbones and seven solvent molecules forming a central four-membered K2O2 ring perpendicular to an eight-membered structure formed also by K and O atoms spanning over the two ligand moieties.

Chirality-selected phase behaviour in ionic polypeptide complexes

DOE PAGES

Perry, Sarah L.; Leon, Lorraine; Hoffmann, Kyle Q.; ...

2015-01-14

In this study, polyelectrolyte complexes present new opportunities for self-assembled soft matter. Factors determining whether the phase of the complex is solid or liquid remain unclear. Ionic polypeptides enable examination of the effects of stereochemistry on complex formation. Here we demonstrate that chirality determines the state of polyelectrolyte complexes, formed from mixing dilute solutions of oppositely charged polypeptides, via a combination of electrostatic and hydrogen-bonding interactions. Fluid complexes occur when at least one of the polypeptides in the mixture is racemic, which disrupts backbone hydrogen-bonding networks. Pairs of purely chiral polypeptides, of any sense, form compact, fibrillar solids with amore » β-sheet structure. Analogous behaviour occurs in micelles formed from polypeptide block copolymers with polyethylene oxide, where assembly into aggregates with either solid or fluid cores, and eventually into ordered phases at high concentrations, is possible. Chirality is an exploitable tool for manipulating material properties in polyelectrolyte complexation.« less

(PS)2: protein structure prediction server version 3.0.

PubMed

Huang, Tsun-Tsao; Hwang, Jenn-Kang; Chen, Chu-Huang; Chu, Chih-Sheng; Lee, Chi-Wen; Chen, Chih-Chieh

2015-07-01

Protein complexes are involved in many biological processes. Examining coupling between subunits of a complex would be useful to understand the molecular basis of protein function. Here, our updated (PS)(2) web server predicts the three-dimensional structures of protein complexes based on comparative modeling; furthermore, this server examines the coupling between subunits of the predicted complex by combining structural and evolutionary considerations. The predicted complex structure could be indicated and visualized by Java-based 3D graphics viewers and the structural and evolutionary profiles are shown and compared chain-by-chain. For each subunit, considerations with or without the packing contribution of other subunits cause the differences in similarities between structural and evolutionary profiles, and these differences imply which form, complex or monomeric, is preferred in the biological condition for the subunit. We believe that the (PS)(2) server would be a useful tool for biologists who are interested not only in the structures of protein complexes but also in the coupling between subunits of the complexes. The (PS)(2) is freely available at http://ps2v3.life.nctu.edu.tw/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Structural Reorganization and the Cooperative Binding of Single-stranded Telomere DNA in Sterkiella nova*

PubMed Central

Buczek, Pawel; Horvath, Martin P.

2009-01-01

In Sterkiella nova, α and β telomere proteins bind cooperatively with single-stranded DNA to form a ternary α·β·DNA complex. Association of telomere protein subunits is DNA-dependent, and α-β association enhances DNA affinity. To further understand the molecular basis for binding cooperativity, we characterized several possible stepwise assembly pathways using isothermal titration calorimetry. In one path, α and DNA first form a stable α·DNA complex followed by addition of β in a second step. Binding energy accumulates with nearly equal free energy of association for each of these steps. Heat capacity is nonetheless dramatically different with ΔCp = −305 ± 3 cal mol−1 K−1 for α binding with DNA and ΔCp = −2010 ± 20 cal mol−1 K−1 for addition of β to complete the α·β·DNA complex. By examining alternate routes including titration of single-stranded DNA with a preformed α·β complex, a significant portion of binding energy and heat capacity could be assigned to structural reorganization involving protein-protein interactions and repositioning of the DNA. Structural reorganization probably affords a mechanism to regulate high affinity binding of telomere single-stranded DNA with important implications for telomere biology. Regulation of telomere complex dissociation is thought to involve post-translational modifications in the lysine-rich C-terminal portion of β. We observed no difference in binding energetics or crystal structure when comparing complexes prepared with full-length β or a C-terminally truncated form, supporting interesting parallels between the intrinsically disordered regions of histones and this portion of β. PMID:17082188

The complex evolutionary history of big-eared horseshoe bats (Rhinolophus macrotis complex): insights from genetic, morphological and acoustic data

PubMed Central

Sun, Keping; Kimball, Rebecca T.; Liu, Tong; Wei, Xuewen; Jin, Longru; Jiang, Tinglei; Lin, Aiqing; Feng, Jiang

2016-01-01

Palaeoclimatic oscillations and different landscapes frequently result in complex population-level structure or the evolution of cryptic species. Elucidating the potential mechanisms is vital to understanding speciation events. However, such complex evolutionary patterns have rarely been reported in bats. In China, the Rhinolophus macrotis complex contains a large form and a small form, suggesting the existence of a cryptic bat species. Our field surveys found these two sibling species have a continuous and widespread distribution with partial sympatry. However, their evolutionary history has received little attention. Here, we used extensive sampling, morphological and acoustic data, as well as different genetic markers to investigate their evolutionary history. Genetic analyses revealed discordance between the mitochondrial and nuclear data. Mitochondrial data identified three reciprocally monophyletic lineages: one representing all small forms from Southwest China, and the other two containing all large forms from Central and Southeast China, respectively. The large form showed paraphyly with respect to the small form. However, clustering analyses of microsatellite and Chd1 gene sequences support two divergent clusters separating the large form and the small form. Moreover, morphological and acoustic analyses were consistent with nuclear data. This unusual pattern in the R. macrotis complex might be accounted for by palaeoclimatic oscillations, shared ancestral polymorphism and/or interspecific hybridization. PMID:27748429

EPR Characterization of Dinitrosyl Iron Complexes with Thiol-Containing Ligands as an Approach to Their Identification in Biological Objects: An Overview.

PubMed

Vanin, Anatoly F

2018-06-01

The overview demonstrates how the use of only one physico-chemical approach, viz., the electron paramagnetic resonance method, allowed detection and identification of dinitrosyl iron complexes with thiol-containing ligands in various animal and bacterial cells. These complexes are formed in biological objects in the paramagnetic (electron paramagnetic resonance-active) mononuclear and diamagnetic (electron paramagnetic resonance-silent) binuclear forms and control the activity of nitrogen monoxide, one of the most universal regulators of metabolic processes in the organism. The analysis of electronic and spatial structures of dinitrosyl iron complex sheds additional light on the mechanism whereby dinitrosyl iron complex with thiol-containing ligands function in human and animal cells as donors of nitrogen monoxide and its ionized form, viz., nitrosonium ions (NO + ).

Archaeal MCM Proteins as an Analog for the Eukaryotic Mcm2–7 Helicase to Reveal Essential Features of Structure and Function

PubMed Central

Miller, Justin M.; Enemark, Eric J.

2015-01-01

In eukaryotes, the replicative helicase is the large multisubunit CMG complex consisting of the Mcm2–7 hexameric ring, Cdc45, and the tetrameric GINS complex. The Mcm2–7 ring assembles from six different, related proteins and forms the core of this complex. In archaea, a homologous MCM hexameric ring functions as the replicative helicase at the replication fork. Archaeal MCM proteins form thermostable homohexamers, facilitating their use as models of the eukaryotic Mcm2–7 helicase. Here we review archaeal MCM helicase structure and function and how the archaeal findings relate to the eukaryotic Mcm2–7 ring. PMID:26539061

Theoretical study of mixed MLaX(4) (M = Na, K, Cs; X = F, Cl, Br, I) rare earth/alkali metal halide complexes.

PubMed

Groen, Cornelis Petrus; Oskam, Ad; Kovács, Attila

2003-02-10

The structure, bonding, and vibrational properties of the mixed MLaX(4) (M = Na, K, Cs; X = F, Cl, Br, I) rare earth/alkali metal halide complexes have been studied using the MP2 method in conjunction with polarized triple-zeta valence basis sets and quasi-relativistic effective core potentials for the heavy atoms. From the three characteristic structures, possessing 1- (C(3)(v)), 2- (C(2)(v)), or 3-fold coordination (C(3)(v)) between the alkali metal and the bridging halide atoms, the bi- and tridentate forms are stable isomers with close dissociation energies. In general, for the complexes existing of lighter alkali metals and halogens, the bidentate structure corresponds to the global minimum of the potential energy surface, while the heavier analogues favor the tridentate structure. At experimentally relevant temperatures (T > 800 K), however, the isomerization entropy leads to a domination of the bidentate structures over the tridentate forms for all complexes. An important effect of the size of the alkali metal is manifested in the larger stabilities of the K and Cs complexes. The natural atomic charges are in agreement with strong electrostatic interactions in the title complexes. The marginal covalent contributions show a slight increasing trend in the heavier analogues. The calculated vibrational data indicate that infrared spectroscopy may be an effective tool for experimental investigation and characterization of MLaX(4) molecules.

Synthesis and characterization of a series of transition metal complexes with a new symmetrical polyoxaaza macroacyclic Schiff base ligand: X-ray crystal structure of cobalt(II) and nickel(II) complexes and their antibacterial properties

NASA Astrophysics Data System (ADS)

Keypour, Hassan; Shayesteh, Maryam; Rezaeivala, Majid; Chalabian, Firoozeh; Valencia, Laura

2013-01-01

A new symmetrical [N4O2] hexadentate Schiff base ligand, (E)-N-(pyridin-2-ylmethylene)-2-(3-(2-((E)-pyridin-2-lmethyleneamino)phenoxy)naphthalen-2-yloxy)benzenamine, abbreviated to L, and its complexes of Ni(II), Cu(II), Zn(II), Co(II), Cd(II) and Mn(II) have been synthesized in the presence of metal ions. The complexes were structurally characterized by elemental analyses, IR, UV-Vis, NMR and molar conductivity. The crystal structures of two complexes, [NiL(ONO2)2]·2H2O and [CoLCl2]CH3OH·0.5H2O, have been determined by a single crystal X-ray diffraction study. In these complexes, the ligand is coordinated in a neutral form via pyridine and azomethine nitrogen atoms. The metal ions complete their six coordination with two coordinated nitrate or chloride ions, forming a distorted octahedral geometry. The synthesized compounds have antibacterial activity against the three Gram-positive bacteria: Enterococcus faecalis, Bacillus cereus and Staphylococcus epid and also against the three Gram-negative bacteria: Citrobacter freundii, Enterobacter aerogenes and Salmonella typhi. The activity data show that the complexes are more potent antibacterials than the parent Schiff base.

Molecular Architecture of Plant Thylakoids under Physiological and Light Stress Conditions: A Study of Lipid–Light-Harvesting Complex II Model Membranes[C][W

PubMed Central

Janik, Ewa; Bednarska, Joanna; Zubik, Monika; Puzio, Michal; Luchowski, Rafal; Grudzinski, Wojciech; Mazur, Radoslaw; Garstka, Maciej; Maksymiec, Waldemar; Kulik, Andrzej; Dietler, Giovanni; Gruszecki, Wieslaw I.

2013-01-01

In this study, we analyzed multibilayer lipid-protein membranes composed of the photosynthetic light-harvesting complex II (LHCII; isolated from spinach [Spinacia oleracea]) and the plant lipids monogalcatosyldiacylglycerol and digalactosyldiacylglycerol. Two types of pigment-protein complexes were analyzed: those isolated from dark-adapted leaves (LHCII) and those from leaves preilluminated with high-intensity light (LHCII-HL). The LHCII-HL complexes were found to be partially phosphorylated and contained zeaxanthin. The results of the x-ray diffraction, infrared imaging microscopy, confocal laser scanning microscopy, and transmission electron microscopy revealed that lipid-LHCII membranes assemble into planar multibilayers, in contrast with the lipid-LHCII-HL membranes, which form less ordered structures. In both systems, the protein formed supramolecular structures. In the case of LHCII-HL, these structures spanned the multibilayer membranes and were perpendicular to the membrane plane, whereas in LHCII, the structures were lamellar and within the plane of the membranes. Lamellar aggregates of LHCII-HL have been shown, by fluorescence lifetime imaging microscopy, to be particularly active in excitation energy quenching. Both types of structures were stabilized by intermolecular hydrogen bonds. We conclude that the formation of trans-layer, rivet-like structures of LHCII is an important determinant underlying the spontaneous formation and stabilization of the thylakoid grana structures, since the lamellar aggregates are well suited to dissipate excess energy upon overexcitation. PMID:23898030

Molecular architecture of plant thylakoids under physiological and light stress conditions: a study of lipid-light-harvesting complex II model membranes.

PubMed

Janik, Ewa; Bednarska, Joanna; Zubik, Monika; Puzio, Michal; Luchowski, Rafal; Grudzinski, Wojciech; Mazur, Radoslaw; Garstka, Maciej; Maksymiec, Waldemar; Kulik, Andrzej; Dietler, Giovanni; Gruszecki, Wieslaw I

2013-06-01

In this study, we analyzed multibilayer lipid-protein membranes composed of the photosynthetic light-harvesting complex II (LHCII; isolated from spinach [Spinacia oleracea]) and the plant lipids monogalcatosyldiacylglycerol and digalactosyldiacylglycerol. Two types of pigment-protein complexes were analyzed: those isolated from dark-adapted leaves (LHCII) and those from leaves preilluminated with high-intensity light (LHCII-HL). The LHCII-HL complexes were found to be partially phosphorylated and contained zeaxanthin. The results of the x-ray diffraction, infrared imaging microscopy, confocal laser scanning microscopy, and transmission electron microscopy revealed that lipid-LHCII membranes assemble into planar multibilayers, in contrast with the lipid-LHCII-HL membranes, which form less ordered structures. In both systems, the protein formed supramolecular structures. In the case of LHCII-HL, these structures spanned the multibilayer membranes and were perpendicular to the membrane plane, whereas in LHCII, the structures were lamellar and within the plane of the membranes. Lamellar aggregates of LHCII-HL have been shown, by fluorescence lifetime imaging microscopy, to be particularly active in excitation energy quenching. Both types of structures were stabilized by intermolecular hydrogen bonds. We conclude that the formation of trans-layer, rivet-like structures of LHCII is an important determinant underlying the spontaneous formation and stabilization of the thylakoid grana structures, since the lamellar aggregates are well suited to dissipate excess energy upon overexcitation.

Structure of a Yeast Dyn2-Nup159 Complex and Molecular Basis for Dynein Light Chain-Nuclear Pore Interaction*

PubMed Central

Romes, Erin M.; Tripathy, Ashutosh; Slep, Kevin C.

2012-01-01

The nuclear pore complex gates nucleocytoplasmic transport through a massive, eight-fold symmetric channel capped by a nucleoplasmic basket and structurally unique, cytoplasmic fibrils whose tentacles bind and regulate asymmetric traffic. The conserved Nup82 complex, composed of Nsp1, Nup82, and Nup159, forms the unique cytoplasmic fibrils that regulate mRNA nuclear export. Although the nuclear pore complex plays a fundamental, conserved role in nuclear trafficking, structural information about the cytoplasmic fibrils is limited. Here, we investigate the structural and biochemical interactions between Saccharomyces cerevisiae Nup159 and the nucleoporin, Dyn2. We find that Dyn2 is predominantly a homodimer and binds arrayed sites on Nup159, promoting the Nup159 parallel homodimerization. We present the first structure of Dyn2, determined at 1.85 Å resolution, complexed with a Nup159 target peptide. Dyn2 resembles homologous metazoan dynein light chains, forming homodimeric composite substrate binding sites that engage two independent 10-residue target motifs, imparting a β-strand structure to each peptide via antiparallel extension of the Dyn2 core β-sandwich. Dyn2 recognizes a highly conserved QT motif while allowing sequence plasticity in the flanking residues of the peptide. Isothermal titration calorimetric analysis of the comparative binding of Dyn2 to two Nup159 target sites shows similar affinities (18 and 13 μm), but divergent thermal binding modes. Dyn2 homodimers are arrayed in the crystal lattice, likely mimicking the arrayed architecture of Dyn2 on the Nup159 multivalent binding sites. Crystallographic interdimer interactions potentially reflect a cooperative basis for Dyn2-Nup159 complex formation. Our data highlight the determinants that mediate oligomerization of the Nup82 complex and promote a directed, elongated cytoplasmic fibril architecture. PMID:22411995

The structure and protein binding of amyloid-specific dye reagents.

PubMed

Stopa, Barbara; Piekarska, Barbara; Konieczny, Leszek; Rybarska, Janina; Spólnik, Paweł; Zemanek, Grzegorz; Roterman, Irena; Król, Marcin

2003-01-01

The self-assembling tendency and protein complexation capability of dyes related to Congo red and also some dyes of different structure were compared to explain the mechanism of Congo red binding and the reason for its specific affinity for beta-structure. Complexation with proteins was measured directly and expressed as the number of dye molecules bound to heat-aggregated IgG and to two light chains with different structural stability. Binding of dyes to rabbit antibodies was measured indirectly as the enhancement effect of the dye on immune complex formation. Self-assembling was tested using dynamic light scattering to measure the size of the supramolecular assemblies. In general the results show that the supramolecular form of a dye is the main factor determining its complexation capability. Dyes that in their compact supramolecular organization are ribbon-shaped may adhere to polypeptides of beta-conformation due to the architectural compatibility in this unique structural form. The optimal fit in complexation seems to depend on two contradictory factors involving, on the one hand, the compactness of the non-covalently stabilized supramolecular ligand, and the dynamic character producing its plasticity on the other. As a result, the highest protein binding capability is shown by dyes with a moderate self-assembling tendency, while those arranging into either very rigid or very unstable supramolecular entities are less able to bind.

Sugar-induced conformational change found in the HA-33/HA-17 trimer of the botulinum toxin complex.

PubMed

Sagane, Yoshimasa; Hayashi, Shintaro; Matsumoto, Takashi; Miyashita, Shin-Ichiro; Inui, Ken; Miyata, Keita; Yajima, Shunsuke; Suzuki, Tomonori; Hasegawa, Kimiko; Yamano, Akihito; Nishikawa, Atsushi; Ohyama, Tohru; Watanabe, Toshihiro; Niwa, Koichi

2013-08-30

Large-sized botulinum toxin complex (L-TC) is formed by conjugation of neurotoxin, nontoxic nonhemagglutinin and hemagglutinin (HA) complex. The HA complex is formed by association of three HA-70 molecules and three HA-33/HA-17 trimers, comprised of a single HA-17 and two HA-33 proteins. The HA-33/HA-17 trimer isolated from serotype D L-TC has the ability to bind to and penetrate through the intestinal epithelial cell monolayer in a sialic acid-dependent manner, and thus it plays an important role in toxin delivery through the intestinal cell wall. In this study, we determined the solution structure of the HA-33/HA-17 trimer by using small-angle X-ray scattering (SAXS). The SAXS image of HA-33/HA-17 exhibited broadly similar appearance to the crystal image of the complex. On the other hand, in the presence of N-acetylneuraminic acid, glucose and galactose, the solution structure of the HA-33/HA-17 trimer was drastically altered compared to the structure in the absence of the sugars. Sugar-induced structural change of the HA-33/HA-17 trimer may contribute to cell binding and subsequent transport across the intestinal cell layer. Copyright © 2013 Elsevier Inc. All rights reserved.

Phosphate barrier on pore-filled cation-exchange membrane for blocking complexing ions in presence of non-complexing ions

NASA Astrophysics Data System (ADS)

Chavan, Vivek; Agarwal, Chhavi; Shinde, Rakesh N.

2018-06-01

In present work, an approach has been used to form a phosphate groups bearing surface barrier on a cation-exchange membrane (CEM). Using optimized conditions, the phosphate bearing monomer bis[2-(methacryloyloxy)ethyl] phosphate has been grafted on the surface of the host poly(ethersulfone) membranes using UV light induced polymerization. The detailed characterizations have shown that less than a micron layer of phosphate barrier is formed without disturbing the original microporous structure of the host membrane. The pores of thus formed membrane have been blocked by cationic-gel formed by in situ UV-initiator induced polymerization of 2-acrylamido-2-methyl-1-propane sulphonic acid along with crosslinker ethylene glycol dimethacrylate in the pores of the membrane. UV-initiator is required for pore-filling as UV light would not penetrate the interior matrix of the membrane. The phosphate functionalized barrier membrane has been examined for permselectivity using a mixture of representative complexing Am3+ ions and non-complexing Cs+ ions. This experiment has demonstrated that complex forming Am3+ ions are blocked by phosphate barrier layer while non-complexing Cs+ ions are allowed to pass through the channels formed by the crosslinked cationic gel.

Host-guest capability of a three-dimensional heterometallic macrocycle.

PubMed

Fan, Qi-Jia; Lin, Yue-Jian; Hahn, F Ekkehardt; Jin, Guo-Xin

2018-02-13

A three-dimensional heterometallic coordination macrocycle is found to be capable of encapsulating planar pyrene (G1), coronene (G4) and non-planar corannulene (G2) guest molecules in high yields, giving rise to 1 : 1 host-guest complexes. The bowl-shaped guest corannulene is found to be significantly flattened upon inclusion within the cavity. However, macrocyclic compounds with larger cavity sizes, which form 1 : 1 stoichiometry assemblies with a naphthalene bisimide planar molecule (G3), are more inclined to form infinite sandwich structures. Furthermore, these heterometallic coordination macrocycles can be destroyed in the presence of a soft base to form hexanuclear triangular prism complexes. These structures are unambiguously revealed by single-crystal X-ray analysis.

Azide and acetate complexes plus two iron-depleted crystal structures of the di-iron enzyme delta9 stearoyl-acyl carrier protein desaturase. Implications for oxygen activation and catalytic intermediates.

PubMed

Moche, Martin; Shanklin, John; Ghoshal, Alokesh; Lindqvist, Ylva

2003-07-04

Delta9 stearoyl-acyl carrier protein (ACP) desaturase is a mu-oxo-bridged di-iron enzyme, which belongs to the structural class I of large helix bundle proteins and that catalyzes the NADPH and O2-dependent formation of a cis-double bond in stearoyl-ACP. The crystal structures of complexes with azide and acetate, respectively, as well as the apoand single-iron forms of Delta9 stearoyl-ACP desaturase from Ricinus communis have been determined. In the azide complex, the ligand forms a mu-1,3-bridge between the two iron ions in the active site, replacing a loosely bound water molecule. The structure of the acetate complex is similar, with acetate bridging the di-iron center in the same orientation with respect to the di-iron center. However, in this complex, the iron ligand Glu196 has changed its coordination mode from bidentate to monodentate, the first crystallographic observation of a carboxylate shift in Delta9 stearoyl-ACP desaturase. The two complexes are proposed to mimic a mu-1,2 peroxo intermediate present during catalytic turnover. There are striking structural similarities between the di-iron center in the Delta9 stearoyl-ACP desaturase-azide complex and in the reduced rubrerythrin-azide complex. This suggests that Delta9 stearoyl-ACP desaturase might catalyze the formation of water from exogenous hydrogen peroxide at a low rate. From the similarity in iron center structure, we propose that the mu-oxo-bridge in oxidized desaturase is bound to the di-iron center as in rubrerythrin and not as reported for the R2 subunit of ribonucleotide reductase and the hydroxylase subunit of methane monooxygenase. The crystal structure of the one-iron depleted desaturase species demonstrates that the affinities for the two iron ions comprising the di-iron center are not equivalent, Fe1 being the higher affinity site and Fe2 being the lower affinity site.

Structural Basis for Reversible and Irreversible Inhibition of Human Cathepsin L by their Respective dipeptidyl glyoxal and diazomethylketone Inhibitors

DOE Office of Scientific and Technical Information (OSTI.GOV)

R Shenoy; J Sivaraman

Cathepsin L plays a key role in many pathophysiological conditions including rheumatoid arthritis, tumor invasion and metastasis, bone resorption and remodeling. Here we report the crystal structures of two analogous dipeptidyl inhibitor complexes which inhibit human cathepsin L in reversible and irreversible modes, respectively. To-date, there are no crystal structure reports of complexes of proteases with their glyoxal inhibitors or complexes of cathepsin L and their diazomethylketone inhibitors. These two inhibitors - inhibitor 1, an {alpha}-keto-{beta}-aldehyde and inhibitor 2, a diazomethylketone, have different groups in the S1 subsite. Inhibitor 1 [Z-Phe-Tyr (OBut)-COCHO], with a Ki of 0.6 nM, is themore » most potent, reversible, synthetic peptidyl inhibitor of cathepsin L reported to-date. The structure of the inhibitor 1 complex was refined up to 2.2 {angstrom} resolution. The structure of the complex of the inhibitor 2 [Z-Phe-Tyr (t-Bu)-diazomethylketone], an irreversible inhibitor that can inactivate cathepsin L at {micro}M concentrations, was refined up to 1.76 {angstrom} resolution. These two inhibitors have substrate-like interactions with the active site cysteine (Cys25). Inhibitor 1 forms a tetrahedral hemithioacetal adduct, whereas the inhibitor 2 forms a thioester with Cys25. The inhibitor 1 {beta}-aldehyde group is shown to make a hydrogen bond with catalytic His163, whereas the ketone carbonyl oxygen of the inhibitor 2 interacts with the oxyanion hole. tert-Butyl groups of both inhibitors are found to make several non-polar contacts with S' subsite residues of cathepsin L. These studies, combined with other complex structures of cathepsin L, reveal the structural basis for their potency and selectivity.« less

Homodimeric cross-over structure of the human granulocyte colony-stimulating factor (GCSF) receptor signaling complex

PubMed Central

Tamada, Taro; Honjo, Eijiro; Maeda, Yoshitake; Okamoto, Tomoyuki; Ishibashi, Matsujiro; Tokunaga, Masao; Kuroki, Ryota

2006-01-01

A crystal structure of the signaling complex between human granulocyte colony-stimulating factor (GCSF) and a ligand binding region of GCSF receptor (GCSF-R), has been determined to 2.8 Å resolution. The GCSF:GCSF-R complex formed a 2:2 stoichiometry by means of a cross-over interaction between the Ig-like domains of GCSF-R and GCSF. The conformation of the complex is quite different from that between human GCSF and the cytokine receptor homologous domain of mouse GCSF-R, but similar to that of the IL-6/gp130 signaling complex. The Ig-like domain cross-over structure necessary for GCSF-R activation is consistent with previously reported thermodynamic and mutational analyses. PMID:16492764

Reaction of Pb(II) and Zn(II) with Ethyl Linoleate To Form Structured Hybrid Inorganic–Organic Complexes: A Model for Degradation in Historic Paint Films

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacDonald, Margaret G.; Palmer, Michael R.; Suchomel, Matthew R.

To investigate soap formation in drying oils in historic paints, the reaction between metal acetates (K +, Zn 2+, Pb 2+) and ethyl linoleate (EL) was studied using optical microscopy, X-ray powder diffraction, and electron microscopy. Pb(II) and Zn(II) react rapidly with EL to form highly structured, spherulitic, luminescent crystallites that aggregate. Evidence from Fourier transform infrared (FTIR) and scanning electron microscopy/energy dispersive X-ray analysis and high-resolution synchrotron powder X-ray diffraction indicates that these are organic-inorganic hybrid complexes or coordination polymers. FTIR absorbance peaks at ca. 1540 cm -1 for Pb(II) and ca. 1580 cm -1 for Zn(II) are consistentmore » with the formation of carboxylate complexes. The complexes formed offer insight into the degradation processes observed in oil paint films, suggesting that soap formation is rapid when metal ions are solubilized and can occur with unsaturated fatty acids that are present in fresh oils. Finally, these complexes may account for the atypical luminescence observed in lead-containing cured oil paint films.« less

Reaction of Pb(II) and Zn(II) with Ethyl Linoleate To Form Structured Hybrid Inorganic–Organic Complexes: A Model for Degradation in Historic Paint Films

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacDonald, Margaret G.; Palmer, Michael R.; Suchomel, Matthew R.

To investigate soap formation in drying oils in historic paints, the reaction between metal acetates (K +, Zn 2+, Pb 2+) and ethyl linoleate (EL) was studied using optical microscopy, X-ray powder diffraction, and electron microscopy. Pb(II) and Zn(II) react rapidly with EL to form highly structured, spherulitic, luminescent crystallites that aggregate. Evidence from Fourier transform infrared (FTIR) and scanning electron microscopy/energy dispersive X-ray analysis and high-resolution synchrotron powder X-ray diffraction indicates that these are organic–inorganic hybrid complexes or coordination polymers. FTIR absorbance peaks at ca. 1540 cm –1 for Pb(II) and ca. 1580 cm –1 for Zn(II) are consistentmore » with the formation of carboxylate complexes. The complexes formed offer insight into the degradation processes observed in oil paint films, suggesting that soap formation is rapid when metal ions are solubilized and can occur with unsaturated fatty acids that are present in fresh oils. These complexes may account for the atypical luminescence observed in lead-containing cured oil paint films.« less

Reaction of Pb(II) and Zn(II) with Ethyl Linoleate To Form Structured Hybrid Inorganic–Organic Complexes: A Model for Degradation in Historic Paint Films

DOE PAGES

MacDonald, Margaret G.; Palmer, Michael R.; Suchomel, Matthew R.; ...

2016-09-07

To investigate soap formation in drying oils in historic paints, the reaction between metal acetates (K +, Zn 2+, Pb 2+) and ethyl linoleate (EL) was studied using optical microscopy, X-ray powder diffraction, and electron microscopy. Pb(II) and Zn(II) react rapidly with EL to form highly structured, spherulitic, luminescent crystallites that aggregate. Evidence from Fourier transform infrared (FTIR) and scanning electron microscopy/energy dispersive X-ray analysis and high-resolution synchrotron powder X-ray diffraction indicates that these are organic-inorganic hybrid complexes or coordination polymers. FTIR absorbance peaks at ca. 1540 cm -1 for Pb(II) and ca. 1580 cm -1 for Zn(II) are consistentmore » with the formation of carboxylate complexes. The complexes formed offer insight into the degradation processes observed in oil paint films, suggesting that soap formation is rapid when metal ions are solubilized and can occur with unsaturated fatty acids that are present in fresh oils. Finally, these complexes may account for the atypical luminescence observed in lead-containing cured oil paint films.« less

Structural and functional characterization of a cell cycle associated HDAC1/2 complex reveals the structural basis for complex assembly and nucleosome targeting

PubMed Central

Itoh, Toshimasa; Fairall, Louise; Muskett, Frederick W.; Milano, Charles P.; Watson, Peter J.; Arnaudo, Nadia; Saleh, Almutasem; Millard, Christopher J.; El-Mezgueldi, Mohammed; Martino, Fabrizio; Schwabe, John W.R.

2015-01-01

Recent proteomic studies have identified a novel histone deacetylase complex that is upregulated during mitosis and is associated with cyclin A. This complex is conserved from nematodes to man and contains histone deacetylases 1 and 2, the MIDEAS corepressor protein and a protein called DNTTIP1 whose function was hitherto poorly understood. Here, we report the structures of two domains from DNTTIP1. The amino-terminal region forms a tight dimerization domain with a novel structural fold that interacts with and mediates assembly of the HDAC1:MIDEAS complex. The carboxy-terminal domain of DNTTIP1 has a structure related to the SKI/SNO/DAC domain, despite lacking obvious sequence homology. We show that this domain in DNTTIP1 mediates interaction with both DNA and nucleosomes. Thus, DNTTIP1 acts as a dimeric chromatin binding module in the HDAC1:MIDEAS corepressor complex. PMID:25653165

Ab initio and DFT study of hydrogen bond interactions between ascorbic acid and dimethylsulfoxide based on FT-IR and FT-Raman spectra

NASA Astrophysics Data System (ADS)

Niazazari, Naser; Zatikyan, Ashkhen L.; Markarian, Shiraz A.

2013-06-01

The hydrogen bonding of 1:1 complexes formed between L-ascorbic acid (LAA) and dimethylsulfoxide (DMSO) has been studied by means of ab initio and density functional theory (DFT) calculations. Solutions of L-ascorbic acid (AA) in dimethylsulfoxide (DMSO) have been studied by means of both FT-IR (4000-220 cm-1) and FT-Raman spectroscopy. Ab initio Hartree-Fock (HF) and DFT methods have been used to determine the structure and energies of stable conformers of various types of L-AA/DMSO complexes in gas phase and solution. The basis sets 6-31++G∗∗ and 6-311+G∗ were used to describe the structure, energy, charges and vibrational frequencies of interacting complexes in the gas phase. The optimized geometric parameters and interaction energies for various complexes at different theories have been estimated. Binding energies have been corrected for basis set superposition error (BSSE) and harmonic vibrational frequencies of the structures have been calculated to obtain the stable forms of the complexes. The self-consistent reaction field (SCRF) has been used to calculate the effect of DMSO as the solvent on the geometry, energy and charges of complexes. The solvent effect has been studied using the Onsager models. It is shown that the polarity of the solvent plays an important role on the structures and relative stabilities of different complexes. The results obtained show that there is a satisfactory correlation between experimental and theoretical predictions.

Structure of soybean serine acetyltransferase and formation of the cysteine regulatory complex as a molecular chaperone

USDA-ARS?s Scientific Manuscript database

Serine acetyltransferase (SAT) catalyzes the limiting reaction in plant and microbial biosynthesis of cysteine. In addition to its enzymatic function, SAT forms a macromolecular complex with O-acetylserine sulfhydrylase (OASS). Formation of the cysteine regulatory complex (CRC) is a critical biochem...

Is Structure Dependence an Innate Constraint? New Experimental Evidence from Children's Complex-Question Production

ERIC Educational Resources Information Center

Ambridge, Ben; Rowland, Caroline F.; Pine, Julian M.

2008-01-01

According to Crain and Nakayama (1987), when forming complex yes/no questions, children do not make errors such as "Is the boy who smoking is crazy?" because they have innate knowledge of "structure dependence" and so will not move the auxiliary from the relative clause. However, simple recurrent networks are also able to avoid…

Histone H3 phosphorylation near the nucleosome dyad alters chromatin structure

PubMed Central

North, Justin A.; Šimon, Marek; Ferdinand, Michelle B.; Shoffner, Matthew A.; Picking, Jonathan W.; Howard, Cecil J.; Mooney, Alex M.; van Noort, John; Poirier, Michael G.; Ottesen, Jennifer J.

2014-01-01

Nucleosomes contain ∼146 bp of DNA wrapped around a histone protein octamer that controls DNA accessibility to transcription and repair complexes. Posttranslational modification (PTM) of histone proteins regulates nucleosome function. To date, only modest changes in nucleosome structure have been directly attributed to histone PTMs. Histone residue H3(T118) is located near the nucleosome dyad and can be phosphorylated. This PTM destabilizes nucleosomes and is implicated in the regulation of transcription and repair. Here, we report gel electrophoretic mobility, sucrose gradient sedimentation, thermal disassembly, micrococcal nuclease digestion and atomic force microscopy measurements of two DNA–histone complexes that are structurally distinct from nucleosomes. We find that H3(T118ph) facilitates the formation of a nucleosome duplex with two DNA molecules wrapped around two histone octamers, and an altosome complex that contains one DNA molecule wrapped around two histone octamers. The nucleosome duplex complex forms within short ∼150 bp DNA molecules, whereas altosomes require at least ∼250 bp of DNA and form repeatedly along 3000 bp DNA molecules. These results are the first report of a histone PTM significantly altering the nucleosome structure. PMID:24561803

Spectroscopic and structural study of the newly synthesized heteroligand complex of copper with creatinine and urea.

PubMed

Gangopadhyay, Debraj; Singh, Sachin Kumar; Sharma, Poornima; Mishra, Hirdyesh; Unnikrishnan, V K; Singh, Bachcha; Singh, Ranjan K

2016-02-05

Study of copper complex of creatinine and urea is very important in life science and medicine. In this paper, spectroscopic and structural study of a newly synthesized heteroligand complex of copper with creatinine and urea has been discussed. Structural studies have been carried out using DFT calculations and spectroscopic analyses were carried out by FT-IR, Raman, UV-vis absorption and fluorescence techniques. The copper complex of creatinine and the heteroligand complex were found to have much increased water solubility as compared to pure creatinine. The analysis of FT-IR and Raman spectra helps to understand the coordination properties of the two ligands and to determine the probable structure of the heteroligand complex. The LIBS spectra of the heteroligand complex reveal that the complex is free from other metal impurities. UV-visible absorption spectra and the fluorescence emission spectra of the aqueous solution of Cu-Crn-urea heteroligand complex at different solute concentrations have been analyzed and the complex is found to be rigid and stable in its monomeric form at very low concentrations. Copyright © 2015 Elsevier B.V. All rights reserved.

Solution structure of the phosphoryl transfer complex between the cytoplasmic A domain of the mannitol transporter IIMannitol and HPr of the Escherichia coli phosphotransferase system.

PubMed

Cornilescu, Gabriel; Lee, Byeong Ryong; Cornilescu, Claudia C; Wang, Guangshun; Peterkofsky, Alan; Clore, G Marius

2002-11-01

The solution structure of the complex between the cytoplasmic A domain (IIA(Mtl)) of the mannitol transporter II(Mannitol) and the histidine-containing phosphocarrier protein (HPr) of the Escherichia coli phosphotransferase system has been solved by NMR, including the use of conjoined rigid body/torsion angle dynamics, and residual dipolar couplings, coupled with cross-validation, to permit accurate orientation of the two proteins. A convex surface on HPr, formed by helices 1 and 2, interacts with a complementary concave depression on the surface of IIA(Mtl) formed by helix 3, portions of helices 2 and 4, and beta-strands 2 and 3. The majority of intermolecular contacts are hydrophobic, with a small number of electrostatic interactions at the periphery of the interface. The active site histidines, His-15 of HPr and His-65 of IIA(Mtl), are in close spatial proximity, and a pentacoordinate phosphoryl transition state can be readily accommodated with no change in protein-protein orientation and only minimal perturbations of the backbone immediately adjacent to the histidines. Comparison with two previously solved structures of complexes of HPr with partner proteins of the phosphotransferase system, the N-terminal domain of enzyme I (EIN) and enzyme IIA(Glucose) (IIA(Glc)), reveals a number of common features despite the fact that EIN, IIA(Glc), and IIA(Mtl) bear no structural resemblance to one another. Thus, entirely different underlying structural elements can form binding surfaces for HPr that are similar in terms of both shape and residue composition. These structural comparisons illustrate the roles of surface and residue complementarity, redundancy, incremental build-up of specificity and conformational side chain plasticity in the formation of transient specific protein-protein complexes in signal transduction pathways.

alpha-Lactalbumin species variation, HAMLET formation, and tumor cell death.

PubMed

Pettersson, Jenny; Mossberg, Ann-Kristin; Svanborg, Catharina

2006-06-23

HAMLET (human alpha-lactalbumin made lethal to tumor cells) is a tumoricidal complex of apo alpha-lactalbumin and oleic acid, formed in casein after low pH treatment of human milk. This study examined if HAMLET-like complexes are present in casein from different species and if isolated alpha-lactalbumin from those species can form such complexes with oleic acid. Casein from human, bovine, equine, and porcine milk was separated by ion exchange chromatography and active complexes were only found in human casein. This was not explained by alpha-lactalbumin sequence variation, as purified bovine, equine, porcine, and caprine alpha-lactalbumins formed complexes with oleic acid with biological activity similar to HAMLET. We conclude that structural variation of alpha-lactalbumins does not preclude the formation of HAMLET-like complexes and that natural HAMLET formation in casein was unique to human milk, which also showed the highest oleic acid content.

Tiopronin Gold Nanoparticle Precursor Forms Aurophilic Ring Tetramer

PubMed Central

Simpson, Carrie A.; Farrow, Christopher L.; Tian, Peng; Billinge, Simon J.L.; Huffman, Brian J.; Harkness, Kellen M.; Cliffel, David E.

2010-01-01

In the two step synthesis of thiolate-monolayer protected clusters (MPCs), the first step of the reaction is a mild reduction of gold(III) by thiols that generates gold(I) thiolate complexes as intermediates. Using tiopronin (Tio) as the thiol reductant, the characterization of the intermediate Au4Tio4 complex was accomplished with various analytical and structural techniques. Nuclear magnetic resonance (NMR), elemental analysis, thermogravimetric analysis (TGA), and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) were all consistent with a cyclic gold(I)-thiol tetramer structure, and final structural analysis was gathered through the use of powder diffraction and pair distribution functions (PDF). Crystallographic data has proved challenging for almost all previous gold(I)-thiolate complexes. Herein, a novel characterization technique when combined with standard analytical assessment to elucidate structure without crystallographic data proved invaluable to the study of these complexes. This in conjunction with other analytical techniques, in particular mass spectrometry, can elucidate a structure when crystallographic data is unavailable. In addition, luminescent properties provided evidence of aurophilicity within the molecule. The concept of aurophilicity has been introduced to describe a select group of gold-thiolate structures, which possess unique characteristics, mainly red photoluminescence and a distinct Au-Au intramolecular distance indicating a weak metal-metal bond as also evidenced by the structural model of the tetramer. Significant features of both the tetrameric and aurophilic properties of the intermediate gold(I) tiopronin complex are retained after borohydride reduction to form the MPC, including gold(I) tiopronin partial rings as capping motifs, or “staples”, and weak red photoluminescence that extends into the Near Infrared region. PMID:21067183

Systems Modeling in Developmental Toxicity

EPA Science Inventory

An individual starts off as a single cell, the progeny of which form complex structures that are themselves integrated into progressively larger systems. Developmental biology is concerned with how this cellular complexity and patterning arises through orchestration of cell divi...

Crystal Structure of a CRISPR RNA-guided Surveillance Complex Bound to a ssDNA Target

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mulepati, Sabin; Heroux, Annie; Bailey, Scott

In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of proteinmore » subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.« less

Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target

PubMed Central

Mulepati, Sabin; Héroux, Annie; Bailey, Scott

2015-01-01

In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kDa complex is called Cascade. Here we report the 3.03Å crystal structure of Cascade bound to a single-stranded DNA target. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This non-canonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding. PMID:25123481

Structural mechanism of JH delivery in hemolymph by JHBP of silkworm, Bombyx mori

PubMed Central

Suzuki, Rintaro; Fujimoto, Zui; Shiotsuki, Takahiro; Tsuchiya, Wataru; Momma, Mitsuru; Tase, Akira; Miyazawa, Mitsuhiro; Yamazaki, Toshimasa

2011-01-01

Juvenile hormone (JH) plays crucial roles in many aspects of the insect life. All the JH actions are initiated by transport of JH in the hemolymph as a complex with JH-binding protein (JHBP) to target tissues. Here, we report structural mechanism of JH delivery by JHBP based upon the crystal and solution structures of apo and JH-bound JHBP. In solution, apo-JHBP exists in equilibrium of multiple conformations with different orientations of the gate helix for the hormone-binding pocket ranging from closed to open forms. JH-binding to the gate-open form results in the fully closed JHBP-JH complex structure where the bound JH is completely buried inside the protein. JH-bound JHBP opens the gate helix to release the bound hormone likely by sensing the less polar environment at the membrane surface of target cells. This is the first report that provides structural insight into JH signaling. PMID:22355650

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Liwei; Yang, Jin Kuk; Kabaleeswaran, Venkataraman

The death-inducing signaling complex (DISC) formed by the death receptor Fas, the adaptor protein FADD and caspase-8 mediates the extrinsic apoptotic program. Mutations in Fas that disrupt the DISC cause autoimmune lymphoproliferative syndrome (ALPS). Here we show that the Fas-FADD death domain (DD) complex forms an asymmetric oligomeric structure composed of 5-7 Fas DD and 5 FADD DD, whose interfaces harbor ALPS-associated mutations. Structure-based mutations disrupt the Fas-FADD interaction in vitro and in living cells; the severity of a mutation correlates with the number of occurrences of a particular interaction in the structure. The highly oligomeric structure explains the requirementmore » for hexameric or membrane-bound FasL in Fas signaling. It also predicts strong dominant negative effects from Fas mutations, which are confirmed by signaling assays. The structure optimally positions the FADD death effector domain (DED) to interact with the caspase-8 DED for caspase recruitment and higher-order aggregation.« less

Epoxy blanket protects milled part during explosive forming

NASA Technical Reports Server (NTRS)

1966-01-01

Epoxy blanket protects chemically milled or machined sections of large, complex structural parts during explosive forming. The blanket uniformly covers all exposed surfaces and fills any voids to support and protect the entire part.

Unbound Young Stellar Systems: Star Formation on the Loose

NASA Astrophysics Data System (ADS)

Gouliermis, Dimitrios A.

2018-07-01

Unbound young stellar systems, the loose ensembles of physically related young bright stars, trace the typical regions of recent star formation in galaxies. Their morphologies vary from small few pc-size associations of newly formed stars to enormous few kpc-size complexes composed of stars few 100 Myr old. These stellar conglomerations are located within the disks and along the spiral arms and rings of star-forming disk galaxies, and they are the active star-forming centers of dwarf and starburst galaxies. Being associated with star-forming regions of various sizes, these stellar structures trace the regions where stars form at various length- and timescales, from compact clusters to whole galactic disks. Stellar associations, the prototypical unbound young systems, and their larger counterparts, stellar aggregates, and stellar complexes, have been the focus of several studies for quite a few decades, with special interest on their demographics, classification, and structural morphology. The compiled surveys of these loose young stellar systems demonstrate that the clear distinction of these systems into well-defined classes is not as straightforward as for stellar clusters, due to their low densities, asymmetric shapes and variety in structural parameters. These surveys also illustrate that unbound stellar structures follow a clear hierarchical pattern in the clustering of their stars across various scales. Stellar associations are characterized by significant sub-structure with bound stellar clusters being their most compact parts, while associations themselves are the brighter denser parts of larger stellar aggregates and stellar complexes, which are members of larger super-structures up to the scale of a whole star-forming galaxy. This structural pattern, which is usually characterized as self-similar or fractal, appears to be identical to that of star-forming giant molecular clouds and interstellar gas, driven mainly by turbulence cascade. In this short review, I make a concise compilation of our understanding of unbound young stellar systems across various environments in the local universe, as it is developed during the last 60 years. I present a factual assessment of the clustering behavior of star formation, as revealed from the assembling pattern of stars across loose stellar structures and its relation to the interstellar medium and the environmental conditions. I also provide a consistent account of the processes that possibly play important role in the formation of unbound stellar systems, compiled from both theoretical and observational investigations on the field.

Differential global structural changes in the core particle of yeast and mouse proteasome induced by ligand binding

PubMed Central

Arciniega, Marcelino; Beck, Philipp; Lange, Oliver F.; Groll, Michael; Huber, Robert

2014-01-01

Two clusters of configurations of the main proteolytic subunit β5 were identified by principal component analysis of crystal structures of the yeast proteasome core particle (yCP). The apo-cluster encompasses unliganded species and complexes with nonpeptidic ligands, and the pep-cluster comprises complexes with peptidic ligands. The murine constitutive CP structures conform to the yeast system, with the apo-form settled in the apo-cluster and the PR-957 (a peptidic ligand) complex in the pep-cluster. In striking contrast, the murine immune CP classifies into the pep-cluster in both the apo and the PR-957–liganded species. The two clusters differ essentially by multiple small structural changes and a domain motion enabling enclosure of the peptidic ligand and formation of specific hydrogen bonds in the pep-cluster. The immune CP species is in optimal peptide binding configuration also in its apo form. This favors productive ligand binding and may help to explain the generally increased functional activity of the immunoproteasome. Molecular dynamics simulations of the representative murine species are consistent with the experimentally observed configurations. A comparison of all 28 subunits of the unliganded species with the peptidic liganded forms demonstrates a greatly enhanced plasticity of β5 and suggests specific signaling pathways to other subunits. PMID:24979800

Free-Energy Landscape of Protein-Ligand Interactions Coupled with Protein Structural Changes.

PubMed

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2017-02-02

Protein-ligand interactions are frequently coupled with protein structural changes. Focusing on the coupling, we present the free-energy surface (FES) of the ligand-binding process for glutamine-binding protein (GlnBP) and its ligand, glutamine, in which glutamine binding accompanies large-scale domain closure. All-atom simulations were performed in explicit solvents by multiscale enhanced sampling (MSES), which adopts a multicopy and multiscale scheme to achieve enhanced sampling of systems with a large number of degrees of freedom. The structural ensemble derived from the MSES simulation yielded the FES of the coupling, described in terms of both the ligand's and protein's degrees of freedom at atomic resolution, and revealed the tight coupling between the two degrees of freedom. The derived FES led to the determination of definite structural states, which suggested the dominant pathways of glutamine binding to GlnBP: first, glutamine migrates via diffusion to form a dominant encounter complex with Arg75 on the large domain of GlnBP, through strong polar interactions. Subsequently, the closing motion of GlnBP occurs to form ligand interactions with the small domain, finally completing the native-specific complex structure. The formation of hydrogen bonds between glutamine and the small domain is considered to be a rate-limiting step, inducing desolvation of the protein-ligand interface to form the specific native complex. The key interactions to attain high specificity for glutamine, the "door keeper" existing between the two domains (Asp10-Lys115) and the "hydrophobic sandwich" formed between the ligand glutamine and Phe13/Phe50, have been successfully mapped on the pathway derived from the FES.

A comparative study of the microstructures observed in statically cast and continuously cast Bi-In-Sn ternary eutectic alloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sengupta, S.; Soda, H.; McLean, A.

2000-01-01

A ternary eutectic alloy with a composition of 57.2 pct Bi, 24.8 pct In, and 18 pct Sn was continuously cast into wire of 2 mm diameter with casting speeds of 14 and 79 mm/min using the Ohno Continuous Casting (OCC) process. The microstructures obtained were compared with those of statically cast specimens. Extensive segregation of massive Bi blocks, Bi complex structures, and tin-rich dendrites was found in specimens that were statically cast. Decomposition of {radical}Sn by a eutectoid reaction was confirmed based on microstructural evidence. Ternary eutectic alloy with a cooling rate of approximately 1 C/min formed a doublemore » binary eutectic. The double binary eutectic consisted of regions of BiIn and decomposed {radical}Sn in the form of a dendrite cell structure and regions of Bi and decomposed {radical}Sn in the form of a complex-regular cell. The Bi complex-regular cells, which are a ternary eutectic constituent, existed either along the boundaries of the BiIn-decomposed {radical}Sn dendrite cells or at the front of elongated dendrite cell structures. In the continuously cast wires, primary Sn dendrites coupled with a small Bi phase were uniformly distributed within the Bi-In alloy matrix. Neither massive Bi phase, Bi complex-regular cells, no BiIn eutectic dendrite cells were observed, resulting in a more uniform microstructure in contrast to the heavily segregated structures of the statically cast specimens.« less

Self-assembly of polyelectrolyte surfactant complexes using large scale MD simulation

NASA Astrophysics Data System (ADS)

Goswami, Monojoy; Sumpter, Bobby

2014-03-01

Polyelectrolytes (PE) and surfactants are known to form interesting structures with varied properties in aqueous solutions. The morphological details of the PE-surfactant complexes depend on a combination of polymer backbone, electrostatic interactions and hydrophobic interactions. We study the self-assembly of cationic PE and anionic surfactants complexes in dilute condition. The importance of such complexes of PE with oppositely charged surfactants can be found in biological systems, such as immobilization of enzymes in polyelectrolyte complexes or nonspecific association of DNA with protein. Many useful properties of PE surfactant complexes come from the highly ordered structures of surfactant self-assembly inside the PE aggregate which has applications in industry. We do large scale molecular dynamics simulation using LAMMPS to understand the structure and dynamics of PE-surfactant systems. Our investigation shows highly ordered pearl-necklace structures that have been observed experimentally in biological systems. We investigate many different properties of PE-surfactant complexation for different parameter ranges that are useful for pharmaceutical, engineering and biological applications.

Who is Mr. HAMLET? Interaction of human alpha-lactalbumin with monomeric oleic acid.

PubMed

Knyazeva, Ekaterina L; Grishchenko, Valery M; Fadeev, Roman S; Akatov, Vladimir S; Permyakov, Sergei E; Permyakov, Eugene A

2008-12-09

A specific state of the human milk Ca(2+) binding protein alpha-lactalbumin (hLA) complexed with oleic acid (OA) prepared using an OA-pretreated ion-exchange column (HAMLET) triggers several cell death pathways in various tumor cells. The possibility of preparing a hLA-OA complex with structural and cytotoxic properties similar to those of the HAMLET but under solution conditions has been explored. The complex was formed by titration of hLA by OA at pH 8.3 up to OA critical micelle concentration. We have shown that complex formation strongly depends on calcium, ionic strength, and temperature; the optimal conditions were established. The spectrofluorimetrically estimated number of OA molecules irreversibly bound per hLA molecule (after dialysis of the OA-loaded preparation against water followed by lyophilization) depends upon temperature: 2.9 at 17 degrees C (native apo-hLA; resulting complex referred to as LA-OA-17 state) and 9 at 45 degrees C (thermally unfolded apo-hLA; LA-OA-45). Intrinsic tryptophan fluorescence measurements revealed substantially decreased thermal stability of Ca(2+)-free forms of HAMLET, LA-OA-45, and OA-saturated protein. The irreversibly bound OA does not affect the Ca(2+) association constant of the protein. Phase plot analysis of fluorimetric and CD data indicates that the OA binding process involves several hLA intermediates. The effective pseudoequilibrium OA association constants for Ca(2+)-free hLA were estimated. The far-UV CD spectra of Ca(2+)-free hLA show that all OA-bound forms of the protein are characterized by elevated content of alpha-helical structure. The various hLA-OA complexes possess similar cytotoxic activities against human epidermoid larynx carcinoma cells. Overall, the LA-OA-45 complex possesses physicochemical, structural, and cytotoxic properties closely resembling those of HAMLET. The fact that the HAMLET-like complex can be formed in aqueous solution makes the process of its preparation more transparent and controllable, opening up opportunities for formation of active complexes with specific properties.

The structure and organization of lanceolate mechanosensory complexes at mouse hair follicles

PubMed Central

Li, Lishi; Ginty, David D

2014-01-01

In mouse hairy skin, lanceolate complexes associated with three types of hair follicles, guard, awl/auchene and zigzag, serve as mechanosensory end organs. These structures are formed by unique combinations of low-threshold mechanoreceptors (LTMRs), Aβ RA-LTMRs, Aδ-LTMRs, and C-LTMRs, and their associated terminal Schwann cells (TSCs). In this study, we investigated the organization, ultrastructure, and maintenance of longitudinal lanceolate complexes at each hair follicle subtype. We found that TSC processes at hair follicles are tiled and that individual TSCs host axonal endings of more than one LTMR subtype. Electron microscopic analyses revealed unique ultrastructural features of lanceolate complexes that are proposed to underlie mechanotransduction. Moreover, Schwann cell ablation leads to loss of LTMR terminals at hair follicles while, in contrast, TSCs remain associated with hair follicles following skin denervation in adult mice and, remarkably, become re-associated with newly formed axons, indicating a TSC-dependence of lanceolate complex maintenance and regeneration in adults. DOI: http://dx.doi.org/10.7554/eLife.01901.001 PMID:24569481

The structure and organization of lanceolate mechanosensory complexes at mouse hair follicles.

PubMed

Li, Lishi; Ginty, David D

2014-02-25

In mouse hairy skin, lanceolate complexes associated with three types of hair follicles, guard, awl/auchene and zigzag, serve as mechanosensory end organs. These structures are formed by unique combinations of low-threshold mechanoreceptors (LTMRs), Aβ RA-LTMRs, Aδ-LTMRs, and C-LTMRs, and their associated terminal Schwann cells (TSCs). In this study, we investigated the organization, ultrastructure, and maintenance of longitudinal lanceolate complexes at each hair follicle subtype. We found that TSC processes at hair follicles are tiled and that individual TSCs host axonal endings of more than one LTMR subtype. Electron microscopic analyses revealed unique ultrastructural features of lanceolate complexes that are proposed to underlie mechanotransduction. Moreover, Schwann cell ablation leads to loss of LTMR terminals at hair follicles while, in contrast, TSCs remain associated with hair follicles following skin denervation in adult mice and, remarkably, become re-associated with newly formed axons, indicating a TSC-dependence of lanceolate complex maintenance and regeneration in adults. DOI: http://dx.doi.org/10.7554/eLife.01901.001.

Incremental electrohydraulic forming - A new approach for the manufacture of structured multifunctional sheet metal blanks

NASA Astrophysics Data System (ADS)

Djakow, Eugen; Springer, Robert; Homberg, Werner; Piper, Mark; Tran, Julian; Zibart, Alexander; Kenig, Eugeny

2017-10-01

Electrohydraulic Forming (EHF) processes permit the production of complex, sharp-edged geometries even when high-strength materials are used. Unfortunately, the forming zone is often limited as compared to other sheet metal forming processes. The use of a special industrial-robot-based tool setup and an incremental process strategy could provide a promising solution for this problem. This paper describes such an innovative approach using an electrohydraulic incremental forming machine, which can be employed to manufacture the large multifunctional and complex part geometries in steel, aluminium, magnesium and reinforced plastic that are employed in lightweight constructions or heating elements.

Modular fabrication and characterization of complex silicon carbide composite structures Advanced Reactor Technologies (ART) Research Final Report (Feb 2015 – May 2017)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khalifa, Hesham

Advanced ceramic materials exhibit properties that enable safety and fuel cycle efficiency improvements in advanced nuclear reactors. In order to fully exploit these desirable properties, new processing techniques are required to produce the complex geometries inherent to nuclear fuel assemblies and support structures. Through this project, the state of complex SiC-SiC composite fabrication for nuclear components has advanced significantly. New methods to produce complex SiC-SiC composite structures have been demonstrated in the form factors needed for in-core structural components in advanced high temperature nuclear reactors. Advanced characterization techniques have been employed to demonstrate that these complex SiC-SiC composite structures providemore » the strength, toughness and hermeticity required for service in harsh reactor conditions. The complex structures produced in this project represent a significant step forward in leveraging the excellent high temperature strength, resistance to neutron induced damage, and low neutron cross section of silicon carbide in nuclear applications.« less

Superplastic forming of Al-Li alloys for lightweight, low-cost structures

NASA Technical Reports Server (NTRS)

Hales, Stephen J.; Wagner, John A.

1991-01-01

Superplastic forming of advanced aluminum alloys is being evaluated as an approach for fabricating low-cost, light-weight, cryogenic propellant tanks. Built-up structure concepts (with inherent reduced scrap rate) are under investigation to offset the additional raw material expenses incurred by using aluminum lithium alloys. This approach to fabrication offers the potential for significant improvements in both structural efficiency and overall manufacturing costs. Superplasticity is the ability of specially processed material to sustain very large forming strains without failure at elevated temperatures under controlled deformation conditions. It was demonstrated that superplastic forming technology can be used to fabricate complex structural components in a single operation and increase structural efficiency by as much as 60 percent compared to conventional configurations in skin-stiffened structures. Details involved in the application of this technology to commercial grade superplastic aluminum lithium material are presented. Included are identification of optimum forming parameters, development of forming procedures, and assessment of final part quality in terms of cavitation volume and thickness variation.

Diamond-like nanoparticles influence on flavonoids transport: molecular modelling

NASA Astrophysics Data System (ADS)

Plastun, Inna L.; Agandeeva, Ksenia E.; Bokarev, Andrey N.; Zenkin, Nikita S.

2017-03-01

Intermolecular interaction of diamond-like nanoparticles and flavonoids is investigated by numerical simulation. Using molecular modelling by the density functional theory method, we analyze hydrogen bonds formation and their influence on IR - spectra and structure of molecular complex which is formed due to interaction between flavonoids and nanodiamonds surrounded with carboxylic groups. Enriched adamantane (1,3,5,7 - adamantanetetracarboxylic acid) is used as an example of diamond-like nanoparticles. Intermolecular forces and structure of hydrogen bonds are investigated. IR - spectra and structure parameters of quercetin - adamantanetetracarboxylic acid molecular complex are obtained by numerical simulation using the Gaussian software complex. Received data coincide well with experimental results. Intermolecular interactions and hydrogen bonding structure in the obtained molecular complex are examined. Possibilities of flavonoids interaction with DNA at the molecular level are also considered.

Crystal Structure of the Complex Between Programmed Death-1 (PD-1) and its Ligand PD-L2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lazar-Molnar,E.; Yan, Q.; Cao, E.

2008-01-01

Programmed death-1 (PD-1) is a member of the CD28/B7 superfamily that delivers negative signals upon interaction with its two ligands, PD-L1 or PD-L2. The high-resolution crystal structure of the complex formed by the complete ectodomains of murine PD-1 and PD-L2 revealed a 1:1 receptor:ligand stoichiometry and displayed a binding interface and overall molecular organization distinct from that observed in the CTLA-4/B7 inhibitory complexes. Furthermore, our structure also provides insights into the association between PD-1 and PD-L1 and highlights differences in the interfaces formed by the two PD-1 ligands (PD-Ls) Mutagenesis studies confirmed the details of the proposed PD-1/PD-L binding interfacesmore » and allowed for the design of a mutant PD-1 receptor with enhanced affinity. These studies define spatial and organizational constraints that control the localization and signaling of PD-1/PD-L complexes within the immunological synapse and provide a basis for manipulating the PD-1 pathways for immunotherapy.« less

Four-Stranded Dna Formed by Isoguanine Quartets: Complex Stoichiometry, Thermal Stability and Resistance Against Exonucleases

NASA Astrophysics Data System (ADS)

Seela, Frank; Wei, Changfu; Melenewski, Alexander

1997-12-01

Single stranded DNA-fragments containing short runs of isoguanine such as d(T_4iG_4T_4) (5) or d(iG_4T_4) (6) form quartet structures by self-assembly of the isoguanine residues. The stoichiometry of the complexes is deduced from mixed aggregates formed between d(T_4iG_4T_4) and d(iG_4T_4). The iG_d-tetrads are more stable with regard to their thermal denaturation and to their resistance against enzymatic phosphodiester hydrolysis than those formed by dG.

Crystal structures of resorcin[4]arene and pyrogallol[4]arene complexes with DL-pipecolinic acid. Model compounds for the recognition of the pipecolinyl ring, a key fragment of FK506, through C-H⋯π interaction

NASA Astrophysics Data System (ADS)

Fujisawa, Ikuhide; Kitamura, Yuji; Kato, Ryo; Murayama, Kazutaka; Aoki, Katsuyuki

2014-01-01

Resorcin[4]arene (resorcinol cyclic tetramer, abbreviated as RCT) or pyrogallol[4]arene (pyrogallol cyclic tetramer, PCT) form host-guest 1:1 complexes with DL-pipecolinic acid (DL-pipeH), RCT·DL-pipeH·EtOH·8H2O (1), PCT DL-pipeH·EtOH·4H2O (2), and PCT·DL-pipeH·3H2O (3), whose crystal structures have been determined. In each complex, the pipeH ligand is incorporated into the bowl-shaped cavity of the RCT or PCT host molecules through C-H⋯π interactions between alkyl protons of the piperidine ring of pipeH and π-rings of RCT or PCT, forming an [(RCT/PCT)·pipeH] structural fragment. In 1 and 3, two [(RCT/PCT) pipeH] fragments self-associate across an inversion center to form a guest-mediated, obliquely declined dimeric structure [(RCT/PCT)·L-pipeH·D-pipeH (RCT/PCT)]. In 2, each PCT-capped pipeH ligand bridges to two adjacent PCT molecules to form guest-mediated, optically-discrete helical polymers [PCT·L-pipeH]n or [PCT·D-pipeH]n. An 1H NMR experiment shows that the complexation through C-H⋯π interaction between the piperidine ring of pipeH and π-rings of RCT or PCT occurs also in solution, with the binding constants of 9.7 ± 0.6 M-1 for RCT and 26.5 ± 1.5 M-1 for PCT. These complexes provide a synthetic model for the recognition of the pipecolinyl-ring moiety, a key constituent of immunosuppressant drugs such as FK506, FK520 or rapamycin, by their binding proteins through C-H⋯π interaction.

Combinatorial operad actions on cochains

NASA Astrophysics Data System (ADS)

Berger, Clemens; Fresse, Benoit

2004-07-01

A classical E-infinity operad is formed by the bar construction of the symmetric groups. Such an operad has been introduced by M. Barratt and P. Eccles in the context of simplicial sets in order to have an analogue of the Milnor FK-construction for infinite loop spaces. The purpose of this paper is to prove that the associative algebra structure on the normalized cochain complex of a simplicial set extends to the structure of an algebra over the Barratt-Eccles operad. We also prove that differential graded algebras over the Barratt-Eccles operad form a closed model category. Similar results hold for the normalized Hochschild cochain complex of an associative algebra. More precisely, the Hochschild cochain complex is acted on by a suboperad of the Barratt-Eccles operad which is equivalent to the classical little squares operad.

Crystallographic and theoretical studies of an inclusion complex of β-cyclodextrin with fentanyl.

PubMed

Ogawa, Noriko; Nagase, Hiromasa; Loftsson, Thorsteinn; Endo, Tomohiro; Takahashi, Chisato; Kawashima, Yoshiaki; Ueda, Haruhisa; Yamamoto, Hiromitsu

2017-10-15

The crystal structure of an inclusion complex of β-cyclodextrin (β-CD) with fentanyl was determined by single crystal X-ray diffraction analysis. The crystal belongs to the triclinic space group P1 and the complex comprises one fentanyl, two β-CD, and several water molecules. β-CD and fentanyl form a host-guest inclusion complex at a ratio of 2:1 and the asymmetric unit of the complex contains two host molecules (β-CDs) in a head-to-head arrangement that form dimers through hydrogen bonds between the secondary hydroxyl groups of β-CD and one guest molecule. Fentanyl is totally contained within the β-CD cavity and the structure of the phenylethyl part of fentanyl inside the dimeric cavity of the complex is disordered. Furthermore, theoretical molecular conformational calculations were conducted to clarify the mobility of the guest molecule in the β-CD cavity using CONFLEX software. Crystal optimization and crystal energy calculations were also conducted. The results of the theoretical calculations confirmed that the conformation of disorder part 1, which was high in occupancy by crystal structure analysis, was more stable. The phenylethyl part of fentanyl existed in several stable conformations. Copyright © 2017 Elsevier B.V. All rights reserved.

The central element of the synaptonemal complex in mice is organized as a bilayered junction structure.

PubMed

Hernández-Hernández, Abrahan; Masich, Sergej; Fukuda, Tomoyuki; Kouznetsova, Anna; Sandin, Sara; Daneholt, Bertil; Höög, Christer

2016-06-01

The synaptonemal complex transiently stabilizes pairing interactions between homologous chromosomes during meiosis. Assembly of the synaptonemal complex is mediated through integration of opposing transverse filaments into a central element, a process that is poorly understood. We have, here, analyzed the localization of the transverse filament protein SYCP1 and the central element proteins SYCE1, SYCE2 and SYCE3 within the central region of the synaptonemal complex in mouse spermatocytes using immunoelectron microscopy. Distribution of immuno-gold particles in a lateral view of the synaptonemal complex, supported by protein interaction data, suggest that the N-terminal region of SYCP1 and SYCE3 form a joint bilayered central structure, and that SYCE1 and SYCE2 localize in between the two layers. We find that disruption of SYCE2 and TEX12 (a fourth central element protein) localization to the central element abolishes central alignment of the N-terminal region of SYCP1. Thus, our results show that all four central element proteins, in an interdependent manner, contribute to stabilization of opposing N-terminal regions of SYCP1, forming a bilayered transverse-filament-central-element junction structure that promotes synaptonemal complex formation and synapsis. © 2016. Published by The Company of Biologists Ltd.

Plasma adiponectin complexes have distinct biochemical characteristics.

PubMed

Schraw, Todd; Wang, Zhao V; Halberg, Nils; Hawkins, Meredith; Scherer, Philipp E

2008-05-01

Adipocytes release the secretory protein adiponectin in a number of different higher-order complexes. Once synthesized and assembled in the secretory pathway of the adipocyte, these complexes circulate as biochemically distinct and stable entities with little evidence of interchange between the different forms that include a high-molecular-weight (HMW) species, a hexamer (low-molecular-weight form), and a trimeric form of the complexes. Here, we validate a high-resolution gel filtration method that reproducibly separates the three complexes in recombinant adiponectin and adiponectin from human and murine samples. We demonstrate that the HMW form is prominently reduced in male vs. female subjects and in obese, insulin-resistant vs. lean, insulin-sensitive individuals. A direct comparison of human and mouse adiponectin demonstrates that the trimer is generally more abundant in human serum. Furthermore, when the production of adiponectin is reduced, either by obesity or in mice carrying only a single functional allele of the adiponectin locus, then the amount of the HMW form is selectively reduced in circulation. The complex distribution of adiponectin can be regulated in several ways. Both mouse and human HMW adiponectin are very stable under basic conditions but are exquisitely labile under acidic conditions below pH 7. Murine and human adiponectin HMW forms also display differential susceptibility to the presence of calcium in the buffer. A mutant form of adiponectin unable to bind calcium is less susceptible to changes in calcium concentrations. However, the lack of calcium binding results in a destabilization of the structure. Disulfide bond formation (at position C39) is also important for complex formation. A mutant form of adiponectin lacking C39 prominently forms HMW and trimer but not the low-molecular-weight form. Injection of adiponectin with a fluorescent label reveals that over time, the various complexes do not interconvert in vivo. The stability of adiponectin complexes highlights that the production and secretion of these forms from fat cells has a major influence on the circulating levels of each complex.

Trans-acting RNAs as molecular probes for monitoring time-dependent structural change of an RNA complex adapting two structures.

PubMed

Maeda, Yuri; Furuta, Hiroyuki; Ikawa, Yoshiya

2011-03-01

As dynamic structural changes are pivotal for the functions of some classes of RNA molecule, it is important to develop methods to monitor structural changes in RNA in a time-dependent manner without chemical modification. Based on previous reports that trans-acting RNAs can be used as probes for analysis and control of 3D structures of target RNAs, we applied this method to monitor time-dependent structural changes in RNA. We designed and performed a proof-of-principle study using a simple model RNA complex that adopts two different structures as a target. The time-dependent structural changes in the target RNA were successfully monitored using two trans-acting RNAs, which stably form a ternary complex with the bimolecular target RNA and act as a catalyst to join two RNA fragments of the target complex, respectively. Copyright © 2010 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Polymeric Cd(II), trinuclear and mononuclear Ni(II) complexes of 5-methyl-4-phenyl-1,2,4-triazole-3-thione: Synthesis, structural characterization, thermal behaviour, fluorescence properties and antibacterial activity

NASA Astrophysics Data System (ADS)

Bharty, M. K.; Paswan, S.; Dani, R. K.; Singh, N. K.; Sharma, V. K.; Kharwar, R. N.; Butcher, R. J.

2017-02-01

Syntheses of a polymeric Cd(II) complex, [Cd(mptt)2]n (1), a trinuclear Ni(II) complex, [Ni3(μ-mptt)4(μ-H2O)2(H2O)2(ttfa)2]·3H2O (2) and a mononuclear Ni(II) complex [Ni(mptt)2(en)2] (3) have been performed using the ligand 5-methyl-4-phenyl-1,2,4-triazole-3-thione (Hmptt) and nickel(II)/cadmium(II) salts {ttfa = thenoyltrifluroacetonate). The ligand and the complexes have been characterized by various physicochemical methods in addition to their single crystal X-ray structure. The Cd centre in complex 1 adopts a distorted tetrahedral geometry with one sulfur atom and two mptt ligands provide three nitrogen atoms from three triazole units. The sulfur atom of the ligand binds covalently and overall the ligand acts as uninigative N,S/N,N bidentate moiety. The polymeric structure of complex 1 results from the N atoms of the neighboring triazole units coordinating with the Cd(II) centre. The three Ni(II) centres in the trinuclear Ni(II) complex 2 form a linear arrangement and all have six coordinated arrangements. The middle Ni(II) binds with four deprotonated triazole ring nitrogens and two water molecules form two bridges. The terminal Ni(II) centres bind through two thenoyl oxygens, two triazole nitrogens and water molecules that formed bridges with the middle Ni centre. In complex 3, the nickel(II) centre is covalently bonded through two deprotonated triazole ring nitrogens from two ligand moieties and other four sites are occupied by four nitrogens from two bidentate en ligands. Thermogravimetric analyses (TGA) of the complexes indicated for NiO as the final residue. The bioefficacy of the ligand and complexes 2 and 3 have been examined against the growth of bacteria to evaluate their anti-microbial potential. Complex 2 showed high antibacterial activity as compared to the ligand and complex 3. Complexes 1, 2 and 3 are fluorescent materials with maximum emissions at 425, 421 and 396 nm at an excitation wavelength of 323, 348 and 322 nm, respectively.

Nucleoplasmin-like domain of FKBP39 from Drosophila melanogaster forms a tetramer with partly disordered tentacle-like C-terminal segments

PubMed Central

Kozłowska, Małgorzata; Tarczewska, Aneta; Jakób, Michał; Bystranowska, Dominika; Taube, Michał; Kozak, Maciej; Czarnocki-Cieciura, Mariusz; Dziembowski, Andrzej; Orłowski, Marek; Tkocz, Katarzyna; Ożyhar, Andrzej

2017-01-01

Nucleoplasmins are a nuclear chaperone family defined by the presence of a highly conserved N-terminal core domain. X-ray crystallographic studies of isolated nucleoplasmin core domains revealed a β-propeller structure consisting of a set of five monomers that together form a stable pentamer. Recent studies on isolated N-terminal domains from Drosophila 39-kDa FK506-binding protein (FKBP39) and from other chromatin-associated proteins showed analogous, nucleoplasmin-like (NPL) pentameric structures. Here, we report that the NPL domain of the full-length FKBP39 does not form pentameric complexes. Multi-angle light scattering (MALS) and sedimentation equilibrium ultracentrifugation (SE AUC) analyses of the molecular mass of the full-length protein indicated that FKBP39 forms homotetrameric complexes. Molecular models reconstructed from small-angle X-ray scattering (SAXS) revealed that the NPL domain forms a stable, tetrameric core and that FK506-binding domains are linked to it by intrinsically disordered, flexible chains that form tentacle-like segments. Analyses of full-length FKBP39 and its isolated NPL domain suggested that the distal regions of the polypeptide chain influence and determine the quaternary conformation of the nucleoplasmin-like protein. These results provide new insights regarding the conserved structure of nucleoplasmin core domains and provide a potential explanation for the importance of the tetrameric structural organization of full-length nucleoplasmins. PMID:28074868

A gatekeeper chaperone complex directs translocator secretion during Type Three Secretion

DOE PAGES

Archuleta, Tara L.; Spiller, Benjamin W.; Kubori, Tomoko

2014-11-06

Many Gram-negative bacteria use Type Three Secretion Systems (T3SS) to deliver effector proteins into host cells. These protein delivery machines are composed of cytosolic components that recognize substrates and generate the force needed for translocation, the secretion conduit, formed by a needle complex and associated membrane spanning basal body, and translocators that form the pore in the target cell. A defined order of secretion in which needle component proteins are secreted first, followed by translocators, and finally effectors, is necessary for this system to be effective. While the secreted effectors vary significantly between organisms, the ~20 individual protein components thatmore » form the T3SS are conserved in many pathogenic bacteria. One such conserved protein, referred to as either a plug or gatekeeper, is necessary to prevent unregulated effector release and to allow efficient translocator secretion. The mechanism by which translocator secretion is promoted while effector release is inhibited by gatekeepers is unknown. We present the structure of the Chlamydial gatekeeper, CopN, bound to a translocator-specific chaperone. The structure identifies a previously unknown interface between gatekeepers and translocator chaperones and reveals that in the gatekeeper-chaperone complex the canonical translocator-binding groove is free to bind translocators. Thus, structure-based mutagenesis of the homologous complex in Shigella reveals that the gatekeeper-chaperone-translocator complex is essential for translocator secretion and for the ordered secretion of translocators prior to effectors.« less

Colorimetric detection of hydrogen peroxide by dioxido-vanadium(V) complex containing hydrazone ligand: synthesis and crystal structure

NASA Astrophysics Data System (ADS)

Kurbah, Sunshine D.; Syiemlieh, Ibanphylla; Lal, Ram A.

2018-03-01

Dioxido-vanadium(V) complex has been synthesized in good yield, the complex was characterized by IR, UV-visible and 1H NMR spectroscopy. Single crystal X-ray crystallography techniques were used to assign the structure of the complex. Complex crystallized with monoclinic P21/c space group with cell parameters a (Å) = 39.516(5), b (Å) = 6.2571(11), c (Å) = 17.424(2), α (°) = 90, β (°) = 102.668(12) and γ (°) = 90. The hydrazone ligand is coordinate to metal ion in tridentate fashion through -ONO- donor atoms forming a distorted square pyramidal geometry around the metal ion.

Molecular Investigations of the Structure and Function of the Protein Phosphatase 1:Spinophilin:Inhibitor-2 Heterotrimeric Complex

PubMed Central

Dancheck, Barbara; Ragusa, Michael J.; Allaire, Marc; Nairn, Angus C.; Page, Rebecca; Peti, Wolfgang

2011-01-01

Regulation of the major ser/thr phosphatase Protein Phosphatase 1 (PP1) is controlled by a diverse array of targeting and inhibitor proteins. Though many PP1 regulatory proteins share at least one PP1 binding motif, usually the RVxF motif, it was recently discovered that certain pairs of targeting and inhibitor proteins bind PP1 simultaneously to form PP1 heterotrimeric complexes. To date, structural information for these heterotrimeric complexes, and, in turn, how they direct PP1 activity is entirely lacking. Using a combination of NMR spectroscopy, biochemistry and small angle X-ray scattering (SAXS), we show that major structural rearrangements in both spinophilin (targeting) and Inhibitor-2 (I-2, inhibitor) are essential for the formation of the heterotrimeric PP1:spinophilin:I-2 (PSI) complex. The RVxF motif of I-2 is released from PP1 during the formation of PSI, making the less prevalent SILK motif of I-2 essential for complex stability. The release of the I-2 RVxF motif allows for enhanced flexibility of both I-2 and spinophilin in the heterotrimeric complex. In addition, we used inductively coupled plasma atomic emission spectroscopy to show that PP1 contains two metals in both heterodimeric complexes (PP1:spinophilin and PP1:I2) and PSI, demonstrating that PSI retains the biochemical characteristics of the PP1:I2 holoenzyme. Finally, we combined the NMR and biochemical data with SAXS and molecular dynamics simulations to generate a structural model of the full heterotrimeric PSI complex. Collectively, these data reveal the molecular events that enable PP1 heterotrimeric complexes to exploit both the targeting and inhibitory features of the PP1-regulatory proteins to form multi-functional PP1 holoenzymes. PMID:21218781

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hartwig, J.F.

The products and mechanisms of the thermal reactions of several complexes of the general structure (PMe{sub 3}){sub 4}Ru(X)(Y) and (DMPM){sub 2}Ru(X)(Y) where X and Y are hydride, aryl, and benzyl groups, have been investigated. The mechanism of decomposition depends critically on the structure of the complex and the medium in which the thermolysis is carried out. The alkyl hydride complexes are do not react with alkane solvent, but undergo C-H activation processes with aromatic solvents by several different mechanisms. Thermolysis of (PMe{sub 3}){sub 4}Ru(Ph)(Me) or (PMe{sub 3}){sub 4}Ru(Ph){sub 2} leads to the ruthenium benzyne complex (PMe{sub 3}){sub 4}Ru({eta}{sup 2}-C{sub 6}H{submore » 4}) (1) by a mechanism which involves reversible dissociation of phosphine. In many ways its chemistry is analogous to that of early rather than late organo transition metal complexes. The synthesis, structure, variable temperature NMR spectroscopy and reactivity of ruthenium complexes containing aryloxide or arylamide ligands are reported. These complexes undergo cleavage of a P-C bond in coordinated trimethylphosphine, insertion of CO and CO{sub 2} and hydrogenolysis. Mechanistic studies on these reactions are described. The generation of a series of reactive ruthenium complexes of the general formula (PMe{sub 3}){sub 4}Ru(R)(enolate) is reported. Most of these enolates have been shown to bind to the ruthenium center through the oxygen atom. Two of the enolate complexes 8 and 9 exist in equilibrium between the O- and C-bound forms. The reactions of these compounds are reported, including reactions to form oxygen-containing metallacycles. The structure and reactivity of these ruthenium metallacycles is reported, including their thermal chemistry and reactivity toward protic acids, electrophiles, carbon monoxide, hydrogen and trimethylsilane. 243 refs., 10 tabs.« less

Structural basis for the inhibition of insulin-like growth factors by insulin-like growth factor-binding proteins

PubMed Central

Sitar, Tomasz; Popowicz, Grzegorz M.; Siwanowicz, Igor; Huber, Robert; Holak, Tad A.

2006-01-01

Insulin-like growth factor-binding proteins (IGFBPs) control bioavailability, activity, and distribution of insulin-like growth factor (IGF)1 and -2 through high-affinity IGFBP/IGF complexes. IGF-binding sites are found on N- and C-terminal fragments of IGFBPs, the two conserved domains of IGFBPs. The relative contributions of these domains to IGFBP/IGF complexation has been difficult to analyze, in part, because of the lack of appropriate three-dimensional structures. To analyze the effects of N- and C-terminal domain interactions, we determined several x-ray structures: first, of a ternary complex of N- and C-terminal domain fragments of IGFBP4 and IGF1 and second, of a “hybrid” ternary complex using the C-terminal domain fragment of IGFBP1 instead of IGFBP4. We also solved the binary complex of the N-terminal domains of IGFBP4 and IGF1, again to analyze C- and N-terminal domain interactions by comparison with the ternary complexes. The structures reveal the mechanisms of IGF signaling regulation via IGFBP binding. This finding supports research into the design of IGFBP variants as therapeutic IGF inhibitors for diseases of IGF disregulation. In IGFBP4, residues 1–38 form a rigid disulphide bond ladder-like structure, and the first five N-terminal residues bind to IGF and partially mask IGF residues responsible for the type 1 IGF receptor binding. A high-affinity IGF1-binding site is located in a globular structure between residues 39 and 82. Although the C-terminal domains do not form stable binary complexes with either IGF1 or the N-terminal domain of IGFBP4, in the ternary complex, the C-terminal domain contacts both and contributes to blocking of the IGF1 receptor-binding region of IGF1. PMID:16924115

Mechanism for priming DNA synthesis by yeast DNA Polymerase α

PubMed Central

Perera, Rajika L; Torella, Rubben; Klinge, Sebastian; Kilkenny, Mairi L; Maman, Joseph D; Pellegrini, Luca

2013-01-01

The DNA Polymerase α (Pol α)/primase complex initiates DNA synthesis in eukaryotic replication. In the complex, Pol α and primase cooperate in the production of RNA-DNA oligonucleotides that prime synthesis of new DNA. Here we report crystal structures of the catalytic core of yeast Pol α in unliganded form, bound to an RNA primer/DNA template and extending an RNA primer with deoxynucleotides. We combine the structural analysis with biochemical and computational data to demonstrate that Pol α specifically recognizes the A-form RNA/DNA helix and that the ensuing synthesis of B-form DNA terminates primer synthesis. The spontaneous release of the completed RNA-DNA primer by the Pol α/primase complex simplifies current models of primer transfer to leading- and lagging strand polymerases. The proposed mechanism of nucleotide polymerization by Pol α might contribute to genomic stability by limiting the amount of inaccurate DNA to be corrected at the start of each Okazaki fragment. DOI: http://dx.doi.org/10.7554/eLife.00482.001 PMID:23599895

ESI-MS of Cucurbituril Complexes Under Negative Polarity.

PubMed

Rodrigues, Maria A A; Mendes, Débora C; Ramamurthy, Vaidhyanathan; Da Silva, José P

2017-11-01

Electrospray ionization mass spectrometry (ESI-MS) is a powerful tool to study host-guest supramolecular interactions. ESI-MS can be used for detailed gas-phase reactivity studies, to clarify the structure, or simply to verify the formation of complexes. Depending on the structure of the host and of the guest, negative and/or positive ESI are used. Here we report the unexpected formation of host-guest complexes between cucurbit[n]urils (n = 7, 8, CB[n]) and amine, styryl pyridine, and styryl pyridine dimer cations, under negative ESI. Non-complexed CB[n] form double charged halide (Br - , Cl - , F - ) adducts. Under negative ESI, halide ions interact with CB[n] outer surface hydrogen atoms. One to one host-guest complexes (1:1) of CB[n] with positive charged guests were also observed as single and double charged ions under negative ESI. The positive charge of guests is neutralized by ion-pairing with halide anions. Depending on the number of positive charges guests retain in the gas phase, one or two additional halide ions are required for neutralization. Complexes 1:2 of CB[8] with styryl pyridines retain two halide ions in the gas phase, one per guest. Styryl pyridine dimers form 1:1 complexes possessing a single extra halide ion and therefore a single positive charge. Negative ESI is sensitive to small structural differences between complexes, distinguishing between 1:2 complexes of styryl pyridine-CB[8] and corresponding 1:1 complexes with the dimer. Negative ESI gives simpler spectra than positive ESI and allows the determination of guest charge state of CB[n] complexes in the gas phase. Graphical Abstract ᅟ.

Complex Nano-Scale Structures for Unprecedented Properties in Steels

DOE PAGES

Caballero, Francisca G.; Poplawsky, Jonathan D.; Yen, Hung Wei; ...

2016-11-01

Processing bulk nanoscrystalline materials for structural applications still poses a rather large challenge, particularly in achieving an industrially viable process. In this context, recent work has proved that complex nanoscale steel structures can be formed by solid reaction at low temperatures. These nanocrystalline bainitic steels present the highest strength ever recorded, unprecedented ductility, fatigue on par with commercial bearing steels and exceptional rolling-sliding wear performances. In this paper, a description of the characteristics and significance of these remarkable structures in the context of the atomic mechanism of transformation is provided.

Genetic Organization of the Chromosome Region Surrounding mecA in Clinical Staphylococcal Strains: Role of IS431-Mediated mecI Deletion in Expression of Resistance in mecA-Carrying, Low-Level Methicillin- Resistant Staphylococcus haemolyticus

PubMed Central

Katayama, Yuki; Ito, Teruyo; Hiramatsu, Keiichi

2001-01-01

We report on the structural diversity of mecA gene complexes carried by 38 methicillin-resistant Staphylococcus aureus and 91 methicillin-resistant coagulase-negative Staphylococcus strains of seven different species with a special reference to its correlation with phenotypic expression of methicillin resistance. The most prevalent and widely disseminated mec complex had the structure mecI-mecR1-mecA-IS431R (or IS431mec), designated the class A mecA gene complex. In contrast, in S. haemolyticus, mecA was bracketed by two copies of IS431, forming the structure IS431L-mecA-IS431R. Of the 38 S. haemolyticus strains, 5 had low-level methicillin resistance (MIC, 1 to 4 mg/liter) and characteristic heterogeneous methicillin resistance as judged by population analysis. In these five strains, IS431L was located to the left of an intact mecI gene, forming the structure IS431L-class A mecA-gene complex. In other S. haemolyticus strains, IS431L was associated with the deletion of mecI and mecR1, forming the structure IS431L-ΔmecR1-mecA-IS431mec, designated the class C mecA gene complex. Mutants with the class C mecA gene complex were obtained in vitro by selecting strain SH621, containing the IS431L-class A mecA gene complex with low concentrations of methicillin (1 and 3 mg/liter). The mutants had intermediate level of methicillin resistance (MIC, 16 to 64 mg/liter). The mecA gene transcription was shown to be derepressed in a representative mutant strain, SH621-37. Our study indicated that the mecI-encoded repressor function is responsible for the low-level methicillin resistance of some S. haemolyticus clinical strains and that the IS431-mediated mecI gene deletion causes the expression of methicillin resistance through the derepression of mecA gene transcription. PMID:11408208

Structural basis of carbohydrate recognition by lectin II from Ulex europaeus, a protein with a promiscuous carbohydrate-binding site.

PubMed

Loris, R; De Greve, H; Dao-Thi, M H; Messens, J; Imberty, A; Wyns, L

2000-08-25

Protein-carbohydrate interactions are the language of choice for inter- cellular communication. The legume lectins form a large family of homologous proteins that exhibit a wide variety of carbohydrate specificities. The legume lectin family is therefore highly suitable as a model system to study the structural principles of protein-carbohydrate recognition. Until now, structural data are only available for two specificity families: Man/Glc and Gal/GalNAc. No structural data are available for any of the fucose or chitobiose specific lectins. The crystal structure of Ulex europaeus (UEA-II) is the first of a legume lectin belonging to the chitobiose specificity group. The complexes with N-acetylglucosamine, galactose and fucosylgalactose show a promiscuous primary binding site capable of accommodating both N-acetylglucos amine or galactose in the primary binding site. The hydrogen bonding network in these complexes can be considered suboptimal, in agreement with the low affinities of these sugars. In the complexes with chitobiose, lactose and fucosyllactose this suboptimal hydrogen bonding network is compensated by extensive hydrophobic interactions in a Glc/GlcNAc binding subsite. UEA-II thus forms the first example of a legume lectin with a promiscuous binding site and illustrates the importance of hydrophobic interactions in protein-carbohydrate complexes. Together with other known legume lectin crystal structures, it shows how different specificities can be grafted upon a conserved structural framework. Copyright 2000 Academic Press.

Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simonetti, Angelita; Marzi, Stefano; Fabbretti, Attilio

2013-06-01

The crystal structures of the eubacterial translation initiation factor 2 in apo form and with bound GDP and GTP reveal conformational changes upon nucleotide binding and hydrolysis, notably of the catalytically important histidine in the switch II region. Translation initiation factor 2 (IF2) is involved in the early steps of bacterial protein synthesis. It promotes the stabilization of the initiator tRNA on the 30S initiation complex (IC) and triggers GTP hydrolysis upon ribosomal subunit joining. While the structure of an archaeal homologue (a/eIF5B) is known, there are significant sequence and functional differences in eubacterial IF2, while the trimeric eukaryotic IF2more » is completely unrelated. Here, the crystal structure of the apo IF2 protein core from Thermus thermophilus has been determined by MAD phasing and the structures of GTP and GDP complexes were also obtained. The IF2–GTP complex was trapped by soaking with GTP in the cryoprotectant. The structures revealed conformational changes of the protein upon nucleotide binding, in particular in the P-loop region, which extend to the functionally relevant switch II region. The latter carries a catalytically important and conserved histidine residue which is observed in different conformations in the GTP and GDP complexes. Overall, this work provides the first crystal structure of a eubacterial IF2 and suggests that activation of GTP hydrolysis may occur by a conformational repositioning of the histidine residue.« less

Beacon Hill end moraine, Boston: new explanation of an important urban feature

USGS Publications Warehouse

Kaye, Clifford A.; Coates, Donald R.

1976-01-01

The usefulness of geology to engineers is in direct proportion to how well it helps us predict the subsurface; these predictions, in turn, depend on our knowledge of the geomorphic processes that molded the terrain. The uncertainties of interpretation are particularly great in glaciated terrain because our understanding of both glacial processes and history is so incomplete, a fact well illustrated in Beacon Hill. Recent construction activities in the eastern part of the hill, until now classified as a drumlin, have shown that it is better interpreted as an end moraine formed by a Wisconsonian glacial readvance. Instead of the firm till that was anticipated as foundation material, excavations exposed a complex of sand, gravel, and clay, with only minor zones of till. The structure of these deposits strongly suggests that originally they were plates of the glacial bed that froze to the glacier and were transported englacially. Thrust faulting and other deformations are glacial structures formed within the ice in the glacier's terminal zone. In spite of the complex englacial history, these deposits lost little of their original appearance and intergranular relationships. Upon deglaciation, the frozen moraine thawed, and slumping formed complex secondary structures on the ridge's lower flanks.

Complex between α-bungarotoxin and an α7 nicotinic receptor ligand-binding domain chimaera

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Sun; Li, Shu-Xing; Bren, Nina

2013-09-01

To identify high-affinity interactions between long-chain α-neurotoxins and nicotinic receptors, we determined the crystal structure of the complex between α-btx (α-bungarotoxin) and a pentameric ligand-binding domain constructed from the human α7 AChR (acetylcholine receptor) and AChBP (acetylcholine-binding protein). The complex buries ~2000 Å 2 (1 Å=0.1 nm) of surface area, within which Arg 36 and Phe 32 from finger II of α-btx form a π-cation stack that aligns edge-to-face with the conserved Tyr 184 from loop-C of α7, while Asp 30 of α-btx forms a hydrogen bond with the hydroxy group of Tyr 184. These inter-residue interactions diverge from thosemore » in a 4.2 Å structure of α-ctx (α-cobratoxin) bound to AChBP, but are similar to those in a 1.94 Å structure of α-btx bound to the monomeric α1 extracellular domain, although compared with the monomer-bound complex, the α-btx backbone exhibits a large shift relative to the protein surface. Mutational analyses show that replacing Tyr 184 with a threonine residue abolishes high-affinity α-btx binding, whereas replacing with a phenylalanine residue maintains high affinity. Comparison of the α-btx complex with that coupled to the agonist epibatidine reveals structural rearrangements within the binding pocket and throughout each subunit. The overall findings highlight structural principles by which α-neurotoxins interact with nicotinic receptors.« less

Crystal structure of a complex between the phosphorelay protein YPD1 and the response regulator domain of SLN1 bound to a phosphoryl analog

PubMed Central

Zhao, Xiaodong; Copeland, Daniel M.; Soares, Alexei S.; West, Ann H.

2008-01-01

Summary The crystal structure of the yeast SLN1 response regulator domain bound to both a phosphoryl analog (BeF3−) and Mg2+ ion in complex with its downstream phosphorelay signaling partner YPD1 has been determined at a resolution of 1.70 Å. Comparisons between the beryllium fluoride-activated complex and the unliganded (or apo) complex determined previously reveal modest but important differences. The SLN1-R1•Mg2+•BeF3− structure from the complex provides evidence for the first time that the mechanism of phosphorylation-induced activation is highly conserved between bacterial response regulator domains and this example from a eukaryotic organism. Residues in and around the active site undergo slight rearrangements in order to form bonds to the essential divalent cation and fluorine atoms of BeF3−. Two conserved switch-like residues (Thr 1173 and Phe 1192) occupy distinctly different positions in the apo- versus BeF3−-bound structures consistent with the “Y-T” coupling mechanism proposed for activation of CheY and other bacterial response regulators. Several loop regions and the α4-β5-α5 surface of the SLN1-R1 domain undergo subtle conformational changes (∼1-3 Å displacements relative to the apo-structure) that lead to significant changes in terms of contacts that are formed with YPD1. Detailed structural comparisons of protein-protein interactions in the apo- and BeF3−-bound complexes suggest at least a two-state equilibrium model for formation of a transient encounter complex, in which phosphorylation of the response regulator promotes the formation of a phosphotransfer-competent complex. In the BeF3−-activated complex, the position of His 64 from YPD1 is within ideal distance and near linear geometry with Asp 1144 from the SLN1-R1 domain for phosphotransfer to occur. The ground state structure presented here suggests that phosphoryl transfer will likely proceed through an associative mechanism involving formation of a pentacoordinate phosphorus intermediate. PMID:18076904

Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex*

PubMed Central

Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina; Pellarin, Riccardo; Kim, Seung Joong; Williams, Rosemary; Schneidman-Duhovny, Dina; Sali, Andrej; Rout, Michael P.; Chait, Brian T.

2014-01-01

Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope. PMID:25161197

Complexity of Curved Glass Structures

NASA Astrophysics Data System (ADS)

Kosić, T.; Svetel, I.; Cekić, Z.

2017-11-01

Despite the increasing number of research on the architectural structures of curvilinear forms and technological and practical improvement of the glass production observed over recent years, there is still a lack of comprehensive codes and standards, recommendations and experience data linked to real-life curved glass structures applications regarding design, manufacture, use, performance and economy. However, more and more complex buildings and structures with the large areas of glass envelope geometrically complex shape are built every year. The aim of the presented research is to collect data on the existing design philosophy on curved glass structure cases. The investigation includes a survey about how architects and engineers deal with different design aspects of curved glass structures with a special focus on the design and construction process, glass types and structural and fixing systems. The current paper gives a brief overview of the survey findings.

Study of base pair mutations in proline-rich homeodomain (PRH)-DNA complexes using molecular dynamics.

PubMed

Jalili, Seifollah; Karami, Leila; Schofield, Jeremy

2013-06-01

Proline-rich homeodomain (PRH) is a regulatory protein controlling transcription and gene expression processes by binding to the specific sequence of DNA, especially to the sequence 5'-TAATNN-3'. The impact of base pair mutations on the binding between the PRH protein and DNA is investigated using molecular dynamics and free energy simulations to identify DNA sequences that form stable complexes with PRH. Three 20-ns molecular dynamics simulations (PRH-TAATTG, PRH-TAATTA and PRH-TAATGG complexes) in explicit solvent water were performed to investigate three complexes structurally. Structural analysis shows that the native TAATTG sequence forms a complex that is more stable than complexes with base pair mutations. It is also observed that upon mutation, the number and occupancy of the direct and water-mediated hydrogen bonds decrease. Free energy calculations performed with the thermodynamic integration method predict relative binding free energies of 0.64 and 2 kcal/mol for GC to AT and TA to GC mutations, respectively, suggesting that among the three DNA sequences, the PRH-TAATTG complex is more stable than the two mutated complexes. In addition, it is demonstrated that the stability of the PRH-TAATTA complex is greater than that of the PRH-TAATGG complex.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chumakov, Yu. M.; Paholnitcaia, A. Yu.; Petrenko, P. A.

Two crystal modifications of nitrato-(2-[2-(1-pyridine-2-ylethylidene)hydrazine]-1,3-benzothiazolo) aquacopper (I and II) and two modifications of chloro-(2-[2-phenyl(pyridine-2-ylethylidene)hydrazine]-1,3-benzothiazolo) copper (III and IV) have been synthesized and studied by X-ray diffraction. In structures I and II, the copper atoms coordinate a monodeprotonated molecule of the organic ligand, nitrate ions, and a water molecule. In crystals of I, the complexes are monomeric, whereas complexes II are linked via nitrate ions to form polymeric chains. In both structures the coordination polyhedron of the copper atom can be described as a distorted tetragonal bipyramid—(4 + 1 + 1) in I and (4 + 2) in II. These coordinationmore » polyherdra have different compositions. In structures III and IV, the metal atoms coordinate a monodeprotonated (2-[2-phenyl(pyridine-2-ylethylidene)hydrazine]-1,3-benzothiazole molecule and chloride ions. In III the complex-forming ion has square-planar coordination geometry, whereas structure IV consists of centrosymmetric dimers with two bridging chlorine atoms. It was found that nitrato-(2-[2-(1-pyridine-2-ylethylidene)hydrazine]-1,3-benzothiazolo) aquacopper possesses antitumor activity.« less

CASPT2 study of inverse sandwich-type dinuclear Cr(I) and Fe(I) complexes of the dinitrogen molecule: significant differences in spin multiplicity and coordination structure between these two complexes.

PubMed

Nakagaki, Masayuki; Sakaki, Shigeyoshi

2014-02-20

Inverse sandwich-type complexes (ISTCs), (μ-N2)[M(AIP)]2 (AIPH = (Z)-1-amino-3-imino-prop-1-ene; M = Cr and Fe), were investigated with the CASPT2 method. In the ISTC of Cr, the ground state takes a singlet spin multiplicity. However, the singlet to nonet spin states are close in energy to each other. The thermal average of effective magnetic moments (μeff) of these spin multiplicities is close to the experimental value. The η(2)-side-on coordination structure of N2 is calculated to be more stable than the η(1)-end-on coordination one. This is because the d-orbital of Cr forms a strong dπ-π* bonding interaction with the π* orbital of N2 in molecular plane. In the ISTC of Fe, on the other hand, the ground state takes a septet spin multiplicity, which agrees well with the experimentally reported μeff value. The η(1)-end-on structure of N2 is more stable than the η(2)-side-on structure. In the η(1)-end-on structure, two doubly occupied d-orbitals of Fe can form two dπ-π* bonding interactions. The negative spin density is found on the bridging N2 ligand in the Fe complex but is not in the Cr complex. All these interesting differences between ISTCs of Cr and Fe are discussed on the basis of the electronic structure and bonding nature.

Spectroscopic and quantum chemical study of the structure of a new paramagnetic dimeric palladium(II,III) complex with creatine

NASA Astrophysics Data System (ADS)

Mitewa, Mariana; Enchev, Venelin; Bakalova, Tatyana

2002-05-01

The structure and coordination mode of the newly synthesized dimeric paramagnetic Pd(II,III) complex are studied using magneto-chemical, EPR and IR spectroscopic methods. In order to perform reliable assignment of the IR bands, the structure and IR spectrum of the free creatine were calculated using ab initio method. For calculation of the configuration of its deprotonated and doubly deprotonated forms the semiempirical AM1 method was used.

Structure of solvates of o-hydroxybenzoic acid in supercritical CO2-cosolvent media, according to molecular dynamics data

NASA Astrophysics Data System (ADS)

Petrenko, V. E.; Antipova, M. L.; Gurina, D. L.

2015-03-01

Three-component supercritical carbon dioxide-cosolvent (methanol, ethanol, water)- o-hydroxybenzoic acid ( o-HBA) mixtures at a density of 0.7 g/cm3 and temperatures of 318 and 348 K are simulated by means of molecular dynamics. The solvate structures are investigated. It is shown that the solvation mechanism of o-HBA (particularly the o-HBA molecule forming a stable solvate complex with one molecule of a cosolvent via a hydrogen bond through the carboxyl group) does not depend on the temperature or the cosolvent. It is noted that the form of the cosolvent in a supercritical fluid varies: alcohols are distributed in the bulk in the form of monomers and hydrogen-bonded dimers, and water molecules tend to form microclusters along with chained and spatially branched structures by means of hydrogen bonds. It is established that the local molar fraction of cosolvent around the solvate complexes grows. It is concluded that the solvation of o-HBA is determined by the behavior of cosolvent in media of supercritical CO2.

Lipidomics of glycosphingolipids.

PubMed

Farwanah, Hany; Kolter, Thomas

2012-02-02

Glycosphingolipids (GSLs) contain one or more sugars that are attached to a sphingolipid moiety, usually to a ceramide, but in rare cases also to a sphingoid base. A large structural heterogeneity results from differences in number, identity, linkage, and anomeric configuration of the carbohydrate residues, and also from structural differences within the hydrophobic part. GSLs form complex cell-type specific patterns, which change with the species, the cellular differentiation state, viral transformation, ontogenesis, and oncogenesis. Although GSL structures can be assigned to only a few series with a common carbohydrate core, their structural variety and the complex pattern are challenges for their elucidation and quantification by mass spectrometric techniques. We present a general overview of the application of lipidomics for GSL determination. This includes analytical procedures and instrumentation together with recent correlations of GSL molecular species with human diseases. Difficulties such as the structural complexity and the lack of standard substances for complex GSLs are discussed.

Lipidomics of Glycosphingolipids

PubMed Central

Farwanah, Hany; Kolter, Thomas

2012-01-01

Glycosphingolipids (GSLs) contain one or more sugars that are attached to a sphingolipid moiety, usually to a ceramide, but in rare cases also to a sphingoid base. A large structural heterogeneity results from differences in number, identity, linkage, and anomeric configuration of the carbohydrate residues, and also from structural differences within the hydrophobic part. GSLs form complex cell-type specific patterns, which change with the species, the cellular differentiation state, viral transformation, ontogenesis, and oncogenesis. Although GSL structures can be assigned to only a few series with a common carbohydrate core, their structural variety and the complex pattern are challenges for their elucidation and quantification by mass spectrometric techniques. We present a general overview of the application of lipidomics for GSL determination. This includes analytical procedures and instrumentation together with recent correlations of GSL molecular species with human diseases. Difficulties such as the structural complexity and the lack of standard substances for complex GSLs are discussed. PMID:24957371

Rubber pad forming - Efficient approach for the manufacturing of complex structured sheet metal blanks for food industry

NASA Astrophysics Data System (ADS)

Spoelstra, Paul; Djakow, Eugen; Homberg, Werner

2017-10-01

The production of complex organic shapes in sheet metals is gaining more importance in the food industry due to increasing functional and hygienic demands. Hence it is necessary to produce parts with complex geometries promoting cleanability and general sanitation leading to improvement of food safety. In this context, and especially when stainless steel has to be formed into highly complex geometries while maintaining desired surface properties, it is inevitable that alternative manufacturing processes will need to be used which meet these requirements. Rubber pad forming offers high potential when it comes to shaping complex parts with excellent surface quality, with virtually no tool marks and scratches. Especially in cases where only small series are to be produced, rubber pad forming processes offers both technological and economic advantages. Due to the flexible punch, variation in metal thickness can be used with the same forming tool. The investments to set-up Rubber pad forming is low in comparison to conventional sheet metal forming processes. The process facilitates production of shallow sheet metal parts with complex contours and bends. Different bending sequences in a multiple tool set-up can also be conducted. The planned contribution thus describes a brief overview of the rubber pad technology. It shows the prototype rubber pad forming machine which can be used to perform complex part geometries made from stainless steel (1.4301). Based on an analysis of the already existing systems and new machines for rubber pad forming processes, together with their process properties, influencing variables and areas of application, some relevant parts for the food industry are presented.

Non-Canonical G-quadruplexes cause the hCEB1 minisatellite instability in Saccharomyces cerevisiae

PubMed Central

Piazza, Aurèle; Cui, Xiaojie; Adrian, Michael; Samazan, Frédéric; Heddi, Brahim; Phan, Anh-Tuan; Nicolas, Alain G

2017-01-01

G-quadruplexes (G4) are polymorphic four-stranded structures formed by certain G-rich nucleic acids in vitro, but the sequence and structural features dictating their formation and function in vivo remains uncertain. Here we report a structure-function analysis of the complex hCEB1 G4-forming sequence. We isolated four G4 conformations in vitro, all of which bear unusual structural features: Form 1 bears a V-shaped loop and a snapback guanine; Form 2 contains a terminal G-triad; Form 3 bears a zero-nucleotide loop; and Form 4 is a zero-nucleotide loop monomer or an interlocked dimer. In vivo, Form 1 and Form 2 differently account for 2/3rd of the genomic instability of hCEB1 in two G4-stabilizing conditions. Form 3 and an unidentified form contribute to the remaining instability, while Form 4 has no detectable effect. This work underscores the structural polymorphisms originated from a single highly G-rich sequence and demonstrates the existence of non-canonical G4s in cells, thus broadening the definition of G4-forming sequences. DOI: http://dx.doi.org/10.7554/eLife.26884.001 PMID:28661396

Chitin-Like Molecules Associate with Cryptococcus neoformans Glucuronoxylomannan To Form a Glycan Complex with Previously Unknown Properties

PubMed Central

Ramos, Caroline L.; Fonseca, Fernanda L.; Rodrigues, Jessica; Guimarães, Allan J.; Cinelli, Leonardo P.; Miranda, Kildare; Nimrichter, Leonardo; Casadevall, Arturo; Travassos, Luiz R.

2012-01-01

In prior studies, we demonstrated that glucuronoxylomannan (GXM), the major capsular polysaccharide of the fungal pathogen Cryptococcus neoformans, interacts with chitin oligomers at the cell wall-capsule interface. The structural determinants regulating these carbohydrate-carbohydrate interactions, as well as the functions of these structures, have remained unknown. In this study, we demonstrate that glycan complexes composed of chitooligomers and GXM are formed during fungal growth and macrophage infection by C. neoformans. To investigate the required determinants for the assembly of chitin-GXM complexes, we developed a quantitative scanning electron microscopy-based method using different polysaccharide samples as inhibitors of the interaction of chitin with GXM. This assay revealed that chitin-GXM association involves noncovalent bonds and large GXM fibers and depends on the N-acetyl amino group of chitin. Carboxyl and O-acetyl groups of GXM are not required for polysaccharide-polysaccharide interactions. Glycan complex structures composed of cryptococcal GXM and chitin-derived oligomers were tested for their ability to induce pulmonary cytokines in mice. They were significantly more efficient than either GXM or chitin oligomers alone in inducing the production of lung interleukin 10 (IL-10), IL-17, and tumor necrosis factor alpha (TNF-α). These results indicate that association of chitin-derived structures with GXM through their N-acetyl amino groups generates glycan complexes with previously unknown properties. PMID:22562469

The Emergence of Organizing Structure in Conceptual Representation.

PubMed

Lake, Brenden M; Lawrence, Neil D; Tenenbaum, Joshua B

2018-06-01

Both scientists and children make important structural discoveries, yet their computational underpinnings are not well understood. Structure discovery has previously been formalized as probabilistic inference about the right structural form-where form could be a tree, ring, chain, grid, etc. (Kemp & Tenenbaum, 2008). Although this approach can learn intuitive organizations, including a tree for animals and a ring for the color circle, it assumes a strong inductive bias that considers only these particular forms, and each form is explicitly provided as initial knowledge. Here we introduce a new computational model of how organizing structure can be discovered, utilizing a broad hypothesis space with a preference for sparse connectivity. Given that the inductive bias is more general, the model's initial knowledge shows little qualitative resemblance to some of the discoveries it supports. As a consequence, the model can also learn complex structures for domains that lack intuitive description, as well as predict human property induction judgments without explicit structural forms. By allowing form to emerge from sparsity, our approach clarifies how both the richness and flexibility of human conceptual organization can coexist. Copyright © 2018 Cognitive Science Society, Inc.

Multimeric complexes among ankyrin-repeat and SOCS-box protein 9 (ASB9), ElonginBC, and Cullin 5: insights into the structure and assembly of ECS-type Cullin-RING E3 ubiquitin ligases.

PubMed

Thomas, Jemima C; Matak-Vinkovic, Dijana; Van Molle, Inge; Ciulli, Alessio

2013-08-06

Proteins of the ankyrin-repeat and SOCS-box (ASB) family act as the substrate-recognition subunits of ECS-type (ElonginBC-Cullin-SOCS-box) Cullin RING E3 ubiquitin ligase (CRL) complexes that catalyze the specific polyubiquitination of cellular proteins to target them for degradation by the proteasome. Therefore, ASB multimeric complexes are involved in numerous cell processes and pathways; however, their interactions, assembly, and biological roles remain poorly understood. To enhance our understanding of ASB CRL systems, we investigated the structure, affinity, and assembly of the quaternary multisubunit complex formed by ASB9, Elongin B, Elongin C (EloBC), and Cullin 5. Here, we describe the application of several biophysical techniques including differential scanning fluorimetry, isothermal titration calorimetry (ITC), nanoelectrospray ionization, and ion-mobility mass spectrometry (IM-MS) to provide structural and thermodynamic information for a quaternary ASB CRL complex. We find that ASB9 is unstable alone but forms a stable ternary complex with EloBC that binds with high affinity to the Cullin 5 N-terminal domain (Cul5NTD) but not to Cul2NTD. The structure of the monomeric ASB9-EloBC-Cul5NTD quaternary complex is revealed by molecular modeling and is consistent with IM-MS and temperature-dependent ITC data. This is the first experimental study to validate structural information for the assembly of the quaternary N-terminal region of an ASB CRL complex. The results suggest that ASB E3 ligase complexes function and assemble in an analogous manner to that of other CRL systems and provide a platform for further molecular investigation of this important protein family. The data reported here will also be of use for the future development of chemical probes to examine the biological function and modulation of other ECS-type CRL systems.

Multimeric Complexes among Ankyrin-Repeat and SOCS-box Protein 9 (ASB9), ElonginBC, and Cullin 5: Insights into the Structure and Assembly of ECS-type Cullin-RING E3 Ubiquitin Ligases

PubMed Central

2013-01-01

Proteins of the ankyrin-repeat and SOCS-box (ASB) family act as the substrate-recognition subunits of ECS-type (ElonginBC–Cullin–SOCS-box) Cullin RING E3 ubiquitin ligase (CRL) complexes that catalyze the specific polyubiquitination of cellular proteins to target them for degradation by the proteasome. Therefore, ASB multimeric complexes are involved in numerous cell processes and pathways; however, their interactions, assembly, and biological roles remain poorly understood. To enhance our understanding of ASB CRL systems, we investigated the structure, affinity, and assembly of the quaternary multisubunit complex formed by ASB9, Elongin B, Elongin C (EloBC), and Cullin 5. Here, we describe the application of several biophysical techniques including differential scanning fluorimetry, isothermal titration calorimetry (ITC), nanoelectrospray ionization, and ion-mobility mass spectrometry (IM–MS) to provide structural and thermodynamic information for a quaternary ASB CRL complex. We find that ASB9 is unstable alone but forms a stable ternary complex with EloBC that binds with high affinity to the Cullin 5 N-terminal domain (Cul5NTD) but not to Cul2NTD. The structure of the monomeric ASB9–EloBC–Cul5NTD quaternary complex is revealed by molecular modeling and is consistent with IM–MS and temperature-dependent ITC data. This is the first experimental study to validate structural information for the assembly of the quaternary N-terminal region of an ASB CRL complex. The results suggest that ASB E3 ligase complexes function and assemble in an analogous manner to that of other CRL systems and provide a platform for further molecular investigation of this important protein family. The data reported here will also be of use for the future development of chemical probes to examine the biological function and modulation of other ECS-type CRL systems. PMID:23837592

Activity of Pt(II) and Ru(III) Triazolopyrimidine Complexes Against Parasites of the Genus Leishmania, Trypanosomas and Phytomonas.

PubMed

Salas, J M; Quirós, M; Abul Haj, M; Magán, R; Marín, C; Sáchez-Moreno, M; Faure, R

2001-01-01

The synthesis and characterization of two Pt(II) Complexes with the isomeric ligands 4,5-dihydro-5-oxo- [1,2,4]triazolo-[ 1,5-a]pyrimidine (5HtpO) and 4,7-dihydro-7-oxo-[ 1,2,4]-triazolo-[ 1,5-a]pyrimidine (7HtpO) are described, as well as a Ru(III) complex with 7HtpO. The crystal structure of cis-[PtCl(2)(7HtpO)(2)].2H(2)O has been solved by X-ray diffraction analysis. In vitro activity of the new isolated complexes against the epimastigote form of T. cruzi, procyclic form of T. b. brucei and promastigote form of L. donnovani and P. characias has also been studied. The three complexes markedly affect the growth of the parasites and none of them shows cytotoxicity against macrophage of the J774.2 line at the heaviest dosages used.

Activity of Pt(II) and Ru(III) Triazolopyrimidine Complexes Against Parasites of the Genus Leishmania, Trypanosomas and Phytomonas

PubMed Central

Quirós, Miguel; Abul Haj, Mohammad; Magán, Rosa; Marín, Clotilde; Sáchez-Moreno, Manuel; Faure, René

2001-01-01

The synthesis and characterization of two Pt(II) Complexes with the isomeric ligands 4,5-dihydro-5-oxo- [1,2,4]triazolo-[ 1,5-a]pyrimidine (5HtpO) and 4,7-dihydro-7-oxo-[ 1,2,4]-triazolo-[ 1,5-a]pyrimidine (7HtpO) are described, as well as a Ru(III) complex with 7HtpO. The crystal structure of cis-[PtCl2(7HtpO)2].2H2O has been solved by X-ray diffraction analysis. In vitro activity of the new isolated complexes against the epimastigote form of T. cruzi, procyclic form of T. b. brucei and promastigote form of L. donnovani and P. characias has also been studied. The three complexes markedly affect the growth of the parasites and none of them shows cytotoxicity against macrophage of the J774.2 line at the heaviest dosages used. PMID:18475985

Synthesis, characterization and biological activities of semicarbazones and their copper complexes.

PubMed

Venkatachalam, Taracad K; Bernhardt, Paul V; Noble, Chris J; Fletcher, Nicholas; Pierens, Gregory K; Thurecht, Kris J; Reutens, David C

2016-09-01

Substituted semicarbazones/thiosemicarbazones and their copper complexes have been prepared and several single crystal structures examined. The copper complexes of these semicarbazone/thiosemicarbazones were prepared and several crystal structures examined. The single crystal X-ray structure of the pyridyl-substituted semicarbazone showed two types of copper complexes, a monomer and a dimer. We also found that the p-nitrophenyl semicarbazone formed a conventional 'magic lantern' acetate-bridged dimer. Electron Paramagnetic Resonance (EPR) of several of the copper complexes was consistent with the results of single crystal X-ray crystallography. The EPR spectra of the p-nitrophenyl semicarbazone copper complex in dimethylsulfoxide (DMSO) showed the presence of two species, confirming the structural information. Since thiosemicarbazones and semicarbazones have been reported to exhibit anticancer activity, we examined the anticancer activity of several of the derivatives reported in the present study and interestingly only the thiosemicarbazone showed activity while the semicarbazones were not active indicating that introduction of sulphur atom alters the biological profile of these thiosemicarbazones. Copyright © 2016 Elsevier Inc. All rights reserved.

Waves associated to COMPLEX EVENTS observed by STEREO

NASA Astrophysics Data System (ADS)

Siu Tapia, A. L.; Blanco-Cano, X.; Kajdic, P.; Aguilar-Rodriguez, E.; Russell, C. T.; Jian, L. K.; Luhmann, J. G.

2012-12-01

Complex Events are formed by two or more large-scale solar wind structures which interact in space. Typical cases are interactions of: (i) a Magnetic Cloud/Interplanetary Coronal Mass Ejection (MC/ICME) with another MC/ICME transient; and (ii) an ICME followed by a Stream Interaction Region (SIR). Complex Events are of importance for space weather studies and studying them can enhance our understanding of collisionless plasma physics. Some of these structures can produce or enhance southward magnetic fields, a key factor in geomagnetic storm generation. Using data from the STEREO mission during the years 2006-2011, we found 17 Complex Events preceded by a shock wave. We use magnetic field and plasma data to study the micro-scale structure of the shocks, and the waves associated to these shocks and within Complex Events structures. To determine wave characteristics we perform Power Spectra and Minimum Variance Analysis. We also use PLASTIC WAP protons data to study foreshock extensions and the relationship between Complex Regions and particle acceleration to suprathermal energies.

FRET analysis of CP12 structural interplay by GAPDH and PRK.

PubMed

Moparthi, Satish Babu; Thieulin-Pardo, Gabriel; de Torres, Juan; Ghenuche, Petru; Gontero, Brigitte; Wenger, Jérôme

2015-03-13

CP12 is an intrinsically disordered protein playing a key role in the regulation of the Benson-Calvin cycle. Due to the high intrinsic flexibility of CP12, it is essential to consider its structural modulation induced upon binding to the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) enzymes. Here, we report for the first time detailed structural modulation about the wild-type CP12 and its site-specific N-terminal and C-terminal disulfide bridge mutants upon interaction with GAPDH and PRK by Förster resonance energy transfer (FRET). Our results indicate an increase in CP12 compactness when the complex is formed with GAPDH or PRK. In addition, the distributions in FRET histograms show the elasticity and conformational flexibility of CP12 in all supra molecular complexes. Contrarily to previous beliefs, our FRET results importantly reveal that both N-terminal and C-terminal site-specific CP12 mutants are able to form the monomeric (GAPDH-CP12-PRK) complex. Copyright © 2015 Elsevier Inc. All rights reserved.

Ocean acidification can mediate biodiversity shifts by changing biogenic habitat

NASA Astrophysics Data System (ADS)

Sunday, Jennifer M.; Fabricius, Katharina E.; Kroeker, Kristy J.; Anderson, Kathryn M.; Brown, Norah E.; Barry, James P.; Connell, Sean D.; Dupont, Sam; Gaylord, Brian; Hall-Spencer, Jason M.; Klinger, Terrie; Milazzo, Marco; Munday, Philip L.; Russell, Bayden D.; Sanford, Eric; Thiyagarajan, Vengatesen; Vaughan, Megan L. H.; Widdicombe, Stephen; Harley, Christopher D. G.

2017-01-01

The effects of ocean acidification (OA) on the structure and complexity of coastal marine biogenic habitat have been broadly overlooked. Here we explore how declining pH and carbonate saturation may affect the structural complexity of four major biogenic habitats. Our analyses predict that indirect effects driven by OA on habitat-forming organisms could lead to lower species diversity in coral reefs, mussel beds and some macroalgal habitats, but increases in seagrass and other macroalgal habitats. Available in situ data support the prediction of decreased biodiversity in coral reefs, but not the prediction of seagrass bed gains. Thus, OA-driven habitat loss may exacerbate the direct negative effects of OA on coastal biodiversity; however, we lack evidence of the predicted biodiversity increase in systems where habitat-forming species could benefit from acidification. Overall, a combination of direct effects and community-mediated indirect effects will drive changes in the extent and structural complexity of biogenic habitat, which will have important ecosystem effects.

Structural insights into RNA processing by the human RISC-loading complex.

PubMed

Wang, Hong-Wei; Noland, Cameron; Siridechadilok, Bunpote; Taylor, David W; Ma, Enbo; Felderer, Karin; Doudna, Jennifer A; Nogales, Eva

2009-11-01

Targeted gene silencing by RNA interference (RNAi) requires loading of a short guide RNA (small interfering RNA (siRNA) or microRNA (miRNA)) onto an Argonaute protein to form the functional center of an RNA-induced silencing complex (RISC). In humans, Argonaute2 (AGO2) assembles with the guide RNA-generating enzyme Dicer and the RNA-binding protein TRBP to form a RISC-loading complex (RLC), which is necessary for efficient transfer of nascent siRNAs and miRNAs from Dicer to AGO2. Here, using single-particle EM analysis, we show that human Dicer has an L-shaped structure. The RLC Dicer's N-terminal DExH/D domain, located in a short 'base branch', interacts with TRBP, whereas its C-terminal catalytic domains in the main body are proximal to AGO2. A model generated by docking the available atomic structures of Dicer and Argonaute homologs into the RLC reconstruction suggests a mechanism for siRNA transfer from Dicer to AGO2.

SnoN Stabilizes the SMAD3/SMAD4 Protein Complex

PubMed Central

Walldén, Karin; Nyman, Tomas; Hällberg, B. Martin

2017-01-01

TGF-β signaling regulates cellular processes such as proliferation, differentiation and apoptosis through activation of SMAD transcription factors that are in turn modulated by members of the Ski-SnoN family. In this process, Ski has been shown to negatively modulate TGF-β signaling by disrupting active R-SMAD/Co-SMAD heteromers. Here, we show that the related regulator SnoN forms a stable complex with the R-SMAD (SMAD3) and the Co-SMAD (SMAD4). To rationalize this stabilization at the molecular level, we determined the crystal structure of a complex between the SAND domain of SnoN and the MH2-domain of SMAD4. This structure shows a binding mode that is compatible with simultaneous coordination of R-SMADs. Our results show that SnoN, and SMAD heteromers can form a joint structural core for the binding of other transcription modulators. The results are of fundamental importance for our understanding of the molecular mechanisms behind the modulation of TGF-β signaling. PMID:28397834

SnoN Stabilizes the SMAD3/SMAD4 Protein Complex.

PubMed

Walldén, Karin; Nyman, Tomas; Hällberg, B Martin

2017-04-11

TGF-β signaling regulates cellular processes such as proliferation, differentiation and apoptosis through activation of SMAD transcription factors that are in turn modulated by members of the Ski-SnoN family. In this process, Ski has been shown to negatively modulate TGF-β signaling by disrupting active R-SMAD/Co-SMAD heteromers. Here, we show that the related regulator SnoN forms a stable complex with the R-SMAD (SMAD3) and the Co-SMAD (SMAD4). To rationalize this stabilization at the molecular level, we determined the crystal structure of a complex between the SAND domain of SnoN and the MH2-domain of SMAD4. This structure shows a binding mode that is compatible with simultaneous coordination of R-SMADs. Our results show that SnoN, and SMAD heteromers can form a joint structural core for the binding of other transcription modulators. The results are of fundamental importance for our understanding of the molecular mechanisms behind the modulation of TGF-β signaling.

Characterization of the interaction between subunits of the botulinum toxin complex produced by serotype D through tryptic susceptibility of the isolated components and complex forms.

PubMed

Suzuki, Tomonori; Watanabe, Toshihiro; Mutoh, Shingo; Hasegawa, Kimiko; Kouguchi, Hirokazu; Sagane, Yoshimasa; Fujinaga, Yukako; Oguma, Keiji; Ohyama, Tohru

2005-05-01

The 650 kDa large toxin complex (L-TC) produced by Clostridium botulinum serotype D strain 4947 (D-4947) has a subunit structure composed of unnicked components, i.e. neurotoxin (NT), non-toxic non-haemagglutinin (NTNHA) and three haemagglutinin subcomponents (HA-70, HA-33 and HA-17). In this study, subunit interactions were investigated through the susceptibilities of the toxin components to limited trypsin proteolysis. Additionally, complex forms were reconstituted in vitro by various combinations of individual components. Trypsin treatment of intact D-4947 L-TC led to the formation of mature L-TC with nicks at specific sites of each component, which is usually observed in other strains of serotype D. NT, NTNHA and HA-17 were cleaved at their specific sites in either the single or complex forms, but HA-33 showed no sign of proteolysis. Unlike the other components, HA-70 was digested into random fragments as a single form, but it was cleaved into two fragments in the complex form. Based on the relative position of exposed or hidden regions of the individual components in the complex derived from their tryptic susceptibilities, an assembly model is proposed for the arrangement of individual subunits in the botulinum L-TC.

Structure and magnetism of a Mn(III)-Mn(II)-Mn(II)-Mn(III) chain complex.

PubMed

Uhrecký, Róbert; Moncoľ, Ján; Koman, Marian; Titiš, Ján; Boča, Roman

2013-07-14

A novel tetranuclear manganese(II/III) complex with anions of pyridine-2,6-dicarboxylic acid (dipicolinic acid) has been synthesised and magneto-structurally characterised. The crystal structure of [Mn(II)2Mn(III)2(dipic)6(H2O)4]·2CH3OH·4H2O has been determined by single-crystal X-ray diffraction. The tetranuclear complex molecule [Mn(II)2Mn(III)2(dipic)6(H2O)4] is centrosymmetric and two manganese(II) and two manganese(III) atoms are bridged by four dipicolinate ligands. The complex molecules and uncoordinated water and methanol molecules are connected through hydrogen bonds and they form a 3D supramolecular hydrogen-bonding network.

Structural and electronic transport properties of compound forming HgPb liquid alloy using ab-initio pseudopotential

NASA Astrophysics Data System (ADS)

Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

2013-02-01

The electrical resistivity of compound forming liquid alloy HgPb is studied as a function of concentration. Hard sphere diameters of Hg and Pb are obtained through the inter-ionic pair potential evaluated using Troullier and Martins ab initio pseudopotential, which have been used to calculate partial structure factors. Considering the liquid alloy to be a ternary mixture Ziman's formula for calculating the resistivity of binary liquid alloys, modified for complex formation, has been used. The concentration dependence in resistivity occurs due to preferential ordering of unlike atoms as nearest neighbours with help of complex formation model. Though the compound HgiPbi as per structure peaks is found to be less stable. However it contributes significantly to resistivity as compared to bare ions.

The disasters of war in Darfur, 1950-2004.

PubMed

Reyna, Stephen P

2010-01-01

This article investigates the conflict that had been developing since the 1950s in Darfur and which in 2003 and 2004 burst into intense warfare. A 'complex-structuring of violence' standpoint explains the warfare. The argument is organised in two parts. The first section formulates the position by introducing Darfur, next evaluating the prevailing barbarisation perspective's attempts to explicate Darfur warring and, finally, formally presenting the complex structuring standpoint. The second section offers evidence bearing upon this standpoint. This involves information showing that four interrelated structural realms form a causal complex producing the violence. The article ends with discussion of the US government's role in Darfurian disasters of war.

Two conformational states of the membrane-associated Bacillus thuringiensis Cry4Ba {delta}-endotoxin complex revealed by electron crystallography: Implications for toxin-pore formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ounjai, Puey; Laboratory of Molecular Biophysics and Structural Biochemistry, Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, Nakornpathom 73170; Unger, Vinzenz M.

The insecticidal nature of Cry {delta}-endotoxins produced by Bacillus thuringiensis is generally believed to be caused by their ability to form lytic pores in the midgut cell membrane of susceptible insect larvae. Here we have analyzed membrane-associated structures of the 65-kDa dipteran-active Cry4Ba toxin by electron crystallography. The membrane-associated toxin complex was crystallized in the presence of DMPC via detergent dialysis. Depending upon the charge of the adsorbed surface, 2D crystals of the oligomeric toxin complex have been captured in two distinct conformations. The projection maps of those crystals have been generated at 17 A resolution. Both complexes appeared tomore » be trimeric; as in one crystal form, its projection structure revealed a symmetrical pinwheel-like shape with virtually no depression in the middle of the complex. The other form revealed a propeller-like conformation displaying an obvious hole in the center region, presumably representing the toxin-induced pore. These crystallographic data thus demonstrate for the first time that the 65-kDa activated Cry4Ba toxin in association with lipid membranes could exist in at least two different trimeric conformations, conceivably implying the closed and open states of the pore.« less

Terminal NiII-OH/-OH2 complexes in trigonal bipyramidal geometries derived from H2O.

PubMed

Lau, Nathanael; Sano, Yohei; Ziller, Joseph W; Borovik, A S

2017-03-29

The preparation and characterization of two Ni II complexes are described, a terminal Ni II -OH complex with the tripodal ligand tris[(N)-tertbutylureaylato)-N-ethyl)]aminato ([H 3 buea] 3- ) and a terminal Ni II -OH 2 complex with the tripodal ligand N , N ', N ″-[2,2',2″-nitrilotris(ethane-2,1-diyl)]tris(2,4,6-trimethylbenzenesulfonamido) ([MST] 3- ). For both complexes, the source of the -OH and -OH 2 ligand is water. The salts K 2 [Ni II H 3 buea(OH)] and NMe 4 [Ni II MST(OH 2 )] were characterized using perpendicular-mode X-band electronic paramagnetic resonance, Fourier transform infrared, UV-visible spectroscopies, and its electrochemical properties were evaluated using cyclic voltammetry. The solid state structures of these complexes determined by X-ray diffraction methods reveal that they adopt a distorted trigonal bipyramidal geometry, an unusual structure for 5-coordinate Ni II complexes. Moreover, the Ni II -OH and Ni II -OH 2 units form intramolecular hydrogen bonding networks with the [H 3 buea] 3- and [MST] 3- ligands. The oxidation chemistry of these complexes was explored by treating the high-spin Ni II compounds with one-electron oxidants. Species were formed with S = 1/2 spin ground states that are consistent with formation of monomeric Ni III species. While the formation of Ni III -OH complexes cannot be ruled out, the lack of observable O-H vibrations from the putative Ni-OH units suggest the possibility that other high valent Ni species are formed.

Structure of a peptide adsorbed on graphene and graphite.

PubMed

Katoch, Jyoti; Kim, Sang Nyon; Kuang, Zhifeng; Farmer, Barry L; Naik, Rajesh R; Tatulian, Suren A; Ishigami, Masa

2012-05-09

Noncovalent functionalization of graphene using peptides is a promising method for producing novel sensors with high sensitivity and selectivity. Here we perform atomic force microscopy, Raman spectroscopy, infrared spectroscopy, and molecular dynamics simulations to investigate peptide-binding behavior to graphene and graphite. We studied a dodecamer peptide identified with phage display to possess affinity for graphite. Optical spectroscopy reveals that the peptide forms secondary structures both in powder form and in an aqueous medium. The dominant structure in the powder form is α-helix, which undergoes a transition to a distorted helical structure in aqueous solution. The peptide forms a complex reticular structure upon adsorption on graphene and graphite, having a helical conformation different from α-helix due to its interaction with the surface. Our observation is consistent with our molecular dynamics calculations, and our study paves the way for rational functionalization of graphene using biomolecules with defined structures and, therefore, functionalities.

3D Complex: A Structural Classification of Protein Complexes

PubMed Central

Levy, Emmanuel D; Pereira-Leal, Jose B; Chothia, Cyrus; Teichmann, Sarah A

2006-01-01

Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes. PMID:17112313

Structure of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase in complex with the feedback inhibitor CoA reveals only one active-site conformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wubben, T.; Mesecar, A.D.; UIC)

Phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway, reversibly transferring an adenylyl group from ATP to 4'-phosphopantetheine to form dephosphocoenzyme A (dPCoA). To complement recent biochemical and structural studies on Mycobacterium tuberculosis PPAT (MtPPAT) and to provide further insight into the feedback regulation of MtPPAT by CoA, the X-ray crystal structure of the MtPPAT enzyme in complex with CoA was determined to 2.11 {angstrom} resolution. Unlike previous X-ray crystal structures of PPAT-CoA complexes from other bacteria, which showed two distinct CoA conformations bound to the active site, only one conformation of CoA is observedmore » in the MtPPAT-CoA complex.« less

ALGORITHM OF CARDIO COMPLEX DETECTION AND SORTING FOR PROCESSING THE DATA OF CONTINUOUS CARDIO SIGNAL MONITORING.

PubMed

Krasichkov, A S; Grigoriev, E B; Nifontov, E M; Shapovalov, V V

The paper presents an algorithm of cardio complex classification as part of processing the data of continuous cardiac monitoring. R-wave detection concurrently with cardio complex sorting is discussed. The core of this approach is the use of prior information about. cardio complex forms, segmental structure, and degree of kindness. Results of the sorting algorithm testing are provided.

Crystal-contact engineering to obtain a crystal form of the Kelch domain of human Keap1 suitable for ligand-soaking experiments.

PubMed

Hörer, Stefan; Reinert, Dirk; Ostmann, Katja; Hoevels, Yvette; Nar, Herbert

2013-06-01

Keap1 is a substrate adaptor protein for a Cul3-dependent ubiquitin ligase complex and plays an important role in the cellular response to oxidative stress. It binds Nrf2 with its Kelch domain and thus triggers the ubiquitinylation and degradation of Nrf2. Oxidative stress prevents the degradation of Nrf2 and leads to the activation of cytoprotective genes. Therefore, Keap1 is an attractive drug target in inflammatory diseases. The support of a medicinal chemistry effort by structural research requires a robust crystallization system in which the crystals are preferably suited for performing soaking experiments. This facilitates the generation of protein-ligand complexes in a routine and high-throughput manner. The structure of human Keap1 has been described previously. In this crystal form, however, the binding site for Nrf2 was blocked by a crystal contact. This interaction was analysed and mutations were introduced to disrupt this crystal contact. One double mutation (E540A/E542A) crystallized in a new crystal form in which the binding site for Nrf2 was not blocked and was accessible to small-molecule ligands. The crystal structures of the apo form of the mutated Keap1 Kelch domain (1.98 Å resolution) and of the complex with an Nrf2-derived peptide obtained by soaking (2.20 Å resolution) are reported.

Form follows function: the importance of endoplasmic reticulum shape.

PubMed

Westrate, L M; Lee, J E; Prinz, W A; Voeltz, G K

2015-01-01

The endoplasmic reticulum (ER) has a remarkably complex structure, composed of a single bilayer that forms the nuclear envelope, along with a network of sheets and dynamic tubules. Our understanding of the biological significance of the complex architecture of the ER has improved dramatically in the last few years. The identification of proteins and forces required for maintaining ER shape, as well as more advanced imaging techniques, has allowed the relationship between ER shape and function to come into focus. These studies have also revealed unexpected new functions of the ER and novel ER domains regulating alterations in ER dynamics. The importance of ER structure has become evident as recent research has identified diseases linked to mutations in ER-shaping proteins. In this review, we discuss what is known about the maintenance of ER architecture, the relationship between ER structure and function, and diseases associated with defects in ER structure.

From SHAPE Signatures to 3-D Structures | Center for Cancer Research

Cancer.gov

RNAs undergo extensive folding to form sophisticated based-paired secondary structures that are, in part, indicators of more complex three-dimensional structures.  These 3-D shapes are an integral part of the cellular gene-expression machinery. Deconstructing these structures is no small matter, yet it is critical to understanding their function.

Synthesis, crystal structures, spectral, thermal and antimicrobial properties of new Zn(II) 5-iodo- and 5-bromosalicylates

NASA Astrophysics Data System (ADS)

Košická, Petra; Győryová, Katarína; Smolko, Lukáš; Gyepes, Róbert; Hudecová, Daniela

2018-03-01

Two new analogous zinc(II) complexes containing 5-iodo- and 5-bromosalicylate ligands, respectively, were prepared in single-crystal form and characterized by IR spectroscopy, thermal analysis and elemental analysis. The solid-state structures of prepared complexes were determined by single crystal X-ray crystallography. Both complexes are isostructural and their crystal structures composed of neutral molecules [Zn(5-Xsal)2(H2O)2] (where X = Br, I, sal = salicylato). Central Zn(II) atom is in both complexes coordinated by six oxygen atoms, four of which are from two chelate bonded 5-halosalicylates and remaining two from coordinated water molecules. The found chelate binding mode is in line with the Δ values calculated from IR spectral data. Antimicrobial activity of prepared complexes was studied against selected bacteria, yeast and filamentous fungi. Obtained results indicate that 5-iodosalicylate complex is more antimicrobially active than its 5-bromo substituted analogue.

Proteins evolve on the edge of supramolecular self-assembly.

PubMed

Garcia-Seisdedos, Hector; Empereur-Mot, Charly; Elad, Nadav; Levy, Emmanuel D

2017-08-10

The self-association of proteins into symmetric complexes is ubiquitous in all kingdoms of life. Symmetric complexes possess unique geometric and functional properties, but their internal symmetry can pose a risk. In sickle-cell disease, the symmetry of haemoglobin exacerbates the effect of a mutation, triggering assembly into harmful fibrils. Here we examine the universality of this mechanism and its relation to protein structure geometry. We introduced point mutations solely designed to increase surface hydrophobicity among 12 distinct symmetric complexes from Escherichia coli. Notably, all responded by forming supramolecular assemblies in vitro, as well as in vivo upon heterologous expression in Saccharomyces cerevisiae. Remarkably, in four cases, micrometre-long fibrils formed in vivo in response to a single point mutation. Biophysical measurements and electron microscopy revealed that mutants self-assembled in their folded states and so were not amyloid-like. Structural examination of 73 mutants identified supramolecular assembly hot spots predictable by geometry. A subsequent structural analysis of 7,471 symmetric complexes showed that geometric hot spots were buffered chemically by hydrophilic residues, suggesting a mechanism preventing mis-assembly of these regions. Thus, point mutations can frequently trigger folded proteins to self-assemble into higher-order structures. This potential is counterbalanced by negative selection and can be exploited to design nanomaterials in living cells.

Proteins evolve on the edge of supramolecular self-assembly

NASA Astrophysics Data System (ADS)

Garcia-Seisdedos, Hector; Empereur-Mot, Charly; Elad, Nadav; Levy, Emmanuel D.

2017-08-01

The self-association of proteins into symmetric complexes is ubiquitous in all kingdoms of life. Symmetric complexes possess unique geometric and functional properties, but their internal symmetry can pose a risk. In sickle-cell disease, the symmetry of haemoglobin exacerbates the effect of a mutation, triggering assembly into harmful fibrils. Here we examine the universality of this mechanism and its relation to protein structure geometry. We introduced point mutations solely designed to increase surface hydrophobicity among 12 distinct symmetric complexes from Escherichia coli. Notably, all responded by forming supramolecular assemblies in vitro, as well as in vivo upon heterologous expression in Saccharomyces cerevisiae. Remarkably, in four cases, micrometre-long fibrils formed in vivo in response to a single point mutation. Biophysical measurements and electron microscopy revealed that mutants self-assembled in their folded states and so were not amyloid-like. Structural examination of 73 mutants identified supramolecular assembly hot spots predictable by geometry. A subsequent structural analysis of 7,471 symmetric complexes showed that geometric hot spots were buffered chemically by hydrophilic residues, suggesting a mechanism preventing mis-assembly of these regions. Thus, point mutations can frequently trigger folded proteins to self-assemble into higher-order structures. This potential is counterbalanced by negative selection and can be exploited to design nanomaterials in living cells.

Conformation Control of a Conjugated Polymer through Complexation with Bile Acids Generates Its Novel Spectral and Morphological Properties.

PubMed

Tsuchiya, Youichi; Noguchi, Takao; Yoshihara, Daisuke; Roy, Bappaditya; Yamamoto, Tatsuhiro; Shinkai, Seiji

2016-11-29

Control of higher-order polymer structures attracts a great deal of interest for many researchers when they lead to the development of materials having various advanced functions. Among them, conjugated polymers that are useful as starting materials in the design of molecular wires are particularly attractive. However, an equilibrium existing between isolated chains and bundled aggregates is inevitable and has made their physical properties very complicated. As an attempt to simplify this situation, we previously reported that a polymer chain of a water-soluble polythiophene could be isolated through complexation with a helix-forming polysaccharide. More recently, a covalently self-threading polythiophene was reported, the main chain of which was physically protected from self-folding and chain-chain π-stacking. In this report, we wish to report a new strategy to isolate a water-soluble polythiophene and to control its higher-order structure by a supramolecular approach: that is, among a few bile acids, lithocholate can form stoichiometric complexes with cationic polythiophene to isolate the polymer chain, and the higher-order structure is changeable by the molar ratio. The optical and morphological studies have been thoroughly performed, and the resultant complex has been applied to the selective recognition of two AMP structural isomers.

Spectroscopic investigations of the charge-transfer interaction between the drug reserpine and different acceptors: Towards understanding of drug-receptor mechanism

NASA Astrophysics Data System (ADS)

Eldaroti, Hala H.; Gadir, Suad A.; Refat, Moamen S.; Adam, Abdel Majid A.

2013-11-01

The study of the charge-transfer interaction of the drugs may be useful in understanding the drug-receptor interactions and the mechanism of drug action. Structural and thermal stability of charge-transfer (CT) complexes formed between the drug reserpine (Res) as a donor and quinol (QL), picric acid (PA), tetracyanoquinodimethane (TCNQ) or dichlorodicyanobenzoquinone (DDQ) as acceptors were reported. Elemental analysis, electronic absorption, spectrophotometric titration, IR, Raman, 1H NMR and X-ray powder diffraction (XRD) were used to characterize the new products. The thermal stability of the synthesized CT complexes was investigated using thermogravimetric (TG) analyses, and the morphology and particle size of these complexes were obtained from scanning electron microscopy (SEM). The stoichiometry of the complexes (donor:acceptor molar ratio) was determined to be 1:1 for all complexes. Accordingly the formed CT complexes could be formulated as [(Res)(QL)], [(Res)(PA)], [(Res)(TCNQ)] and [(Res)(DDQ)]. It was found that the obtained CT complexes are nanoscale, semi-crystalline particles, thermally stable and formed through spontaneous reaction. The results obtained herein are satisfactory for estimation of drug Res in the pharmaceutical form.

Using complexation for the microencapsulation of nisin in biopolymer matrices by spray-drying.

PubMed

Ben Amara, Chedia; Kim, Lanhee; Oulahal, Nadia; Degraeve, Pascal; Gharsallaoui, Adem

2017-12-01

The aim of this study is to investigate the potential of complexation to encapsulate nisin (5g/L concentration) using spray-drying technique and to evaluate how complexation with pectin or alginate (2g/L concentration) can preserve nisin structure and antimicrobial activity. Spray-drying of nisin-low methoxyl pectin or nisin-alginate electrostatic complexes has led to the microencapsulation of the peptide in different networks that were highly influenced by the polysaccharide type. Turbidity and particle size measurements indicated that while spray-drying promoted the aggregation of nisin-pectin complexes, it favored the dissociation of nisin-alginate aggregates to form individual complexes. Structural changes of nisin induced by complexation with pectin or alginate and spray-drying were studied by using UV-Vis absorption and fluorescence spectroscopy. The results showed that complexation with pectin or alginate preserved nisin structure as well as its antimicrobial activity during spray-drying. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Topographical Mapping in Drosophila Central Complex Network and Its Signal Routing

PubMed Central

Chang, Po-Yen; Su, Ta-Shun; Shih, Chi-Tin; Lo, Chung-Chuan

2017-01-01

Neural networks regulate brain functions by routing signals. Therefore, investigating the detailed organization of a neural circuit at the cellular levels is a crucial step toward understanding the neural mechanisms of brain functions. To study how a complicated neural circuit is organized, we analyzed recently published data on the neural circuit of the Drosophila central complex, a brain structure associated with a variety of functions including sensory integration and coordination of locomotion. We discovered that, except for a small number of “atypical” neuron types, the network structure formed by the identified 194 neuron types can be described by only a few simple mathematical rules. Specifically, the topological mapping formed by these neurons can be reconstructed by applying a generation matrix on a small set of initial neurons. By analyzing how information flows propagate with or without the atypical neurons, we found that while the general pattern of signal propagation in the central complex follows the simple topological mapping formed by the “typical” neurons, some atypical neurons can substantially re-route the signal pathways, implying specific roles of these neurons in sensory signal integration. The present study provides insights into the organization principle and signal integration in the central complex. PMID:28443014

Cas5d Protein Processes Pre-crRNA and Assembles into a Cascade-like Interference Complex in Subtype I-C/Dvulg CRISPR-Cas System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nam, Ki Hyun; Haitjema, Charles; Liu, Xueqi

Clustered regularly interspaced short palindromic repeats (CRISPRs), together with an operon of CRISPR-associated (Cas) proteins, form an RNA-based prokaryotic immune system against exogenous genetic elements. Cas5 family proteins are found in several type I CRISPR-Cas systems. Here, we report the molecular function of subtype I-C/Dvulg Cas5d from Bacillus halodurans. We show that Cas5d cleaves pre-crRNA into unit length by recognizing both the hairpin structure and the 3 single stranded sequence in the CRISPR repeat region. Cas5d structure reveals a ferredoxin domain-based architecture and a catalytic triad formed by Y46, K116, and H117 residues. We further show that after pre-crRNA processing,more » Cas5d assembles with crRNA, Csd1, and Csd2 proteins to form a multi-sub-unit interference complex similar to Escherichia coli Cascade (CRISPR-associated complex for antiviral defense) in architecture. Our results suggest that formation of a crRNA-presenting Cascade-like complex is likely a common theme among type I CRISPR subtypes.« less

Diapause hormone in the Helicoverpa/Heliothis complex: a review of gene expression, peptide structure and activity, analog and antagonist development, and the receptor

USDA-ARS?s Scientific Manuscript database

This review summarizes recent studies focusing on diapause hormone (DH) in the Helicoverpa/Heliothis complex of agricultural pests. Moths in this complex overwinter in pupal diapause, a form of developmental arrest used to circumvent unfavorable seasons. DH was originally reported in the silkmoth ...

New Evidence for the Presence of Indigenous Microfossils in Carbonaceous Chondrites

NASA Technical Reports Server (NTRS)

Hoover, Richard B.; Rozanov, Alexei Yu.

2004-01-01

We present additional evidence for the presence of indigenous microfossils in carbonaceous meteorites scanning electron micrograph studies of freshly fractured interior surfaces of pristine samples of the Murchison CM2 carbonaceous meteorite have revealed forms in-situ that are recognizable as biofilms as well as complex and highly structured forms similar to calcareous and siliceous microfossils. Some of the forms encountered are very well-preserved and exhibit complex associated microstructures similar to bacterial flagella. New images will be presented of forms recently encountered in carbonaceous meteorites and they will be compared with those of known microbial extremophiles. KEYWORDS: carbonaceous chondrites, Murchison, microfossils, extremophiles

Designing Effective Web Forms for Older Web Users

ERIC Educational Resources Information Center

Li, Hui; Rau, Pei-Luen Patrick; Fujimura, Kaori; Gao, Qin; Wang, Lin

2012-01-01

This research aims to provide insight for web form design for older users. The effects of task complexity and information structure of web forms on older users' performance were examined. Forty-eight older participants with abundant computer and web experience were recruited. The results showed significant differences in task time and error rate…

Luminescent macrocyclic lanthanide complexes

DOEpatents

Raymond, Kenneth N; Corneillie, Todd M; Xu, Jide

2014-05-20

The present invention provides a novel class of macrocyclic compounds as well as complexes formed between a metal (e.g., lanthanide) ion and the compounds of the invention. Preferred complexes exhibit high stability as well as high quantum yields of lanthanide ion luminescence in aqueous media without the need for secondary activating agents. Preferred compounds incorporate hydroxy-isophthalamide moieties within their macrocyclic structure and are characterized by surprisingly low, non-specific binding to a variety of polypeptides such as antibodies and proteins as well as high kinetic stability. These characteristics distinguish them from known, open-structured ligands.

Crystal structure and functional interpretation of the erythrocyte spectrin tetramerization domain complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ipsaro, Jonathan J.; Harper, Sandra L.; Messick, Troy E.

2010-09-07

As the principal component of the membrane skeleton, spectrin confers integrity and flexibility to red cell membranes. Although this network involves many interactions, the most common hemolytic anemia mutations that disrupt erythrocyte morphology affect the spectrin tetramerization domains. Although much is known clinically about the resulting conditions (hereditary elliptocytosis and pyropoikilocytosis), the detailed structural basis for spectrin tetramerization and its disruption by hereditary anemia mutations remains elusive. Thus, to provide further insights into spectrin assembly and tetramer site mutations, a crystal structure of the spectrin tetramerization domain complex has been determined. Architecturally, this complex shows striking resemblance to multirepeat spectrinmore » fragments, with the interacting tetramer site region forming a central, composite repeat. This structure identifies conformational changes in {alpha}-spectrin that occur upon binding to {beta}-spectrin, and it reports the first structure of the {beta}-spectrin tetramerization domain. Analysis of the interaction surfaces indicates an extensive interface dominated by hydrophobic contacts and supplemented by electrostatic complementarity. Analysis of evolutionarily conserved residues suggests additional surfaces that may form important interactions. Finally, mapping of hereditary anemia-related mutations onto the structure demonstrate that most, but not all, local hereditary anemia mutations map to the interacting domains. The potential molecular effects of these mutations are described.« less

Crystal Structure and Functional Interpretation of the Erythrocyte spectrin Tetramerization Domain Complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

J Ipsaro; S Harper; T Messick

2011-12-31

As the principal component of the membrane skeleton, spectrin confers integrity and flexibility to red cell membranes. Although this network involves many interactions, the most common hemolytic anemia mutations that disrupt erythrocyte morphology affect the spectrin tetramerization domains. Although much is known clinically about the resulting conditions (hereditary elliptocytosis and pyropoikilocytosis), the detailed structural basis for spectrin tetramerization and its disruption by hereditary anemia mutations remains elusive. Thus, to provide further insights into spectrin assembly and tetramer site mutations, a crystal structure of the spectrin tetramerization domain complex has been determined. Architecturally, this complex shows striking resemblance to multirepeat spectrinmore » fragments, with the interacting tetramer site region forming a central, composite repeat. This structure identifies conformational changes in {alpha}-spectrin that occur upon binding to {beta}-spectrin, and it reports the first structure of the {beta}-spectrin tetramerization domain. Analysis of the interaction surfaces indicates an extensive interface dominated by hydrophobic contacts and supplemented by electrostatic complementarity. Analysis of evolutionarily conserved residues suggests additional surfaces that may form important interactions. Finally, mapping of hereditary anemia-related mutations onto the structure demonstrate that most, but not all, local hereditary anemia mutations map to the interacting domains. The potential molecular effects of these mutations are described.« less

Integrating mechanisms of visual guidance in naturalistic language production.

PubMed

Coco, Moreno I; Keller, Frank

2015-05-01

Situated language production requires the integration of visual attention and linguistic processing. Previous work has not conclusively disentangled the role of perceptual scene information and structural sentence information in guiding visual attention. In this paper, we present an eye-tracking study that demonstrates that three types of guidance, perceptual, conceptual, and structural, interact to control visual attention. In a cued language production experiment, we manipulate perceptual (scene clutter) and conceptual guidance (cue animacy) and measure structural guidance (syntactic complexity of the utterance). Analysis of the time course of language production, before and during speech, reveals that all three forms of guidance affect the complexity of visual responses, quantified in terms of the entropy of attentional landscapes and the turbulence of scan patterns, especially during speech. We find that perceptual and conceptual guidance mediate the distribution of attention in the scene, whereas structural guidance closely relates to scan pattern complexity. Furthermore, the eye-voice span of the cued object and its perceptual competitor are similar; its latency mediated by both perceptual and structural guidance. These results rule out a strict interpretation of structural guidance as the single dominant form of visual guidance in situated language production. Rather, the phase of the task and the associated demands of cross-modal cognitive processing determine the mechanisms that guide attention.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faucher, Frédérick; Robey-Bond, Susan M.; Wallace, Susan S.

DNA is subject to a multitude of oxidative damages generated by oxidizing agents from metabolism and exogenous sources and by ionizing radiation. Guanine is particularly vulnerable to oxidation, and the most common oxidative product 8-oxoguanine (8-oxoG) is the most prevalent lesion observed in DNA molecules. 8-OxoG can form a normal Watson-Crick pair with cytosine (8-oxoG:C), but it can also form a stable Hoogsteen pair with adenine (8-oxoG:A), leading to a G:C {yields} T:A transversion after replication. Fortunately, 8-oxoG is recognized and excised by either of two DNA glycosylases of the base excision repair pathway: formamidopyrimidine-DNA glycosylase and 8-oxoguanine DNA glycosylasemore » (Ogg). While Clostridium acetobutylicum Ogg (CacOgg) DNA glycosylase can specifically recognize and remove 8-oxoG, it displays little preference for the base opposite the lesion, which is unusual for a member of the Ogg1 family. This work describes the crystal structures of CacOgg in its apo form and in complex with 8-oxo-2'-deoxyguanosine. A structural comparison between the apo form and the liganded form of the enzyme reveals a structural reorganization of the C-terminal domain upon binding of 8-oxoG, similar to that reported for human OGG1. A structural comparison of CacOgg with human OGG1, in complex with 8-oxoG containing DNA, provides a structural rationale for the lack of opposite base specificity displayed by CacOgg.« less

Structural Behavioral Study on the General Aviation Network Based on Complex Network

NASA Astrophysics Data System (ADS)

Zhang, Liang; Lu, Na

2017-12-01

The general aviation system is an open and dissipative system with complex structures and behavioral features. This paper has established the system model and network model for general aviation. We have analyzed integral attributes and individual attributes by applying the complex network theory and concluded that the general aviation network has influential enterprise factors and node relations. We have checked whether the network has small world effect, scale-free property and network centrality property which a complex network should have by applying degree distribution of functions and proved that the general aviation network system is a complex network. Therefore, we propose to achieve the evolution process of the general aviation industrial chain to collaborative innovation cluster of advanced-form industries by strengthening network multiplication effect, stimulating innovation performance and spanning the structural hole path.

The main principles of formation of structure of cultural-historical landscapes of Central Russia.

NASA Astrophysics Data System (ADS)

Nizovtsev, Vyacheslav; Natalia, Erman

2014-05-01

The forming and development of cultural-historical landscapes (CH) are obligate result of evolution of society and nature, as well as, man and landscapes during their coherent growth. CH landscapes are holistic historic-cultural and nature creations. They reflect the history of land use and spiritual development of ethnic community of concrete territory with determine homogeneous landscape characteristics. The majority of them appertain to the category of relict landscapes, which completed their evolution growth. That means that these are anthropogenic (AL) and cultural (CL) landscapes. They lost anthropogenic management and continue their growth obeying natural logic. These landscapes include elements of morphological structure and natural components, which have been transformed by men, and also artefacts, sociofacts and mental facts. These facts can be considered as peculiar "biographical chronicle" of activity of population in determinate landscape conditions in determinate historical period. These facts are evidences of material and spiritual cultural of society. The first AL begin to arise simultaneously with conversation of appropriating economy into generating economy. There was such conversation in Central Russia (Neolithic revolution) only in Bronze Age. Anthropogenic transformed landscape complexes and even man-made landscape complexes have been formed in Bronze Age. Some of these complexes exist now. Actual anthropogenic and cultural landscapes began to form only in Iron Age while permanent, long existed settlement and agriculture structure has organized. First, These are small settlement anthropogenic landscape complexes (selischa and gorodischa) with applied permanent miniature arable areas. These complexes located on the capes and on the areas between river banks and banks of streams. Second, these are pasture anthropogenic landscape complexes (on the level of podurochische and urochische), located in flood plain and valley-cavin position (pasture plod plain meadow-forest).

Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein–DNA interactions

PubMed Central

Eldar, Amir; Rozenberg, Haim; Diskin-Posner, Yael; Rohs, Remo; Shakked, Zippora

2013-01-01

A p53 hot-spot mutation found frequently in human cancer is the replacement of R273 by histidine or cysteine residues resulting in p53 loss of function as a tumor suppressor. These mutants can be reactivated by the incorporation of second-site suppressor mutations. Here, we present high-resolution crystal structures of the p53 core domains of the cancer-related proteins, the rescued proteins and their complexes with DNA. The structures show that inactivation of p53 results from the incapacity of the mutated residues to form stabilizing interactions with the DNA backbone, and that reactivation is achieved through alternative interactions formed by the suppressor mutations. Detailed structural and computational analysis demonstrates that the rescued p53 complexes are not fully restored in terms of DNA structure and its interface with p53. Contrary to our previously studied wild-type (wt) p53-DNA complexes showing non-canonical Hoogsteen A/T base pairs of the DNA helix that lead to local minor-groove narrowing and enhanced electrostatic interactions with p53, the current structures display Watson–Crick base pairs associated with direct or water-mediated hydrogen bonds with p53 at the minor groove. These findings highlight the pivotal role played by R273 residues in supporting the unique geometry of the DNA target and its sequence-specific complex with p53. PMID:23863845

Crystallization of Mitochondrial Respiratory Complex II from Chicken Heart: a Membrane Protein Complex Diffracting to 2.0 Å.

PubMed Central

Huang, Li-shar; Borders, Toni M.; Shen, John T.; Wang, Chung-Jen; Berry, Edward

2006-01-01

Synopsis A multi-subunit mitochondrial membrane protein complex involved in the Krebs Cycle and respiratory chain has been crystallized in a form suitable for near-atomic resolution structure determination. A procedure is presented for preparation of diffraction-quality crystals of a vertebrate mitochondrial respiratory Complex II. The crystals have the potential to diffract to at least 2.0 Å with optimization of post-crystal-growth treatment and cryoprotection. This should allow determination of the structure of this important and medically relevant membrane protein complex at near-atomic resolution and provide great detail of the mode of binding of substrates and inhibitors at the two substrate-binding sites. PMID:15805592

The Crystal Structure of BRAF in Complex with an Organoruthenium Inhibitor Reveals a Mechanism for Inhibition of an Active Form of BRAF Kinase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Peng; Streu, Craig; Qin, Jie

Substitution mutations in the BRAF serine/threonine kinase are found in a variety of human cancers. Such mutations occur in 70% of human malignant melanomas, and a single hyperactivating V600E mutation is found in the activation segment of the kinase domain and accounts for more than 90% of these mutations. Given this correlation, the molecular mechanism for BRAF regulation as well as oncogenic activation has attracted considerable interest, and activated forms of BRAF, such as BRAF{sup V600E}, have become attractive targets for small molecule inhibition. Here we report on the identification and subsequent optimization of a potent BRAF inhibitor, CS292, basedmore » on an organometallic kinase inhibitor scaffold. A cocrystal structure of CS292 in complex with the BRAF kinase domain reveals that CS292 binds to the ATP binding pocket of the kinase and is an ATP competitive inhibitor. The structure of the kinase-inhibitor complex also demonstrates that CS292 binds to BRAF in an active conformation and suggests a mechanism for regulation of BRAF by phosphorylation and BRAF{sup V600E} oncogene-induced activation. The structure of CS292 bound to the active form of the BRAF kinase also provides a novel scaffold for the design of BRAF{sup V600E} oncogene selective BRAF inhibitors for therapeutic application.« less

Failure of structural elements made of polymer supported composite materials during the multiyear natural aging

NASA Astrophysics Data System (ADS)

Blinkov, Pavel; Ogorodov, Leonid; Grabovyy, Peter

2018-03-01

Modern high-rise construction introduces a number of limitations and tasks. In addition to durability, comfort and profitability, projects should take into account energy efficiency and environmental problems. Polymer building materials are used as substitutes for materials such as brick, concrete, metal, wood and glass, and in addition to traditional materials. Plastic materials are light, can be formed into complex shapes, durable and low, and also possess a wide range of properties. Plastic materials are available in various forms, colors and textures and require minimal or no color. They are resistant to heat transfer and diffusion of moisture and do not suffer from metal corrosion or microbial attack. Polymeric materials, including thermoplastics, thermoset materials and wood-polymer composites, have many structural and non-structural applications in the construction industry. They provide unique and innovative solutions at a low cost, and their use is likely to grow in the future. A number of polymer composite materials form complex material compositions, which are applied in the construction in order to analyze the processes of damage accumulation under the conditions of complex nonstationary loading modes, and to determine the life of structural elements considering the material aging. This paper present the results of tests on short-term compression loading with a deformation rate of v = 2 mm/min using composite samples of various shapes and sizes.

Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease.

PubMed

Nakae, Setsu; Hijikata, Atsushi; Tsuji, Toshiyuki; Yonezawa, Kouki; Kouyama, Ken-Ichi; Mayanagi, Kouta; Ishino, Sonoko; Ishino, Yoshizumi; Shirai, Tsuyoshi

2016-11-01

Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases. In this study, we determined the structure of the EndoMS-DNA complex. The complex structure of the EndoMS dimer with dsDNA unexpectedly revealed that the mismatched bases were flipped out into binding sites, and the overall architecture most resembled that of restriction enzymes. The structure of the apo form was similar to the reported structure of Pyrococcus abyssi NucS, indicating that movement of the C-terminal domain from the resting state was required for activity. In addition, a model of the EndoMS-PCNA-DNA complex was preliminarily verified with electron microscopy. The structures strongly support the idea that EndoMS acts in a mismatch repair pathway. Copyright © 2016 Elsevier Ltd. All rights reserved.

Characterization of physiochemical and biological properties of an insulin/lauryl sulfate complex formed by hydrophobic ion pairing.

PubMed

Dai, Wei-Guo; Dong, Liang C

2007-05-04

An insulin/lauryl sulfate complex was prepared by hydrophobic ion pairing (HIP). The physiochemical and biological properties of the HIP complex were characterized using octanol/water partition measurement, isothermal titration calorimetry (ITC), ultraviolet-circular dichroism (UV-CD) and Fourier transform infrared spectroscopy (FTIR). Sodium dodecyl sulfate (SDS) bound to the insulin in a stoichiometric manner. The formed complex exhibited lipophilicity, and its insulin retained its native structure integrity. The in vivo bioactivity of the complex insulin was evaluated in rats by monitoring the plasma glucose level after intravenous (i.v.) injection, and the glucose level was compared with that for free insulin. The pharmacodynamic study result in rats showed that the complex insulin had in vivo bioactivity comparable to free insulin.

Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5.

PubMed

Swale, Christopher; Monod, Alexandre; Tengo, Laura; Labaronne, Alice; Garzoni, Frédéric; Bourhis, Jean-Marie; Cusack, Stephen; Schoehn, Guy; Berger, Imre; Ruigrok, Rob W H; Crépin, Thibaut

2016-04-20

The genome of influenza A virus (IAV) comprises eight RNA segments (vRNA) which are transcribed and replicated by the heterotrimeric IAV RNA-dependent RNA-polymerase (RdRp). RdRp consists of three subunits (PA, PB1 and PB2) and binds both the highly conserved 3'- and 5'-ends of the vRNA segment. The IAV RdRp is an important antiviral target, but its structural mechanism has remained largely elusive to date. By applying a polyprotein strategy, we produced RdRp complexes and define a minimal human IAV RdRp core complex. We show that PA-PB1 forms a stable heterodimeric submodule that can strongly interact with 5'-vRNA. In contrast, 3'-vRNA recognition critically depends on the PB2 N-terminal domain. Moreover, we demonstrate that PA-PB1 forms a stable and stoichiometric complex with host nuclear import factor RanBP5 that can be modelled using SAXS and we show that the PA-PB1-RanPB5 complex is no longer capable of 5'-vRNA binding. Our results provide further evidence for a step-wise assembly of IAV structural components, regulated by nuclear transport mechanisms and host factor binding.

Mesozoic to Eocene ductile deformation of western Central Iran: From Cimmerian collisional orogeny to Eocene exhumation

NASA Astrophysics Data System (ADS)

Kargaranbafghi, Fariba; Neubauer, Franz; Genser, Johann; Faghih, Ali; Kusky, Timothy

2012-09-01

To advance our understanding of the Mesozoic to Eocene tectonics and kinematics of basement units exposed in the south-western Central Iran plateau, this paper presents new structural and thermochronological data from the Chapedony metamorphic core complex and hangingwall units, particularly from the Posht-e-Badam complex. The overall Paleogene structural characteristics of the area are related to an oblique convergent zone. The Saghand area represents part of a deformation zone between the Arabian and Eurasian plates, and can be interpreted to result from the Central Iran intracontinental deformation acting as a weak zone during Mesozoic to Paleogene times. Field and microstructural evidence reveal that the metamorphic and igneous rocks suffered a ductile shear deformation including mylonitization at the hangingwall boundary of the Eocene Chapedony metamorphic core complex. Comparison of deformation features in the mylonites and other structural features within the footwall unit leads to the conclusion that the mylonites were formed in a subhorizontal shear zone by NE-SW stretching during Middle to Late Eocene extensional tectonics. The Chapedony metamorphic core complex is characterized by amphibolite-facies metamorphism and development of S and S-L tectonic fabrics. The Posht-e-Badam complex was deformed by two stages during Cimmerian tectonic processes forming the Paleo-Tethyan suture.

Pseudoracemic amino acid complexes: blind predictions for flexible two-component crystals.

PubMed

Görbitz, Carl Henrik; Dalhus, Bjørn; Day, Graeme M

2010-08-14

Ab initio prediction of the crystal packing in complexes between two flexible molecules is a particularly challenging computational chemistry problem. In this work we present results of single crystal structure determinations as well as theoretical predictions for three 1 ratio 1 complexes between hydrophobic l- and d-amino acids (pseudoracemates), known from previous crystallographic work to form structures with one of two alternative hydrogen bonding arrangements. These are accurately reproduced in the theoretical predictions together with a series of patterns that have never been observed experimentally. In this bewildering forest of potential polymorphs, hydrogen bonding arrangements and molecular conformations, the theoretical predictions succeeded, for all three complexes, in finding the correct hydrogen bonding pattern. For two of the complexes, the calculations also reproduce the exact space group and side chain orientations in the best ranked predicted structure. This includes one complex for which the observed crystal packing clearly contradicted previous experience based on experimental data for a substantial number of related amino acid complexes. The results highlight the significant recent advances that have been made in computational methods for crystal structure prediction.

Using Gas-Phase Guest-Host Chemistry to Probe the Structures of b Ions of Peptides

NASA Astrophysics Data System (ADS)

Somogyi, Árpád; Harrison, Alex G.; Paizs, Béla

2012-12-01

Middle-sized b n ( n ≥ 5) fragments of protonated peptides undergo selective complex formation with ammonia under experimental conditions typically used to probe hydrogen-deuterium exchange in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Other usual peptide fragments like y, a, a*, etc., and small b n ( n ≤ 4) fragments do not form stable ammonia adducts. We propose that complex formation of b n ions with ammonia is characteristic to macrocyclic isomers of these fragments. Experiments on a protonated cyclic peptide and N-terminal acetylated peptides fully support this hypothesis; the protonated cyclic peptide does form ammonia adducts while linear b n ions of acetylated peptides do not undergo complexation. Density functional theory (DFT) calculations on the proton-bound dimers of all-Ala b 4 , b 5 , and b 7 ions and ammonia indicate that the ionizing proton initially located on the peptide fragment transfers to ammonia upon adduct formation. The ammonium ion is then solvated by N+-H…O H-bonds; this stabilization is much stronger for macrocyclic b n isomers due to the stable cage-like structure formed and entropy effects. The present study demonstrates that gas-phase guest-host chemistry can be used to selectively probe structural features (i.e., macrocyclic or linear) of fragments of protonated peptides. Stable ammonia adducts of b 9 , b 9 -A, and b 9 -2A of A8YA, and b 13 of A20YVFL are observed indicating that even these large b-type ions form macrocyclic structures.

Structural characterization of more potent alternatives to HAMLET, a tumoricidal complex of α-lactalbumin and oleic acid.

PubMed

Nemashkalova, Ekaterina L; Kazakov, Alexei S; Khasanova, Leysan M; Permyakov, Eugene A; Permyakov, Sergei E

2013-09-10

HAMLET is a complex of human α-lactalbumin (hLA) with oleic acid (OA) that kills various tumor cells and strains of Streptococcus pneumoniae. More potent protein-OA complexes were previously reported for bovine α-lactalbumin (bLA) and β-lactoglobulin (bLG), and pike parvalbumin (pPA), and here we explore their structural features. The concentration dependencies of the tryptophan fluorescence of hLA, bLA, and bLG complexes with OA reveal their disintegration at protein concentrations below the micromolar level. Chemical cross-linking experiments provide evidence that association with OA shifts the distribution of oligomeric forms of hLA, bLA, bLG, and pPA toward higher-order oligomers. This effect is confirmed for bLA and bLG using the dynamic light scattering method, while pPA is shown to associate with OA vesicles. Like hLA binding, OA binding increases the affinity of bLG for small unilamellar dipalmitoylphosphatidylcholine vesicles, while pPA efficiently binds to the vesicles irrespective of OA binding. The association of OA with bLG and pPA increases their α-helix and cross-β-sheet content and resistance to enzymatic proteolysis, which is indicative of OA-induced protein structuring. The lack of excess heat sorption during melting of bLG and pPA in complex with OA and the presence of a cooperative thermal transition at the level of their secondary structure suggest that the OA-bound forms of bLG and pPA lack a fixed tertiary structure but exhibit a continuous thermal transition. Overall, despite marked differences, the HAMLET-like complexes that were studied exhibit a common feature: a tendency toward protein oligomerization. Because OA-induced oligomerization has been reported for other proteins, this phenomenon is inherent to many proteins.

Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex.

PubMed

Ortega-Roldan, Jose Luis; Jensen, Malene Ringkjøbing; Brutscher, Bernhard; Azuaga, Ana I; Blackledge, Martin; van Nuland, Nico A J

2009-05-01

The description of the interactome represents one of key challenges remaining for structural biology. Physiologically important weak interactions, with dissociation constants above 100 muM, are remarkably common, but remain beyond the reach of most of structural biology. NMR spectroscopy, and in particular, residual dipolar couplings (RDCs) provide crucial conformational constraints on intermolecular orientation in molecular complexes, but the combination of free and bound contributions to the measured RDC seriously complicates their exploitation for weakly interacting partners. We develop a robust approach for the determination of weak complexes based on: (i) differential isotopic labeling of the partner proteins facilitating RDC measurement in both partners; (ii) measurement of RDC changes upon titration into different equilibrium mixtures of partially aligned free and complex forms of the proteins; (iii) novel analytical approaches to determine the effective alignment in all equilibrium mixtures; and (iv) extraction of precise RDCs for bound forms of both partner proteins. The approach is demonstrated for the determination of the three-dimensional structure of the weakly interacting CD2AP SH3-C:Ubiquitin complex (K(d) = 132 +/- 13 muM) and is shown, using cross-validation, to be highly precise. We expect this methodology to extend the remarkable and unique ability of NMR to study weak protein-protein complexes.

Synthesis, characterization, spectroscopic and theoretical studies of new zinc(II), copper(II) and nickel(II) complexes based on imine ligand containing 2-aminothiophenol moiety

NASA Astrophysics Data System (ADS)

Shafaatian, Bita; Mousavi, S. Sedighe; Afshari, Sadegh

2016-11-01

New dimer complexes of zinc(II), copper(II) and nickel(II) were synthesized using the Schiff base ligand which was formed by the condensation of 2-aminothiophenol and 2-hydroxy-5-methyl benzaldehyde. This tridentate Schiff base ligand was coordinated to the metal ions through the NSO donor atoms. In order to prevent the oxidation of the thiole group during the formation of Schiff base and its complexes, all of the reactions were carried out under an inert atmosphere of argon. The X-ray structure of the Schiff base ligand showed that in the crystalline form the SH groups were oxidized to produce a disulfide Schiff base as a new double Schiff base ligand. The molar conductivity values of the complexes in dichloromethane implied the presence of non-electrolyte species. The fluorescence properties of the Schiff base ligand and its complexes were also studied in dichloromethane. The products were characterized by FT-IR, 1H NMR, UV/Vis spectroscopies, elemental analysis, and conductometry. The crystal structure of the double Schiff base was determined by single crystal X-ray diffraction. Furthermore, the density functional theory (DFT) calculations were performed at the B3LYP/6-31G(d,p) level of theory for the determination of the optimized structures of Schiff base complexes.

Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex

PubMed Central

Ortega-Roldan, Jose Luis; Jensen, Malene Ringkjøbing; Brutscher, Bernhard; Azuaga, Ana I.; Blackledge, Martin; van Nuland, Nico A. J.

2009-01-01

The description of the interactome represents one of key challenges remaining for structural biology. Physiologically important weak interactions, with dissociation constants above 100 μM, are remarkably common, but remain beyond the reach of most of structural biology. NMR spectroscopy, and in particular, residual dipolar couplings (RDCs) provide crucial conformational constraints on intermolecular orientation in molecular complexes, but the combination of free and bound contributions to the measured RDC seriously complicates their exploitation for weakly interacting partners. We develop a robust approach for the determination of weak complexes based on: (i) differential isotopic labeling of the partner proteins facilitating RDC measurement in both partners; (ii) measurement of RDC changes upon titration into different equilibrium mixtures of partially aligned free and complex forms of the proteins; (iii) novel analytical approaches to determine the effective alignment in all equilibrium mixtures; and (iv) extraction of precise RDCs for bound forms of both partner proteins. The approach is demonstrated for the determination of the three-dimensional structure of the weakly interacting CD2AP SH3-C:Ubiquitin complex (Kd = 132 ± 13 μM) and is shown, using cross-validation, to be highly precise. We expect this methodology to extend the remarkable and unique ability of NMR to study weak protein–protein complexes. PMID:19359362

The Shape of Literature.

ERIC Educational Resources Information Center

Lansu, Helvi

1965-01-01

The structural analysis of three short stories, arranged to proceed from an elementary to a complex level of form, can illuminate the secondary school student's understanding of literary structure. Representing plot as structure, the basic elements of Richard Connell's "The Most Dangerous Game" can be quickly reviewed to debate and establish the…

Structural characterization and antioxidant properties of Cu(II) and Ni(II) complexes derived from dicyandiamide

NASA Astrophysics Data System (ADS)

Kertmen, Seda Nur; Gonul, Ilyas; Kose, Muhammet

2018-01-01

New Cu(II) and Ni(II) complexes derived from dicyandiamide were synthesized and characterised by spectroscopic and analytical methods. Molecular structures of the complexes were determined by single crystal X-ray diffraction studies. In the complexes, the Cu(II) or Ni(II) ions are four-coordinate with a slight distorted square planar geometry. The ligands (L-nPen and L-iPen) derived from dicyandiamide formed via nucleophilic addition of alcohol solvent molecule in the presence Cu(II) or Ni(II) ions. Complexes were stabilised by intricate array of hydrogen bonding interactions. Antioxidant activity of the complexes was evaluated by DPPH radical scavenging and CUPRAC methods. The complexes exhibit antioxidant activity, however, their activities were much lower than standard antioxidants (Vitamin C and trolox).

Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.

PubMed

Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina; Pellarin, Riccardo; Kim, Seung Joong; Williams, Rosemary; Schneidman-Duhovny, Dina; Sali, Andrej; Rout, Michael P; Chait, Brian T

2014-11-01

Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼ 600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Large Fluorescence Response by Alcohol from a Bis(benzoxazole)-Zinc(II) Complex: The Role of Excited State Intramolecular Proton Transfer

PubMed Central

Wang, Junfeng; Chu, Qinghui; Liu, Xiumin; Wesdemiotis, Chrys

2013-01-01

The formation of a bis(HBO) anion is known to turn-on the fluorescence to give red emission, via controlling the excited-state intramolecular proton transfer (ESIPT). The poor stability of the formed anion, however, hampered its application. The anion stability is found to be greatly improved by attaching the anion to Zn2+ cation (i.e. forming zinc complex), whose emission is at λem ≈ 550 and 760 nm. Interestingly, addition of methanol to the zinc complex induces a remarkable red fluorescence (λem ≈ 630 nm, ϕfl ≈ 0.8). With the aid of spectroscopic studies (1H NMR, UV-vis, fluorescence, and mass spectra), the structures of the zinc complexes are characterized. The emission species is identified as a dimer-like structure. The study thus reveals an effective fluorescence switching mechanism that could further advance the application of ESIPT-based sensors. PMID:23514312

Structural insights into the roles of the IcmS-IcmW complex in the type IVb secretion system of Legionella pneumophila.

PubMed

Xu, Jianpo; Xu, Dandan; Wan, Muyang; Yin, Li; Wang, Xiaofei; Wu, Lijie; Liu, Yanhua; Liu, Xiaoyun; Zhou, Yan; Zhu, Yongqun

2017-12-19

The type IVb secretion system (T4BSS) of Legionella pneumophila is a multiple-component apparatus that delivers ∼300 virulent effector proteins into host cells. The injected effectors modulate host cellular processes to promote bacterial infection and proliferation. IcmS and IcmW are two conserved small, acidic adaptor proteins that form a binary complex to interact with many effectors and facilitate their translocation. IcmS and IcmW can also interact with DotL, an ATPase of the type IV coupling protein complex (T4CP). However, how IcmS-IcmW recognizes effectors, and what the roles of IcmS-IcmW are in T4BSSs are unclear. In this study, we found that IcmS and IcmW form a 1:1 heterodimeric complex to bind effector substrates. Both IcmS and IcmW adopt new structural folds and have no structural similarities with known effector chaperones. IcmS has a compact global structure with an α/β fold, while IcmW adopts a fully α-folded, relatively loose architecture. IcmS stabilizes IcmW by binding to its two C-terminal α-helices. Photocrosslinking assays revealed that the IcmS-IcmW complex binds its cognate effectors via an extended hydrophobic surface, which can also interact with the C terminus of DotL. A crystal structure of the DotL-IcmS-IcmW complex reveals extensive and highly stable interactions between DotL and IcmS-IcmW. Moreover, IcmS-IcmW recruits LvgA to DotL and assembles a unique T4CP. These data suggest that IcmS-IcmW also functions as an inseparable integral component of the DotL-T4CP complex in the bacterial inner membrane. This study provides molecular insights into the dual roles of the IcmS-IcmW complex in T4BSSs.

Transformation of environmental conditions in large former Soviet countries: regional analysis

NASA Astrophysics Data System (ADS)

Bityukova, V. R.; Borovikov, M. S.

2018-01-01

The article studies changes in the structure of environmental conditions of regions in the large former Soviet countries (case study of Russia and Kazakhstan) that have formed considerable contrasts in the placement of industrial complex and population settlement during the previous development stages. The changes related to the transition to market economy have led to essential transformation of environmental conditions. A complex index allowing to assess changes at the regional level in Kazakhstan and Russia and to reveal main similarities and differences between those changes is applied to studying the transformation of regional and industry structure. The article examines both industry-specific and spatial patterns forming environmental conditions at the regional level.

3-D printed composites with ultrasonically arranged complex microstructure

NASA Astrophysics Data System (ADS)

Llewellyn-Jones, Thomas M.; Drinkwater, Bruce W.; Trask, Richard S.

2016-04-01

This paper demonstrates the efficacy of implementing ultrasonic manipulation within a modified form of stereolithographic 3D printing to form complex microstructures in printed components. Currently 3D printed components are limited both in terms of structural performance and specialised functionality. This study aims to demonstrate a novel method for 3D printing composite materials, by arranging microparticles suspended within a photocurable resin. The resin is selectively cured by a 3-axis gantry-mounted 405nm laser. Ultrasonic forces are used to arrange the microfibres into predetermined patterns within the resin, with unidirectional microfibre alignment and a hexagonal lattice structure demonstrated. An example of dynamic microstructure variation within a single print layer is also presented.

Structural investigations of transition metal (II) tetracyanonickelate complexes of 3-chloropyridine using Fourier transform-infrared and laser Raman spectroscopy

NASA Astrophysics Data System (ADS)

Akyüz, Sevim; Akyüz, Tanil; Eric, J.; Davies, D.

1992-01-01

The FT-IR and laser-Raman spectra of five new complexes of the formula ML 2Ni(CN) 4 (where MMn, Fe, Ni, Zn or Cd; L3-chloropyridine) are reported. The complexes are shown to have a structure consisting of two dimensional polymeric layers formed with Ni(CN) 4 ions bridged by ML 2 cations. For a given series of isomorphous complexes, the effects of metal ligand bond formation on the ligand vibrational modes are examined and the metal-sensitivity sequence of the ligand frequencies is found to be Mn≈Cd

Fluid dynamic instabilities: theory and application to pattern forming in complex media

PubMed Central

Brun, P.-T.

2017-01-01

In this review article, we exemplify the use of stability analysis tools to rationalize pattern formation in complex media. Specifically, we focus on fluid flows, and show how the destabilization of their interface sets the blueprint of the patterns they eventually form. We review the potential use and limitations of the theoretical methods at the end, in terms of their applications to practical settings, e.g. as guidelines to design and fabricate structures while harnessing instabilities. This article is part of the themed issue ‘Patterning through instabilities in complex media: theory and applications’. PMID:28373378

Structural determinants for membrane association and dynamic organization of the hepatitis C virus NS3-4A complex

PubMed Central

Brass, Volker; Berke, Jan Martin; Montserret, Roland; Blum, Hubert E.; Penin, François; Moradpour, Darius

2008-01-01

Hepatitis C virus (HCV) NS3-4A is a membrane-associated multifunctional protein harboring serine protease and RNA helicase activities. It is an essential component of the HCV replication complex and a prime target for antiviral intervention. Here, we show that membrane association and structural organization of HCV NS3-4A are ensured in a cooperative manner by two membrane-binding determinants. We demonstrate that the N-terminal 21 amino acids of NS4A form a transmembrane α-helix that may be involved in intramembrane protein–protein interactions important for the assembly of a functional replication complex. In addition, we demonstrate that amphipathic helix α0, formed by NS3 residues 12–23, serves as a second essential determinant for membrane association of NS3-4A, allowing proper positioning of the serine protease active site on the membrane. These results allowed us to propose a dynamic model for the membrane association, processing, and structural organization of NS3-4A on the membrane. This model has implications for the functional architecture of the HCV replication complex, proteolytic targeting of host factors, and drug design. PMID:18799730

Impact of cationic surfactant on the self-assembly of sodium caseinate.

PubMed

Vinceković, Marko; Curlin, Marija; Jurašin, Darija

2014-08-27

The impact of a cationic surfactant, dodecylammonium chloride (DDACl), on the self-assembly of sodium caseinate (SC) has been investigated by light scattering, zeta potential, and rheological measurements as well as by microscopy (transmission electron and confocal laser scanning microscopy). In SC dilute solutions concentration-dependent self-assembly proceeds through the formation of spherical associates and their aggregation into elongated structures composed of connected spheres. DDACl interacts with SC via its hydrophilic and hydrophobic groups, inducing changes in SC self-assembled structures. These changes strongly depend on the surfactant aggregation states (monomeric or micellar) as well as concentration ratio of both components, leading to the formation of soluble and insoluble complexes of nano- to microdimensions. DDACl monomers interact with SC self-assembled entities in a different way compared to their micelles. Surfactant monomers form soluble complexes (similar to surfactant mixed micelles) at lower SC concentration but insoluble gelatinous complexes at higher SC concentration. At surfactant micellar concentration soluble complexes with casein chains wrapped around surfactant micelles are formed. This study suggests that the use of proper cationic surfactant concentration will allow modification and control of structural changes of SC self-assembled entities.

Crystal structure of a complex of HIV-1 protease with a dihydroxyethylene-containing inhibitor: comparisons with molecular modeling.

PubMed Central

Thanki, N.; Rao, J. K.; Foundling, S. I.; Howe, W. J.; Moon, J. B.; Hui, J. O.; Tomasselli, A. G.; Heinrikson, R. L.; Thaisrivongs, S.; Wlodawer, A.

1992-01-01

The structure of a crystal complex of recombinant human immunodeficiency virus type 1 (HIV-1) protease with a peptide-mimetic inhibitor containing a dihydroxyethylene isostere insert replacing the scissile bond has been determined. The inhibitor is Noa-His-Hch psi [CH(OH)CH(OH)]Vam-Ile-Amp (U-75875), and its Ki for inhibition of the HIV-1 protease is < 1.0 nM (Noa = 1-naphthoxyacetyl, Hch = a hydroxy-modified form of cyclohexylalanine, Vam = a hydroxy-modified form of valine, Amp = 2-pyridylmethylamine). The structure of the complex has been refined to a crystallographic R factor of 0.169 at 2.0 A resolution by using restrained least-squares procedures. Root mean square deviations from ideality are 0.02 A and 2.4 degrees, for bond lengths and angles, respectively. The bound inhibitor diastereomer has the R configurations at both of the hydroxyl chiral carbon atoms. One of the diol hydroxyl groups is positioned such that it forms hydrogen bonds with both the active site aspartates, whereas the other interacts with only one of them. Comparison of this X-ray structure with a model-built structure of the inhibitor, published earlier, reveals similar positioning of the backbone atoms and of the side-chain atoms in the P2-P2' region, where the interaction with the protein is strongest. However, the X-ray structure and the model differ considerably in the location of the P3 and P3' end groups, and also in the positioning of the second of the two central hydroxyl groups. Reconstruction of the central portion of the model revealed the source of the hydroxyl discrepancy, which, when corrected, provided a P1-P1' geometry very close to that seen in the X-ray structure. PMID:1304383

Studies of Toxoplasma gondii and Plasmodium falciparum enoyl acyl carrier protein reductase and implications for the development of antiparasitic agents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muench, Stephen P.; Prigge, Sean T.; McLeod, Rima

2007-03-01

The crystal structures of T. gondii and P. falciparum ENR in complex with NAD{sup +} and triclosan and of T. gondii ENR in an apo form have been solved to 2.6, 2.2 and 2.8 Å, respectively. Recent studies have demonstrated that submicromolar concentrations of the biocide triclosan arrest the growth of the apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii and inhibit the activity of the apicomplexan enoyl acyl carrier protein reductase (ENR). The crystal structures of T. gondii and P. falciparum ENR in complex with NAD{sup +} and triclosan and of T. gondii ENR in an apo form have beenmore » solved to 2.6, 2.2 and 2.8 Å, respectively. The structures of T. gondii ENR have revealed that, as in its bacterial and plant homologues, a loop region which flanks the active site becomes ordered upon inhibitor binding, resulting in the slow tight binding of triclosan. In addition, the T. gondii ENR–triclosan complex reveals the folding of a hydrophilic insert common to the apicomplexan family that flanks the substrate-binding domain and is disordered in all other reported apicomplexan ENR structures. Structural comparison of the apicomplexan ENR structures with their bacterial and plant counterparts has revealed that although the active sites of the parasite enzymes are broadly similar to those of their bacterial counterparts, there are a number of important differences within the drug-binding pocket that reduce the packing interactions formed with several inhibitors in the apicomplexan ENR enzymes. Together with other significant structural differences, this provides a possible explanation of the lower affinity of the parasite ENR enzyme family for aminopyridine-based inhibitors, suggesting that an effective antiparasitic agent may well be distinct from equivalent antimicrobials.« less

Structure and reactivity of oxalate surface complexes on lepidocrocite derived from infrared spectroscopy, DFT-calculations, adsorption, dissolution and photochemical experiments

NASA Astrophysics Data System (ADS)

Borowski, Susan C.; Biswakarma, Jagannath; Kang, Kyounglim; Schenkeveld, Walter D. C.; Hering, Janet G.; Kubicki, James D.; Kraemer, Stephan M.; Hug, Stephan J.

2018-04-01

Oxalate, together with other ligands, plays an important role in the dissolution of iron(hdyr)oxides and the bio-availability of iron. The formation and properties of oxalate surface complexes on lepidocrocite were studied with a combination of infrared spectroscopy (IR), density functional theory (DFT) calculations, dissolution, and photochemical experiments. IR spectra measured as a function of time, concentration, and pH (50-200 μM oxalate, pH 3-7) showed that several surface complexes are formed at different rates and in different proportions. Measured spectra could be separated into three contributions described by Gaussian line shapes, with frequencies that agreed well with the theoretical frequencies of three different surface complexes: an outer-sphere complex (OS), an inner-sphere monodentate mononuclear complex (MM), and a bidentate mononuclear complex (BM) involving one O atom from each carboxylate group. At pH 6, OS was formed at the highest rate. The contribution of BM increased with decreasing pH. In dissolution experiments, lepidocrocite was dissolved at rates proportional to the surface concentration of BM, rather than to the total adsorbed concentration. Under UV-light (365 nm), BM was photolyzed at a higher rate than MM and OS. Although the comparison of measured spectra with calculated frequencies cannot exclude additional possible structures, the combined results allowed the assignment of three main structures with different reactivities consistent with experiments. The results illustrate the importance of the surface speciation of adsorbed ligands in dissolution and photochemical reactions.

An example of complex modelling in dentistry using Markov chain Monte Carlo (MCMC) simulation.

PubMed

Helfenstein, Ulrich; Menghini, Giorgio; Steiner, Marcel; Murati, Francesca

2002-09-01

In the usual regression setting one regression line is computed for a whole data set. In a more complex situation, each person may be observed for example at several points in time and thus a regression line might be calculated for each person. Additional complexities, such as various forms of errors in covariables may make a straightforward statistical evaluation difficult or even impossible. During recent years methods have been developed allowing convenient analysis of problems where the data and the corresponding models show these and many other forms of complexity. The methodology makes use of a Bayesian approach and Markov chain Monte Carlo (MCMC) simulations. The methods allow the construction of increasingly elaborate models by building them up from local sub-models. The essential structure of the models can be represented visually by directed acyclic graphs (DAG). This attractive property allows communication and discussion of the essential structure and the substantial meaning of a complex model without needing algebra. After presentation of the statistical methods an example from dentistry is presented in order to demonstrate their application and use. The dataset of the example had a complex structure; each of a set of children was followed up over several years. The number of new fillings in permanent teeth had been recorded at several ages. The dependent variables were markedly different from the normal distribution and could not be transformed to normality. In addition, explanatory variables were assumed to be measured with different forms of error. Illustration of how the corresponding models can be estimated conveniently via MCMC simulation, in particular, 'Gibbs sampling', using the freely available software BUGS is presented. In addition, how the measurement error may influence the estimates of the corresponding coefficients is explored. It is demonstrated that the effect of the independent variable on the dependent variable may be markedly underestimated if the measurement error is not taken into account ('regression dilution bias'). Markov chain Monte Carlo methods may be of great value to dentists in allowing analysis of data sets which exhibit a wide range of different forms of complexity.

Self-equilibrated Tapered Three-stage Tensegrity Mast

NASA Astrophysics Data System (ADS)

Oh, C. L.; Choong, K. K.; Nishimura, T.; Lee, S. W.

2018-04-01

Investigation of tensegrity structures for the space application is ongoing owing to the characteristics of being lightweight and flexible. Tensegrity structures consist of struts and cables are self-stressed and stable under gravitational loading. Form-finding is an important process to obtain the configuration of tensegrity structures that are in self-equilibrated state. Form-finding of tensegrity structures involves a complex computational strategy in solving the geometrical and forces of the structures. This paper aims to form-finding for a tapered three-stage tensegrity mast. The form-finding strategy involves the assemblage of the tensegrity mast, establishment of equilibrium equations and determination of one possible set of coefficient beta. Several cases of configurations with various twist angles with range of 20°-40° are investigated. A configuration with 9 struts and 42 cables satisfying the material elastic conditions was successfully found. The scalable self-equilibrated tensegrity mast is recommended for space applications.

[Three dimensional mathematical model of tooth for finite element analysis].

PubMed

Puskar, Tatjana; Vasiljević, Darko; Marković, Dubravka; Jevremović, Danimir; Pantelić, Dejan; Savić-Sević, Svetlana; Murić, Branka

2010-01-01

The mathematical model of the abutment tooth is the starting point of the finite element analysis of stress and deformation of dental structures. The simplest and easiest way is to form a model according to the literature data of dimensions and morphological characteristics of teeth. Our method is based on forming 3D models using standard geometrical forms (objects) in programmes for solid modeling. Forming the mathematical model of abutment of the second upper premolar for finite element analysis of stress and deformation of dental structures. The abutment tooth has a form of a complex geometric object. It is suitable for modeling in programs for solid modeling SolidWorks. After analysing the literature data about the morphological characteristics of teeth, we started the modeling dividing the tooth (complex geometric body) into simple geometric bodies (cylinder, cone, pyramid,...). Connecting simple geometric bodies together or substricting bodies from the basic body, we formed complex geometric body, tooth. The model is then transferred into Abaqus, a computational programme for finite element analysis. Transferring the data was done by standard file format for transferring 3D models ACIS SAT. Using the programme for solid modeling SolidWorks, we developed three models of abutment of the second maxillary premolar: the model of the intact abutment, the model of the endodontically treated tooth with two remaining cavity walls and the model of the endodontically treated tooth with two remaining walls and inserted post. Mathematical models of the abutment made according to the literature data are very similar with the real abutment and the simplifications are minimal. These models enable calculations of stress and deformation of the dental structures. The finite element analysis provides useful information in understanding biomechanical problems and gives guidance for clinical research.

Fungal prion HET-s as a model for structural complexity and self-propagation in prions.

PubMed

Wan, William; Stubbs, Gerald

2014-04-08

The highly ordered and reproducible structure of the fungal prion HET-s makes it an excellent model system for studying the inherent properties of prions, self-propagating infectious proteins that have been implicated in a number of fatal diseases. In particular, the HET-s prion-forming domain readily folds into a relatively complex two-rung β-solenoid amyloid. The faithful self-propagation of this fold involves a diverse array of inter- and intramolecular structural features. These features include a long flexible loop connecting the two rungs, buried polar residues, salt bridges, and asparagine ladders. We have used site-directed mutagenesis and X-ray fiber diffraction to probe the relative importance of these features for the formation of β-solenoid structure, as well as the cumulative effects of multiple mutations. Using fibrillization kinetics and chemical stability assays, we have determined the biophysical effects of our mutations on the assembly and stability of the prion-forming domain. We have found that a diversity of structural features provides a level of redundancy that allows robust folding and stability even in the face of significant sequence alterations and suboptimal environmental conditions. Our findings provide fundamental insights into the structural interactions necessary for self-propagation. Propagation of prion structure seems to require an obligatory level of complexity that may not be reproducible in short peptide models.

Nanostructures formed by cyclodextrin covered procainamide through supramolecular self assembly - Spectral and molecular modeling study

NASA Astrophysics Data System (ADS)

Rajendiran, N.; Mohandoss, T.; Sankaranarayanan, R. K.

2015-02-01

Inclusion complexation behavior of procainamide (PCA) with two cyclodextrins (α-CD and β-CD) were analyzed by absorption, fluorescence, scanning electron microscope (SEM), transmission electron microscope (TEM), Raman image, FT-IR, differential scanning colorimeter (DSC), Powder X ray diffraction (XRD) and 1H NMR. Blue shift was observed in β-CD whereas no significant spectral shift observed in α-CD. The inclusion complex formation results suggest that water molecules also present in the inside of the CD cavity. The present study revealed that the phenyl ring of the PCA drug is entrapped in the CD cavity. Cyclodextrin studies show that PCA forms 1:2 inclusion complex with α-CD and β-CD. PCA:α-CD complex form nano-sized particles (46 nm) and PCA:β-CD complex form self-assembled to micro-sized tubular structures. The shape-shifting of 2D nanosheets into 1D microtubes by simple rolling mechanism were analysed by micro-Raman and TEM images. Thermodynamic parameters (ΔH, ΔG and ΔS) of inclusion process were determined from semiempirical PM3 calculations.

Synthesis, structural studies and antimicrobial activity of N'-((2Z, 3E)-3-(hydroxyimino)butan-2-ylidene)-2-phenylacetohydrazide and its Co(II), Ni(II) complexes

NASA Astrophysics Data System (ADS)

Karadeniz, Şeyma; Ataol, Cigdem Yuksektepe; Şahin, Onur; İdil, Önder; Bati, Hümeyra

2018-06-01

A new aroylhydrazoneoxime, N'-((2Z, 3E)-3-(hydroxyimino)butan-2-ylidene)-2-phenylacetohydrazide ligand (LH2) and its Ni(II) and Co(II) complexes, have been synthesized and characterized by elemental and thermal analyses, IR and UV-vis spectroscopy, magnetic moment and X-ray diffraction. The antimicrobial activities of these compounds were tested by using minimal inhibitory concentration method (MIC). The ligand-containing aroylhydrazone and oxime groups and its Ni complex crystallize in the triclinic system and P 1 - space group, while its Co complex crystallizes in the monoclinic system and the C 2/c space group. X-ray results show that the ligand in the keto form is transformed into enolic form when it forms coordination. From elemental analysis data, the stoichiometry of Co(II) complex was found to be 1:2 (metal/ligand), but 1:1 for Ni(II). IR spectra indicate that the ligand acts as monoanionic NNO- tridentate and coordination takes place form through the oxime nitrogen, imine nitrogen, and enolate oxygen atoms.

The conservation and function of RNA secondary structure in plants

PubMed Central

Vandivier, Lee E.; Anderson, Stephen J.; Foley, Shawn W.; Gregory, Brian D.

2016-01-01

RNA transcripts fold into secondary structures via intricate patterns of base pairing. These secondary structures impart catalytic, ligand binding, and scaffolding functions to a wide array of RNAs, forming a critical node of biological regulation. Among their many functions, RNA structural elements modulate epigenetic marks, alter mRNA stability and translation, regulate alternative splicing, transduce signals, and scaffold large macromolecular complexes. Thus, the study of RNA secondary structure is critical to understanding the function and regulation of RNA transcripts. Here, we review the origins, form, and function of RNA secondary structure, focusing on plants. We then provide an overview of methods for probing secondary structure, from physical methods such as X-ray crystallography and nuclear magnetic resonance imaging (NMR) to chemical and nuclease probing methods. Marriage with high-throughput sequencing has enabled these latter methods to scale across whole transcriptomes, yielding tremendous new insights into the form and function of RNA secondary structure. PMID:26865341

Atomic structure and hierarchical assembly of a cross-β amyloid fibril

PubMed Central

Fitzpatrick, Anthony W. P.; Debelouchina, Galia T.; Bayro, Marvin J.; Clare, Daniel K.; Caporini, Marc A.; Bajaj, Vikram S.; Jaroniec, Christopher P.; Wang, Luchun; Ladizhansky, Vladimir; Müller, Shirley A.; MacPhee, Cait E.; Waudby, Christopher A.; Mott, Helen R.; De Simone, Alfonso; Knowles, Tuomas P. J.; Saibil, Helen R.; Vendruscolo, Michele; Orlova, Elena V.; Griffin, Robert G.; Dobson, Christopher M.

2013-01-01

The cross-β amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of β-sheet filaments. These complex aggregates have remarkable chemical and physical properties, and the conversion of normally soluble functional forms of proteins into amyloid structures is linked to many debilitating human diseases, including several common forms of age-related dementia. Despite their importance, however, cross-β amyloid fibrils have proved to be recalcitrant to detailed structural analysis. By combining structural constraints from a series of experimental techniques spanning five orders of magnitude in length scale—including magic angle spinning nuclear magnetic resonance spectroscopy, X-ray fiber diffraction, cryoelectron microscopy, scanning transmission electron microscopy, and atomic force microscopy—we report the atomic-resolution (0.5 Å) structures of three amyloid polymorphs formed by an 11-residue peptide. These structures reveal the details of the packing interactions by which the constituent β-strands are assembled hierarchically into protofilaments, filaments, and mature fibrils. PMID:23513222

TelAP1 links telomere complexes with developmental expression site silencing in African trypanosomes

PubMed Central

Reis, Helena; Schwebs, Marie; Dietz, Sabrina; Janzen, Christian J; Butter, Falk

2018-01-01

Abstract During its life cycle, Trypanosoma brucei shuttles between a mammalian host and the tsetse fly vector. In the mammalian host, immune evasion of T. brucei bloodstream form (BSF) cells relies on antigenic variation, which includes monoallelic expression and periodic switching of variant surface glycoprotein (VSG) genes. The active VSG is transcribed from only 1 of the 15 subtelomeric expression sites (ESs). During differentiation from BSF to the insect-resident procyclic form (PCF), the active ES is transcriptionally silenced. We used mass spectrometry-based interactomics to determine the composition of telomere protein complexes in T. brucei BSF and PCF stages to learn more about the structure and functions of telomeres in trypanosomes. Our data suggest a different telomere complex composition in the two forms of the parasite. One of the novel telomere-associated proteins, TelAP1, forms a complex with telomeric proteins TbTRF, TbRAP1 and TbTIF2 and influences ES silencing kinetics during developmental differentiation. PMID:29385523

A family of silver(I) complexes built with 2-sulfoterephthalic acid monosodium salt and different aminopyridine ligands: Syntheses, structures and properties

NASA Astrophysics Data System (ADS)

Zhang, Jie; Tan, Gai-Xiu; Liu, Bao-Lin; Dai, Yu-Bei; Xu, Na; Wen, Wei-Fen; Cao, Chong; Xiao, Hong-Ping

2017-05-01

Five Ag(I) coordination complexes, namely, [Ag6(2-stp)2(3-methyl-2-apy)3·H2O]n (1), [Ag3(2-stp)(4-methyl-2-apy)3]n (2), [Na2Ag18(2-stp)4(2-Hstp)4(5-methyl-2-apy)16 (H2O)4·11H2O]n (3), Ag3(2-stp)(6-methy-2-apy)4·H2O (4), and [Ag6(2-stp)2(6-methyl-2-apy)8(H2O)2·H2O]n (5) (2-NaH2stp = 2-sulfoterephthalic acid monosodium salt, 3-methyl-2-apy = 3-methyl-2-aminopyridine, 4-methyl-2-apy = 4-methyl-2-aminopyridine, 5-methyl-2-apy = 5-methyl-2-aminopyridine, 6-methyl-2-apy = 6-methyl-2-aminopyridine), have been synthesized and structurally characterized. Complexes 1 and 2 show two-dimensional network. In complex 3, the adjacent Ag10 units are bridged by 5-methyl-2-apy ligands to form a 2D infinite undulated sheet. Adjacent 2D sheets are linked by coordinative bonds between carboxylic oxygen atoms and Na(I) ions to form a 3D coordination polymer. Complex 4 is a 0-D discrete trinuclear molecule, and the self-complementary the Osbnd H⋯O and Nsbnd H⋯O hydrogen bonds incorporating hydrogen bond motifs extend these molecules into a 2D supramolecular framework. Compound 5 exhibits 1D-chain structure. However, complex 5 shows 3D supramolecular structure results from the linkage of neighboring layers through a rich hydrogen-bonding between uncoordinated sulfonates, amino groups and coordinated carboxylates. The thermogravimetric analyses and photoluminescence of the complexes were also investigated.

A Comparison of Prose and Algorithms for Presenting Complex Instructions. Document Design Project, Technical Report No. 17.

ERIC Educational Resources Information Center

Holland, V. Melissa; Rose, Andrew

Complex conditional instructions ("if X, then do Y") are prevalent in public documents, where they typically appear in prose form. Results of two previous studies have shown that conditional instructions become very difficult to process as the structure becomes more complex. A study was designed to investigate whether this difficulty can…

Structural and functional organization of the ESCRT-I trafficking complex

PubMed Central

Kostelansky, Michael S.; Sun, Ji; Lee, Sangho; Kim, Jaewon; Ghirlando, Rodolfo; Hierro, Aitor; Emr, Scott D.; Hurley, James H.

2006-01-01

Summary The Endosomal Sorting Complex Required for Transport (ESCRT) complexes are central to receptor downregulation, lysosome biogenesis, and budding of HIV. The yeast ESCRT-I complex contains the Vps23, Vps28, and Vps37 proteins and its assembly is directed by the C-terminal steadiness box of Vps23, the N-terminal half of Vps28, and the C-terminal half of Vps37. The crystal structures of a Vps23:Vps28 core subcomplex and the Vps23:Vps28:Vps37 core were solved at 2.1 and 2.8 Å resolution. Each subunit contains a structurally similar pair of helices that form the core. The N-terminal domain of Vps28 has a hydrophobic binding site on its surface that is conformationally dynamic. The C-terminal domain of Vps28 binds the ESCRT-II complex. The structure shows how ESCRT-I is assembled by a compact core from which the Vps23 UEVdomain, the Vps28 C-domain, and other domains project to bind their partners. PMID:16615894

Highly Luminescent, Water-Soluble Lanthanide Fluorobenzoates: Syntheses, Structures and Photophysics, Part I: Lanthanide Pentafluorobenzoates.

PubMed

Kalyakina, Alena S; Utochnikova, Valentina V; Bushmarinov, Ivan S; Ananyev, Ivan V; Eremenko, Igor L; Volz, Daniel; Rönicke, Franziska; Schepers, Ute; Van Deun, Rik; Trigub, Alexander L; Zubavichus, Yan V; Kuzmina, Natalia P; Bräse, Stefan

2015-12-01

Highly luminescent, photostable, and soluble lanthanide pentafluorobenzoates have been synthesized and thoroughly characterized, with a focus on Eu(III) and Tb(III) complexes as visible emitters and Nd(III) , Er(III) , and Yb(III) complexes as infrared emitters. Investigation of the crystal structures of the complexes in powder form and as single crystals by using X-ray diffraction revealed five different structural types, including monomeric, dimeric, and polymeric. The local structure in different solutions was studied by using X-ray absorption spectroscopy. The photoluminescence quantum yields (PLQYs) of terbium and europium complexes were 39 and 15 %, respectively; the latter value was increased almost twice by using the heterometallic complex [Tb0.5 Eu0.5 (pfb)3 (H2 O)] (Hpfb=pentafluorobenzoic acid). Due to the effectively utilized sensitization strategy (pfb)(-) →Tb→Eu, a pure europium luminescence with a PLQY of 29 % was achieved. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure and Function of p97 and Pex1/6 Type II AAA+ Complexes.

PubMed

Saffert, Paul; Enenkel, Cordula; Wendler, Petra

2017-01-01

Protein complexes of the Type II AAA+ (ATPases associated with diverse cellular activities) family are typically hexamers of 80-150 kDa protomers that harbor two AAA+ ATPase domains. They form double ring assemblies flanked by associated domains, which can be N-terminal, intercalated or C-terminal to the ATPase domains. Most prominent members of this family include NSF (N-ethyl-maleimide sensitive factor), p97/VCP (valosin-containing protein), the Pex1/Pex6 complex and Hsp104 in eukaryotes and ClpB in bacteria. Tremendous efforts have been undertaken to understand the conformational dynamics of protein remodeling type II AAA+ complexes. A uniform mode of action has not been derived from these works. This review focuses on p97/VCP and the Pex1/6 complex, which both structurally remodel ubiquitinated substrate proteins. P97/VCP plays a role in many processes, including ER- associated protein degradation, and the Pex1/Pex6 complex dislocates and recycles the transport receptor Pex5 from the peroxisomal membrane during peroxisomal protein import. We give an introduction into existing knowledge about the biochemical and cellular activities of the complexes before discussing structural information. We particularly emphasize recent electron microscopy structures of the two AAA+ complexes and summarize their structural differences.

Structural, spectral analysis and DNA studies of heterocyclic thiosemicarbazone ligand and its Cr(III), Fe(III), Co(II) Hg(II), and U(VI) complexes

NASA Astrophysics Data System (ADS)

Yousef, T. A.; Abu El-Reash, G. M.; El Morshedy, R. M.

2013-08-01

The paper presents a combined experimental and computational study of novel Cr(III), Fe(III), Co(II), Hg(II) and U(VI) complexes of (E)-2-((3-hydroxynaphthalen-2-yl)methylene)-N-(pyridin-2-yl)hydrazinecarbothioamide (H2L). The ligand and its complexes have been characterized by elemental analyses, spectral (IR, UV-vis, 1H NMR and 13C NMR), magnetic and thermal studies. IR spectra show that H2L is coordinated to the metal ions in a mononegative bi or tri manner. The structures are suggested to be octahedral for all complexes except Hg(II) complex is tetrahedral. Theoretical calculations have been performed to obtain IR spectra of ligand and its complexes using AM1, MM, Zindo/1, MM+ and PM3, methods. Satisfactory theoretical-experimental agreements were achieved by MM method for the ligand and PM3 for its complexes. DOS calculations carried out by MM (ADF) method for ligand Hg complex from which we concluded that the thiol form of the ligand is more active than thione form and this explains that the most complexation take place in that form. The calculated IR vibrations of the metal complexes, using the PM3 method was the nearest method for the experimental data, and it could be used for all complexes. Also, valuable information are obtained from calculation of molecular parameters for all compounds carried out by the previous methods of calculation (electronegativity of the coordination sites, net dipole moment of the metal complexes, values of heat of formation and binding energy) which approved that the complexes are more stable than ligand. The low value of ΔE could be expected to indicate H2L molecule has high inclination to bind with the metal ions. Furthermore, the kinetic and thermodynamic parameters for the different decomposition steps were calculated using the Coats-Redfern and Horowitz-Metzger methods. Finally, the biochemical studies showed that, complex 2, 4 have powerful and complete degradation effect on DNA. For the foremost majority of cases the activity of the ligand is greatly enhanced by the presence of a metal ion. Thus presented results may be useful in design new more active or specific structures.

Syntheses, crystal structures and magnetic properties of complexes based on [Ni(L-L)3]2+ complex cations with dimethylderivatives of 2,2‧-bipyridine and TCNQ

NASA Astrophysics Data System (ADS)

Černák, Juraj; Hegedüs, Michal; Váhovská, Lucia; Kuchár, Juraj; Šoltésová, Daniela; Čižmár, Erik; Feher, Alexander; Falvello, L. R.

2018-03-01

From the aqueous-methanolic systems Ni(NO3)2 - LiTCNQ - 5,5‧-dmbpy and Ni(NO3)2 - LiTCNQ - 4,4‧-dmbpy three novel complexes [Ni(5,5‧-dmbpy)3](TCNQ)2 (1), [Ni(4,4‧-dmbpy)3](TCNQ)2 (2) and [Ni(4,4‧-dmbpy)3]2(TCNQ-TCNQ)(TCNQ)2•0.60H2O (3), were isolated in single crystal form. The new compounds were identified using chemical analyses and IR spectroscopy. Single crystal studies of all samples corroborated their compositions and have shown that their ionic structures contain the complex cations [Ni(5,5‧-dmbpy)]2+ (1) or [Ni(4,4‧-dmbpy)]2+ (2 and 3). The anionic parts of the respective crystal structures 1-3 are formed by TCNQṡ- anion-radicals and in 3 also by a σ-dimerized dianion (TCNQ-TCNQ)2- with a C-C distance of 1.663(5) Å. The supramolecular structures are governed by weak hydrogen bonding interactions. The variable-temperature (2-300 K) magnetic studies of 1 and 3 confirmed the presence of magnetically active Ni(II) atoms with S = 1 and TCNQṡ- anion-radicals with S = 1/2 while the (TCNQ-TCNQ)2- dianion is magnetically silent. The magnetic behavior was described by a complex magnetic model assuming strong antiferromagnetic interactions between some TCNQṡ- anion-radicals.

Structural Insights into the Assembly of the Adeno-associated Virus Type 2 Rep68 Protein on the Integration Site AAVS1*

PubMed Central

Musayev, Faik N.; Zarate-Perez, Francisco; Bishop, Clayton; Burgner, John W.; Escalante, Carlos R.

2015-01-01

Adeno-associated virus (AAV) is the only eukaryotic virus with the property of establishing latency by integrating site-specifically into the human genome. The integration site known as AAVS1 is located in chromosome 19 and contains multiple GCTC repeats that are recognized by the AAV non-structural Rep proteins. These proteins are multifunctional, with an N-terminal origin-binding domain (OBD) and a helicase domain joined together by a short linker. As a first step to understand the process of site-specific integration, we proceeded to characterize the recognition and assembly of Rep68 onto the AAVS1 site. We first determined the x-ray structure of AAV-2 Rep68 OBD in complex with the AAVS1 DNA site. Specificity is achieved through the interaction of a glycine-rich loop that binds the major groove and an α-helix that interacts with a downstream minor groove on the same face of the DNA. Although the structure shows a complex with three OBD molecules bound to the AAVS1 site, we show by using analytical centrifugation and electron microscopy that the full-length Rep68 forms a heptameric complex. Moreover, we determined that a minimum of two direct repeats is required to form a stable complex and to melt DNA. Finally, we show that although the individual domains bind DNA poorly, complex assembly requires oligomerization and cooperation between its OBD, helicase, and the linker domains. PMID:26370092

Interpolymer complexation: comparisons of bulk and interfacial structures.

PubMed

Cattoz, Beatrice; de Vos, Wiebe M; Cosgrove, Terence; Crossman, Martin; Espidel, Youssef; Prescott, Stuart W

2015-04-14

The interactions between the strong polyelectrolyte sodium poly(styrenesulfonate), NaPSS, and the neutral polymer poly(vinylpyrrolidone), PVP, were investigated in bulk and at the silica/solution interface using a combination of diffusion nuclear magnetic resonance spectroscopy (NMR), small-angle neutron scattering (SANS), solvent relaxation NMR, and ellipsometry. We show for the first time that complex formation occurs between NaPSS and PVP in solution; the complexes formed were shown not to be influenced by pH variation, whereas increasing the ionic strength increases the complexation of NaPSS but does not influence the PVP directly. The complexes formed contained a large proportion of NaPSS. Study of these interactions at the silica interface demonstrated that complexes also form at the nanoparticle interface where PVP is added in the system prior to NaPSS. For a constant PVP concentration and varying NaPSS concentration, the system remains stable until NaPSS is added in excess, which leads to depletion flocculation. Surface complex formation using the layer-by-layer technique was also reported at a planar silica interface.

Zinc(II) complexes with heterocyclic ether, acid and amide. Crystal structure, spectral, thermal and antibacterial activity studies

NASA Astrophysics Data System (ADS)

Jabłońska-Wawrzycka, Agnieszka; Rogala, Patrycja; Czerwonka, Grzegorz; Hodorowicz, Maciej; Stadnicka, Katarzyna

2016-02-01

The reaction of zinc salts with heterocyclic ether (1-ethoxymethyl-2-methylimidazole (1-ExMe-2-MeIm)), acid (pyridine-2,3-dicarboxylic acid (2,3-pydcH2)) and amide (3,5-dimethylpyrazole-1-carboxamide (3,5-DMePzCONH2)) yielded three new zinc complexes formulated as [Zn(1-ExMe-2-MeIm)2Cl2] 1, fac-[Zn(H2O)6][Zn(2,3-pydcH)3]22 and [Zn(3,5-DMePz)2(NCO)2] 3. Complexes of 1 and 3 are four-coordinated with a tetrahedron as coordination polyhedron. However, compound 2 forms an octahedral cation-anion complex. The complex 3 was prepared by eliminating of the carboxamide group from the ligand and then the 3,5-dimethylpyrazole (3,5-DMePz) and isocyanates formed were employed as new ligands. The IR and X-ray studies have confirmed a bidentate fashion of coordination of the 2,3-pydcH and monodentate fashion of coordination of the 1-ExMe-2-MeIm and 3,5-DMePz to the Zn(II) ions. The crystal packing of Zn(II) complexes are stabilized by intermolecular classical hydrogen bonds of O-H⋯O and N-H⋯O types. The most interesting feature of the supramolecular architecture of complexes is the existence of C-H⋯O, C-H⋯Cl and C-H⋯π interactions and π⋯π stacking, which also contributes to structural stabilisation. The correlation between crystal structure and thermal stability of zinc complexes is observed. In all compounds the fragments of ligands donor-atom containing go in the last steps. Additionally, antimicrobial activities of compounds were carried out against certain Gram-positive and Gram-negative bacteria and counts of CFU (colony forming units) were also determined. The achieved results confirmed a significant antibacterial activity of some tested zinc complexes. On the basis of the Δ log CFU values the antibacterial activity of zinc complexes follows the order: 3 > 2 > 1. Influence a number of N-donor atoms in zinc environment on antibacterial activity is also observed.

Assembly of Reconfigurable Colloidal Structures by Multidirectional Field-Induced Interactions.

PubMed

Bharti, Bhuvnesh; Velev, Orlin D

2015-07-28

Field-directed colloidal assembly has shown remarkable recent progress in increasing the complexity, degree of control, and multiscale organization of the structures. This has largely been achieved by using particles of complex shapes and polarizabilites (Janus, patchy, shaped, and faceted). We review the fundamentals of the interactions leading to the directed assembly of such structures, the ways to simulate the dynamics of the process, and the effect of particle size, shape, and properties on the type of structure obtained. We discuss how directional polarization interactions induced by external electric and magnetic fields can be used to assemble complex particles or particle mixtures into lattices of tailored structure. Examples of such systems include isotropic and anisotropic shaped particles with surface patches, which form networks and crystals of unusual symmetry by dipolar, quadrupolar, and multipolar interactions in external fields. The emerging trends in making reconfigurable and dynamic structures are discussed.

Photochemistry of formaldoxime−nitrous acid complexes in an argon matrix: identification of formaldoxime nitrite.

PubMed

Golec, Barbara; Bil, Andrzej; Mielke, Zofia

2009-08-27

We have studied the structure and photochemistry of the formaldoxime−nitrous acid system (CH2NOH−HONO) by help of FTIR matrix isolation spectroscopy and ab initio methods. The MP2/6-311++G(2d,2p) calculations show stability of six isomeric CH2NOH···HONO complexes. The FTIR spectra evidence formation of two hydrogen bonded complexes in an argon matrix whose structures are determined by comparison of the experimental spectra with the calculated ones for the six stable complexes. In the matrix there is present the most stable cyclic complex with two O−H···N bonds; a strong bond is formed between the OH group of HONO and the N atom of CH2NOH and the weaker one between the OH group of CH2NOH and the N atom of HONO. In the other complex present in the matrix the OH group of formaldoxime is attached to the OH group of HONO forming an O−H···O bond. The irradiation of the CH2NOH···HONO complexes with the filtered output of the mercury lamp (λ > 345 nm) leads to the formation of formaldoxime nitrite, CH2NONO, and its two isomeric complexes with water. The main product is the CH2NONO···H2O complex in which water is hydrogen bonded to the N atom of the C═N group. The identity of the photoproducts is confirmed by both FTIR spectroscopy and MP2 or QCISD(full) calculations with the 6-311++G(2d,2p) basis set. The intermediate in this reaction is iminoxyl radical that is formed by abstraction of hydrogen atom from formaldoxime OH group by an OH radical originating from HONO photolysis.

Structural transitions and guest/host complexing of liquid crystal helical nanofilaments induced by nanoconfinement.

PubMed

Kim, Hanim; Ryu, Seong Ho; Tuchband, Michael; Shin, Tae Joo; Korblova, Eva; Walba, David M; Clark, Noel A; Yoon, Dong Ki

2017-02-01

A lamellar liquid crystal (LC) phase of certain bent-core mesogenic molecules can be grown in a manner that generates a single chiral helical nanofilament in each of the cylindrical nanopores of an anodic aluminum oxide (AAO) membrane. By introducing guest molecules into the resulting composite chiral nanochannels, we explore the structures and functionality of the ordered guest/host LC complex, verifying the smectic-like positional order of the fluidic nematic LC phase, which is obtained by the combination of the LC organization and the nanoporous AAO superstructure. The guest nematic LC 4'- n -pentyl-4-cyanobiphenyl is found to form a distinctive fluid layered ordered LC complex at the nanofilament/guest interface with the host 1,3-phenylene bis[4-(4-nonyloxyphenyliminomethyl)benzoate], where this interface contacts the AAO cylinder wall. Filament growth form is strongly influenced by mixture parameters and pore dimensions.

Membranes linked by trans-SNARE complexes require lipids prone to non-bilayer structure for progression to fusion.

PubMed

Zick, Michael; Stroupe, Christopher; Orr, Amy; Douville, Deborah; Wickner, William T

2014-01-01

Like other intracellular fusion events, the homotypic fusion of yeast vacuoles requires a Rab GTPase, a large Rab effector complex, SNARE proteins which can form a 4-helical bundle, and the SNARE disassembly chaperones Sec17p and Sec18p. In addition to these proteins, specific vacuole lipids are required for efficient fusion in vivo and with the purified organelle. Reconstitution of vacuole fusion with all purified components reveals that high SNARE levels can mask the requirement for a complex mixture of vacuole lipids. At lower, more physiological SNARE levels, neutral lipids with small headgroups that tend to form non-bilayer structures (phosphatidylethanolamine, diacylglycerol, and ergosterol) are essential. Membranes without these three lipids can dock and complete trans-SNARE pairing but cannot rearrange their lipids for fusion. DOI: http://dx.doi.org/10.7554/eLife.01879.001.

Gel Phase Formation in Dilute Triblock Copolyelectrolyte Complexes

NASA Astrophysics Data System (ADS)

Srivastava, Samanvaya; Andreev, Marat; Prabhu, Vivek; de Pablo, Juan; Tirrell, Matthew

Assembly of oppositely charged triblock copolyelectrolytes into phase-separated gels at extremely low polymer concentrations (<1 % by mass) has been observed in scattering experiments and molecular dynamics simulations. In contrast to uncharged, amphiphilic block copolymers that form discrete micelles at low concentrations and enter a phase of strongly interacting micelles in a gradual manner with increasing polymer concentrations, the formation of a dilute phase of individual micelles is prevented in polyelectrolyte complexation-driven assemblies of triblock copolyelectrolytes. Gel phases form and phase separate almost instantaneously upon solvation of the copolymers. Furthermore, molecular models of self-assembly demonstrate the presence of oligo-chain aggregates in early stages of triblock copolyelectrolyte assembly, at experimentally unobservable polymer concentrations. Our discoveries not only contribute to our fundamental understanding of the structure and pathways of complexation driven assemblies, but also raise intriguing prospects for formation of gel structures at extraordinarily low concentrations, with applications in tissue engineering, agriculture, water purification and theranostics.

Structural transitions and guest/host complexing of liquid crystal helical nanofilaments induced by nanoconfinement

PubMed Central

Kim, Hanim; Ryu, Seong Ho; Tuchband, Michael; Shin, Tae Joo; Korblova, Eva; Walba, David M.; Clark, Noel A.; Yoon, Dong Ki

2017-01-01

A lamellar liquid crystal (LC) phase of certain bent-core mesogenic molecules can be grown in a manner that generates a single chiral helical nanofilament in each of the cylindrical nanopores of an anodic aluminum oxide (AAO) membrane. By introducing guest molecules into the resulting composite chiral nanochannels, we explore the structures and functionality of the ordered guest/host LC complex, verifying the smectic-like positional order of the fluidic nematic LC phase, which is obtained by the combination of the LC organization and the nanoporous AAO superstructure. The guest nematic LC 4′-n-pentyl-4-cyanobiphenyl is found to form a distinctive fluid layered ordered LC complex at the nanofilament/guest interface with the host 1,3-phenylene bis[4-(4-nonyloxyphenyliminomethyl)benzoate], where this interface contacts the AAO cylinder wall. Filament growth form is strongly influenced by mixture parameters and pore dimensions. PMID:28246642

Solution and electron microscopy characterization of lactococcal phage baseplates expressed in Escherichia coli.

PubMed

Campanacci, Valérie; Veesler, David; Lichière, Julie; Blangy, Stéphanie; Sciara, Giuliano; Moineau, Sylvain; van Sinderen, Douwe; Bron, Patrick; Cambillau, Christian

2010-10-01

We report here the characterization of several large structural protein complexes forming the baseplates (or part of them) of Siphoviridae phages infecting Lactococcus lactis: TP901-1, Tuc2009 and p2. We revisited a "block cloning" expression strategy and extended this approach to genomic fragments encoding proteins whose interacting partners have not yet been clearly identified. Biophysical characterization of some of these complexes using circular dichroism and size exclusion chromatography, coupled with on-line light scattering and refractometry, demonstrated that the over-produced recombinant proteins interact with each other to form large (up to 1.9MDa) and stable baseplate assemblies. Some of these complexes were characterized by electron microscopy confirming their structural homogeneity as well as providing a picture of their overall molecular shapes and symmetry. Finally, using these results, we were able to highlight similarities and differences with the well characterized much larger baseplate of the myophage T4.

Nucleolin forms a specific complex with a fragment of the viral (minus) strand of minute virus of mice DNA.

PubMed Central

Barrijal, S; Perros, M; Gu, Z; Avalosse, B L; Belenguer, P; Amalric, F; Rommelaere, J

1992-01-01

Nucleolin, a major nucleolar protein, forms a specific complex with the genome (a single-stranded DNA molecule of minus polarity) of parvovirus MVMp in vitro. By means of South-western blotting experiments, we mapped the binding site to a 222-nucleotide motif within the non-structural transcription unit, referred to as NUBE (nucleolin-binding element). The specificity of the interaction was confirmed by competitive gel retardation assays. DNaseI and nuclease S1 probing showed that NUBE folds into a secondary structure, in agreement with a computer-assisted conformational prediction. The whole NUBE may be necessary for the interaction with nucleolin, as suggested by the failure of NUBE subfragments to bind the protein and by the nuclease footprinting experiments. The present work extends the previously reported ability of nucleolin to form a specific complex with ribosomal RNA, to a defined DNA substrate. Considering the tropism of MVMp DNA replication for host cell nucleoli, these data raise the possibility that nucleolin may contribute to the regulation of the parvoviral life-cycle. Images PMID:1408821

Supramolecular architectures constructed by lanthanum, amino acids and 1,10-phenanthroline via non-covalent bond interactions

NASA Astrophysics Data System (ADS)

Zheng, Xiang-Jun; Jin, Lin-Pei

2003-07-01

Three supramolecular lanthanum coordination compounds of amino acids, with 1,10-phenanthroline (phen), [La 2(APA) 6(phen) 2(H 2O) 2](ClO 4) 6(phen) 4·2H 2O ( 1), [La 2(ABA) 6(phen) 2(H 2O) 2](ClO 4) 6 (phen) 6·4H 2O ( 2), and [La 2(AHA) 4(phen) 4](ClO 4) 6(phen) 4·2H 2O ( 3) (APA=3-aminopropionic acid; ABA=4-aminobutanoic acid; AHA=6-aminohexanoic acid) were synthesized and characterized by single crystal X-ray diffraction. The results show that the three coordination compounds are all composed of binuclear coordination cations built by metal-ligand coordination. Through hydrogen bonding and π-π stacking interactions, complex 1 forms a two-dimensional supramolecular sheet structure extending in the (001) plane, complex 2 forms a three-dimensional supramolecular network with many cavities occupied by ClO 4- and lattice H 2O molecules, and complex 3 forms a two-dimensional supramolecular lamellar structure in the (100) plane.

Heterobimetallic thiocyanato-bridged coordination polymers based on [Hg(SCN){sub 4}]{sup 2-}: Synthesis, crystal structure, magnetic properties and ESR studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jian Fangfang; Xiao Hailian; Liu Faqian

2006-12-15

Three new M/Hg bimetallic thiocyanato-bridged coordination polymers; [Hg(SCN){sub 4}Ni(Im){sub 3}] {sub {infinity}} 1, [Hg(SCN){sub 4}Mn(Im){sub 2}] {sub {infinity}} 2, and [Hg(SCN){sub 4}Cu(Me-Im){sub 2} Hg(SCN){sub 4}Cu(Me-Im){sub 4}] {sub {infinity}} 3, (Im=imidazole, Me-Im=N-methyl-imidazole), have been synthesized and characterized by means of elemental analysis, ESR, and single-crystal X-ray. X-ray diffraction analysis reveals that these three complexes all form 3D network structure, and their structures all contain a thiocyanato-bridged Hg...Hg chain (M=Mn, Ni, Cu) in which the metal and mercury centers exhibit different coordination environments. In complex 1, the [Hg(SCN){sub 4}]{sup 2-} anion connects three [Ni(Im){sub 3}]{sup 2+} using three SCN ligands giving risemore » to a 3D structure, and in complex 2, four SCN ligands bridge [Hg(SCN){sub 4}]{sup 2-} and [Mn(Im){sub 2}]{sup 2+} to form a 3D structure. The structure of 3 contains two copper atoms with distinct coordination environment; one is coordinated by four N-methyl-imidazole ligands and two axially elongated SCN groups, and another by four SCN groups (two elongated) and two N-methyl-imidazole ligands. The magnetic property of complex 1 has been investigated. The spin state structure in hetermetallic NiHgNi systems of complex 1 is irregular. The ESR spectra results of complex 3 demonstrate Cu{sup 2+} ion lie on octahedral environment. -- Graphical abstract: Three new M/Hg bimetallic thiocyanato-bridged coordination polymers; [Hg(SCN){sub 4}Ni(Im){sub 3}] {sub {infinity}} 1, [Hg(SCN){sub 4}Mn(Im){sub 2}] {sub {infinity}} 2, and [Hg(SCN){sub 4}Cu(Me-Im){sub 2} Hg(SCN){sub 4}Cu(Me-Im){sub 4}] {sub {infinity}} 3, (Im=imidazole, Me-Im=N-methyl-imidazole), have been synthesized and characterized by single-crystal X-ray. All coordination polymers possess 3-D structures, and consist of organic base neutral ligands (imidazole and N-methyl-imidazole) and SCN{sup -1} anions. Their structural difference is maicaused by the role of the organic base and metal ions. The complex 1 shows the irregular spin state structure.« less

Structures of human thymidylate synthase R163K with dUMP, FdUMP and glutathione show asymmetric ligand binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gibson, Lydia M.; Celeste, Lesa R.; Lovelace, Leslie L.

Thymidylate synthase (TS) is a well validated target in cancer chemotherapy. Here, a new crystal form of the R163K variant of human TS (hTS) with five subunits per asymmetric part of the unit cell, all with loop 181-197 in the active conformation, is reported. This form allows binding studies by soaking crystals in artificial mother liquors containing ligands that bind in the active site. Using this approach, crystal structures of hTS complexes with FdUMP and dUMP were obtained, indicating that this form should facilitate high-throughput analysis of hTS complexes with drug candidates. Crystal soaking experiments using oxidized glutathione revealed thatmore » hTS binds this ligand. Interestingly, the two types of binding observed are both asymmetric. In one subunit of the physiological dimer covalent modification of the catalytic nucleophile Cys195 takes place, while in another dimer a noncovalent adduct with reduced glutathione is formed in one of the active sites.« less

Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus vascular endothelial growth factor} protein complex by racemic crystallography.

PubMed

Mandal, Kalyaneswar; Uppalapati, Maruti; Ault-Riché, Dana; Kenney, John; Lowitz, Joshua; Sidhu, Sachdev S; Kent, Stephen B H

2012-09-11

Total chemical synthesis was used to prepare the mirror image (D-protein) form of the angiogenic protein vascular endothelial growth factor (VEGF-A). Phage display against D-VEGF-A was used to screen designed libraries based on a unique small protein scaffold in order to identify a high affinity ligand. Chemically synthesized D- and L- forms of the protein ligand showed reciprocal chiral specificity in surface plasmon resonance binding experiments: The L-protein ligand bound only to D-VEGF-A, whereas the D-protein ligand bound only to L-VEGF-A. The D-protein ligand, but not the L-protein ligand, inhibited the binding of natural VEGF(165) to the VEGFR1 receptor. Racemic protein crystallography was used to determine the high resolution X-ray structure of the heterochiral complex consisting of {D-protein antagonist + L-protein form of VEGF-A}. Crystallization of a racemic mixture of these synthetic proteins in appropriate stoichiometry gave a racemic protein complex of more than 73 kDa containing six synthetic protein molecules. The structure of the complex was determined to a resolution of 1.6 Å. Detailed analysis of the interaction between the D-protein antagonist and the VEGF-A protein molecule showed that the binding interface comprised a contact surface area of approximately 800 Å(2) in accord with our design objectives, and that the D-protein antagonist binds to the same region of VEGF-A that interacts with VEGFR1-domain 2.

A novel subunit structure of Clostridium botulinum serotype D toxin complex with three extended arms.

PubMed

Hasegawa, Kimiko; Watanabe, Toshihiro; Suzuki, Tomonori; Yamano, Akihito; Oikawa, Tetsuo; Sato, Yasuhiko; Kouguchi, Hirokazu; Yoneyama, Tohru; Niwa, Koichi; Ikeda, Toshihiko; Ohyama, Tohru

2007-08-24

The botulinum neurotoxins (BoNTs) are the most potent toxins known in nature, causing the lethal disease known as botulism in humans and animals. The BoNTs act by inhibiting neurotransmitter release from cholinergic synapses. Clostridium botulinum strains produce large BoNTs toxin complexes, which include auxiliary non-toxic proteins that appear not only to protect BoNTs from the hostile environment of the digestive tract but also to assist BoNT translocation across the intestinal mucosal layer. In this study, we visualize for the first time a series of botulinum serotype D toxin complexes using negative stain transmission electron microscopy (TEM). The complexes consist of the 150-kDa BoNT, 130-kDa non-toxic non-hemagglutinin (NTNHA), and three kinds of hemagglutinin (HA) subcomponents: 70-kDa HA-70, 33-kDa HA-33, and 17-kDa HA-17. These components assemble sequentially to form the complex. A novel TEM image of the mature L-TC revealed an ellipsoidal-shaped structure with "three arms" attached. The "body" section was comprised of a single BoNT, a single NTNHA and three HA-70 molecules. The arm section consisted of a complex of HA-33 and HA-17 molecules. We determined the x-ray crystal structure of the complex formed by two HA-33 plus one HA-17. On the basis of the TEM image and biochemical results, we propose a novel 14-mer subunit model for the botulinum toxin complex. This unique model suggests how non-toxic components make up a "delivery vehicle" for BoNT.

CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.

PubMed

Bae, Brian; Chen, James; Davis, Elizabeth; Leon, Katherine; Darst, Seth A; Campbell, Elizabeth A

2015-09-08

A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD. The structures show CarD interacts with the unique DNA topology presented by the upstream double-stranded/single-stranded DNA junction of the transcription bubble. We confirm that our structures correspond to functional activation complexes, and extend our understanding of the role of a conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription initiation complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter complexes, explaining the need for CarD.

The Co(II), Ni(II) and Cu(II) complexes with herbicide 2,4-dichlorophenoxyacetic acid - Synthesis and structural studies

NASA Astrophysics Data System (ADS)

Drzewiecka-Antonik, Aleksandra; Ferenc, Wiesława; Wolska, Anna; Klepka, Marcin T.; Cristóvão, Beata; Sarzyński, Jan; Rejmak, Paweł; Osypiuk, Dariusz

2017-01-01

The Co(II), Ni(II) and Cu(II) complexes with herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) were synthesized and structurally characterized. The geometry of metal-ligand interaction was refined using XAFS and DFT studies. The Co(2,4-D)2·6H2O and Ni(2,4-D)2·4H2O complexes have octahedral geometry with two carboxylate groups of 2,4-D anions and four water molecules in the coordination sphere. The square planar geometry around metal cations formed by the carboxylate groups from two monodentate ligands and two water molecules, is observed for Cu(2,4-D)2·4H2O complex. In the recrystallized Ni(II) complex dinuclear 'Chinese lantern' structures with bridging carboxylate groups of 2,4-D were observed.

Spectroscopic characterization of charge-transfer complexes of morpholine with chloranilic and picric acids in organic media: crystal structure of bis(morpholinium 2,4,6-trinitrocyclohexanolate).

PubMed

Refat, Moamen S; El-Zayat, Lamia A; Yeşilel, Okan Zafer

2010-02-01

Electron donor-acceptor interaction of morpholine (morp) with chloranilic acid (cla) and picric acid (pa) as pi-acceptors was investigated spectrophotometrically and found to form stable charge-transfer (CT) complexes (n-pi*) of [(Hmorp)(2)(cla)] and [(Hmorp)(pa)](2). The donor site involved in CT interaction is morpholine nitrogen. These complexes are easily synthesized from the reaction of morp with cla and pa within MeOH and CHCl(3) solvents, respectively. (1)HNMR, IR, elemental analyses, and UV-vis techniques characterize the two morpholinium charge-transfer complexes. Benesi-Hildebrand and its modification methods were applied to the determination of association constant (K), molar extinction coefficient (epsilon). The X-ray crystal structure was carried out for the interpretation the predict structure of the [(Hmorp)(pa)](2) complex. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Spectroscopic characterization of charge-transfer complexes of morpholine with chloranilic and picric acids in organic media: Crystal structure of bis(morpholinium 2,4,6-trinitrocyclohexanolate)

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; El-Zayat, Lamia A.; Yeşilel, Okan Zafer

2010-02-01

Electron donor-acceptor interaction of morpholine (morp) with chloranilic acid (cla) and picric acid (pa) as π-acceptors was investigated spectrophotometrically and found to form stable charge-transfer (CT) complexes (n-π*) of [(Hmorp) 2(cla)] and [(Hmorp)(pa)] 2. The donor site involved in CT interaction is morpholine nitrogen. These complexes are easily synthesized from the reaction of morp with cla and pa within MeOH and CHCl 3 solvents, respectively. 1HNMR, IR, elemental analyses, and UV-vis techniques characterize the two morpholinium charge-transfer complexes. Benesi-Hildebrand and its modification methods were applied to the determination of association constant ( K), molar extinction coefficient ( ɛ). The X-ray crystal structure was carried out for the interpretation the predict structure of the [(Hmorp)(pa)] 2 complex.

Structural studies of the formation of lipoplexes between siRNA and selected bis-imidazolium gemini surfactants.

PubMed

Andrzejewska, W; Pietralik, Z; Skupin, M; Kozak, M

2016-10-01

Dicationic (gemini) surfactants are agents that can be used for the preparation of stable complexes of nucleic acids, particularly siRNA for therapeutic purposes. In this study, we demonstrated that bis-imidazolium gemini surfactants with variable lengths of dioxyalkyl linker groups (from dioxyethyl to dioxydodecyl) and dodecyl side chains are excellent for the complexation of siRNA. All of these compounds effectively complexed siRNA in a charge ratio range (p/n) of 1.5-10. The low resolution structure of siRNA oligomers was characterised by small angle scattering of synchrotron radiation (SR-SAXS) and ab initio modelling. The structures of the formed complexes were also analysed using SR-SAXS, circular dichroism studies and electrophoretic mobility tests. The most promising agents for complexation with siRNA were the surfactants that contained dioxyethyl and dioxyhexyl spacer groups. Copyright © 2016 Elsevier B.V. All rights reserved.

Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps

PubMed Central

Rakesh, Ramachandran; Joseph, Agnel Praveen; Bhaskara, Ramachandra M.; Srinivasan, Narayanaswamy

2016-01-01

ABSTRACT Pre-mRNA splicing in eukaryotes is performed by the spliceosome, a highly complex macromolecular machine. SF3b is a multi-protein complex which recognizes the branch point adenosine of pre-mRNA as part of a larger U2 snRNP or U11/U12 di-snRNP in the dynamic spliceosome machinery. Although a cryo-EM map is available for human SF3b complex, the structure and relative spatial arrangement of all components in the complex are not yet known. We have recognized folds of domains in various proteins in the assembly and generated comparative models. Using an integrative approach involving structural and other experimental data, guided by the available cryo-EM density map, we deciphered a pseudo-atomic model of the closed form of SF3b which is found to be a “fuzzy complex” with highly flexible components and multiplicity of folds. Further, the model provides structural information for 5 proteins (SF3b10, SF3b155, SF3b145, SF3b130 and SF3b14b) and localization information for 4 proteins (SF3b10, SF3b145, SF3b130 and SF3b14b) in the assembly for the first time. Integration of this model with the available U11/U12 di-snRNP cryo-EM map enabled elucidation of an open form. This now provides new insights on the mechanistic features involved in the transition between closed and open forms pivoted by a hinge region in the SF3b155 protein that also harbors cancer causing mutations. Moreover, the open form guided model of the 5′ end of U12 snRNA, which includes the branch point duplex, shows that the architecture of SF3b acts as a scaffold for U12 snRNA: pre-mRNA branch point duplex formation with potential implications for branch point adenosine recognition fidelity. PMID:27618338

Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase

PubMed Central

Mittag, Tanja; Marsh, Joseph; Grishaev, Alexander; Orlicky, Stephen; Lin, Hong; Sicheri, Frank; Tyers, Mike; Forman-Kay, Julie D.

2010-01-01

Summary Intrinsically disordered proteins can form highly dynamic complexes with partner proteins. One such dynamic complex involves the intrinsically disordered Sic1 with its partner Cdc4 in regulation of yeast cell cycle progression. Phosphorylation of six N-terminal Sic1 sites leads to equilibrium engagement of each phosphorylation site with the primary binding pocket in Cdc4, the substrate recognition subunit of a ubiquitin ligase. ENSEMBLE calculations utilizing experimental NMR and small-angle x-ray scattering data reveal significant transient structure in both phosphorylation states of the isolated ensembles (Sic1 and pSic1) that modulates their electrostatic potential, suggesting a structural basis for the proposed strong contribution of electrostatics to binding. A structural model of the dynamic pSic1-Cdc4 complex demonstrates the spatial arrangements in the ubiquitin ligase complex. These results provide a physical picture of a protein that is predominantly disordered in both its free and bound states, enabling aspects of its structure/function relationship to be elucidated. PMID:20399186

CryoEM and Molecular Dynamics of the Circadian KaiB-KaiC Complex Indicates That KaiB Monomers Interact with KaiC and Block ATP Binding Clefts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Villarreal, Seth A.; Pattanayek, Rekha; Williams, Dewight R.

The circadian control of cellular processes in cyanobacteria is regulated by a posttranslational oscillator formed by three Kai proteins. During the oscillator cycle, KaiA serves to promote autophosphorylation of KaiC while KaiB counteracts this effect. Here, we present a crystallographic structure of the wild-type Synechococcus elongatus KaiB and a cryo-electron microscopy (cryoEM) structure of a KaiBC complex. The crystal structure shows the expected dimer core structure and significant conformational variations of the KaiB C-terminal region, which is functionally important in maintaining rhythmicity. The KaiBC sample was formed with a C-terminally truncated form of KaiC, KaiC-Δ489, which is persistently phosphorylated. Themore » KaiB–KaiC-Δ489 structure reveals that the KaiC hexamer can bind six monomers of KaiB, which form a continuous ring of density in the KaiBC complex. We performed cryoEM-guided molecular dynamics flexible fitting simulations with crystal structures of KaiB and KaiC to probe the KaiBC protein–protein interface. This analysis indicated a favorable binding mode for the KaiB monomer on the CII end of KaiC, involving two adjacent KaiC subunits and spanning an ATP binding cleft. A KaiC mutation, R468C, which has been shown to affect the affinity of KaiB for KaiC and lengthen the period in a bioluminescence rhythm assay, is found within the middle of the predicted KaiBC interface. The proposed KaiB binding mode blocks access to the ATP binding cleft in the CII ring of KaiC, which provides insight into how KaiB might influence the phosphorylation status of KaiC.« less

Clustering of low-valence particles: structure and kinetics.

PubMed

Markova, Olga; Alberts, Jonathan; Munro, Edwin; Lenne, Pierre-François

2014-08-01

We compute the structure and kinetics of two systems of low-valence particles with three or six freely oriented bonds in two dimensions. The structure of clusters formed by trivalent particles is complex with loops and holes, while hexavalent particles self-organize into regular and compact structures. We identify the elementary structures which compose the clusters of trivalent particles. At initial stages of clustering, the clusters of trivalent particles grow with a power-law time dependence. Yet at longer times fusion and fission of clusters equilibrates and clusters form a heterogeneous phase with polydispersed sizes. These results emphasize the role of valence in the kinetics and stability of finite-size clusters.

Crystal structures of the class D beta-lactamase OXA-13 in the native form and in complex with meropenem.

PubMed

Pernot, L; Frénois, F; Rybkine, T; L'Hermite, G; Petrella, S; Delettré, J; Jarlier, V; Collatz, E; Sougakoff, W

2001-07-20

The therapeutic problems posed by class D beta-lactamases, a family of serine enzymes that hydrolyse beta-lactam antibiotics following an acylation-deacylation mechanism, are increased by the very low level of sensitivity of these enzymes to beta-lactamase inhibitors. To gain structural and mechanistic insights to aid the design of new inhibitors, we have determined the crystal structure of OXA-13 from Pseudomonas aeruginosa in the apo form and in complex with the carbapenem meropenem. The native form consisted of a dimer displaying an overall organisation similar to that found in the closely related enzyme OXA-10. In the acyl-enzyme complex, the positioning of the antibiotic appeared to be ensured mainly by (i) the covalent acyl bond and (ii) a strong salt-bridge involving the carboxylate moiety of the drug. Comparison of the structures of OXA-13 in the apo form and in complex with meropenem revealed an unsuspected flexibility in the region of the essential serine 115 residue, with possible consequences for the catalytic properties of the enzyme. In the apo form, the Ser115 side-chain is oriented outside the active site, whereas the general base Lys70 adopts a conformation that seems to be incompatible with the activation of the catalytic water molecule required for the deacylation step. In the OXA-13:meropenem complex, a 3.5 A movement of the backbone of the 114-116 loop towards the side-chain of Lys70 was observed, which seems to be driven by a displacement of the neighbouring 91-104 loop and which results in the repositioning of the side-chain hydroxyl group of Ser115 toward the catalytic centre. Concomitantly, the side-chain of Lys70 is forced to curve in the direction of the deacylating water molecule, which is then strongly bound and activated by this residue. However, a distance of ca 5 A separates the catalytic water molecule from the acyl carbonyl group of meropenem, a structural feature that accounts for the inhibition of OXA-13 by this drug. Finally, the low level of penicillinase activity revealed by the kinetic analysis of OXA-13 could be related to the specific presence in position 73 of a serine residue located close to the general base Lys70, which results in a decrease of the number of hydrogen-bonding interactions stabilising the catalytic water molecule. Copyright 2001 Academic Press.

Substrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition

PubMed Central

Kumar, Prashant; Reithofer, Viktoria; Reisinger, Manuel; Wallner, Silvia; Pavkov-Keller, Tea; Macheroux, Peter; Gruber, Karl

2016-01-01

Human dipeptidyl-peptidase III (hDPP III) is a zinc-dependent hydrolase cleaving dipeptides off the N-termini of various bioactive peptides. Thus, the enzyme is likely involved in a number of physiological processes such as nociception and is also implicated in several forms of cancer. We present high-resolution crystal structures of hDPP III in complex with opioid peptides (Met-and Leu-enkephalin, endomorphin-2) as well as with angiotensin-II and the peptide inhibitor IVYPW. These structures confirm the previously reported large conformational change of the enzyme upon ligand binding and show that the structure of the closed conformation is independent of the nature of the bound peptide. The overall peptide-binding mode is also conserved ensuring the correct positioning of the scissile peptide bond with respect to the catalytic zinc ion. The structure of the angiotensin-II complex shows, how longer peptides are accommodated in the binding cleft of hDPP III. Differences in the binding modes allow a distinction between real substrates and inhibitory peptides or “slow” substrates. The latter displace a zinc bound water molecule necessitating the energetically much less favoured anhydride mechanism as opposed to the favoured promoted-water mechanism. The structural data also form the necessary framework for the design of specific hDPP III inhibitors. PMID:27025154

Small-angle neutron scattering study of specific interaction and coordination structure formed by mono-acetyl-substituted dibenzo-20-crown-6-ether and cesium ions

DOE PAGES

Motokawa, Ryuhei; Kobayashi, Tohru; Endo, Hitoshi; ...

2015-10-26

This study uses small-angle neutron scattering (SANS) to elucidate the coordination structure of the complex of mono-acetyl-substituted dibenzo-20-crown-6-ether (ace-DB20C6) with cesium ions (Cs +). SANS profiles obtained for the complex of ace-DB20C6 and Cs + (ace-DB20C6/Cs) in deuterated dimethyl sulfoxide indicated that Cs + coordination resulted in a more compact structure than the free ace-DB20C6. The data were fitted well with SANS profiles calculated using Debye function for scattering on an absolute scattering intensity scale. For this theoretical calculation of the scattering profiles, the coordination structure proposed based on density functional theory calculation was used. Furthermore, we conclude that themore » SANS analysis experimentally supports the proposed coordination structure of ace-DB20C6/Cs and suggests the following: (1) the complex of ace-DB20C6 and Cs + is formed with an ace-DB20C6/Cs molar ratio of 1/1 and (2) the two benzene rings of ace-DB20C6 fold around Cs + above the center of the crown ether ring of ace-DB20C6.« less

Small-angle neutron scattering study of specific interaction and coordination structure formed by mono-acetyl-substituted dibenzo-20-crown-6-ether and cesium ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Motokawa, Ryuhei; Kobayashi, Tohru; Endo, Hitoshi

This study uses small-angle neutron scattering (SANS) to elucidate the coordination structure of the complex of mono-acetyl-substituted dibenzo-20-crown-6-ether (ace-DB20C6) with cesium ions (Cs +). SANS profiles obtained for the complex of ace-DB20C6 and Cs + (ace-DB20C6/Cs) in deuterated dimethyl sulfoxide indicated that Cs + coordination resulted in a more compact structure than the free ace-DB20C6. The data were fitted well with SANS profiles calculated using Debye function for scattering on an absolute scattering intensity scale. For this theoretical calculation of the scattering profiles, the coordination structure proposed based on density functional theory calculation was used. Furthermore, we conclude that themore » SANS analysis experimentally supports the proposed coordination structure of ace-DB20C6/Cs and suggests the following: (1) the complex of ace-DB20C6 and Cs + is formed with an ace-DB20C6/Cs molar ratio of 1/1 and (2) the two benzene rings of ace-DB20C6 fold around Cs + above the center of the crown ether ring of ace-DB20C6.« less

The three-dimensional structure of the native ternary complex of bovine pancreatic procarboxypeptidase A with proproteinase E and chymotrypsinogen C.

PubMed Central

Gomis-Rüth, F X; Gómez, M; Bode, W; Huber, R; Avilés, F X

1995-01-01

The metalloexozymogen procarboxypeptidase A is mainly secreted in ruminants as a ternary complex with zymogens of two serine endoproteinases, chymotrypsinogen C and proproteinase E. The bovine complex has been crystallized, and its molecular structure analysed and refined at 2.6 A resolution to an R factor of 0.198. In this heterotrimer, the activation segment of procarboxypeptidase A essentially clamps the other two subunits, which shield the activation sites of the former from tryptic attack. In contrast, the propeptides of both serine proproteinases are freely accessible to trypsin. This arrangement explains the sequential and delayed activation of the constituent zymogens. Procarboxypeptidase A is virtually identical to the homologous monomeric porcine form. Chymotrypsinogen C displays structural features characteristic for chymotrypsins as well as elastases, except for its activation domain; similar to bovine chymotrypsinogen A, its binding site is not properly formed, while its surface located activation segment is disordered. The proproteinase E structure is fully ordered and strikingly similar to active porcine elastase; its specificity pocket is occluded, while the activation segment is fixed to the molecular surface. This first structure of a native zymogen from the proteinase E/elastase family does not fundamentally differ from the serine proproteinases known so far. Images PMID:7556081

Cardiolipin synthesizing enzymes form a complex that interacts with cardiolipin-dependent membrane organizing proteins.

PubMed

Serricchio, Mauro; Vissa, Adriano; Kim, Peter K; Yip, Christopher M; McQuibban, G Angus

2018-04-01

The mitochondrial glycerophospholipid cardiolipin plays important roles in mitochondrial biology. Most notably, cardiolipin directly binds to mitochondrial proteins and helps assemble and stabilize mitochondrial multi-protein complexes. Despite their importance for mitochondrial health, how the proteins involved in cardiolipin biosynthesis are organized and embedded in mitochondrial membranes has not been investigated in detail. Here we show that human PGS1 and CLS1 are constituents of large protein complexes. We show that PGS1 forms oligomers and associates with CLS1 and PTPMT1. Using super-resolution microscopy, we observed well-organized nanoscale structures formed by PGS1. Together with the observation that cardiolipin and CLS1 are not required for PGS1 to assemble in the complex we predict the presence of a PGS1-centered cardiolipin-synthesizing scaffold within the mitochondrial inner membrane. Using an unbiased proteomic approach we found that PGS1 and CLS1 interact with multiple cardiolipin-binding mitochondrial membrane proteins, including prohibitins, stomatin-like protein 2 and the MICOS components MIC60 and MIC19. We further mapped the protein-protein interaction sites between PGS1 and itself, CLS1, MIC60 and PHB. Overall, this study provides evidence for the presence of a cardiolipin synthesis structure that transiently interacts with cardiolipin-dependent protein complexes. Copyright © 2018 Elsevier B.V. All rights reserved.

Co(II) and Ni(II) complexes based on anthraquinone-1,4,5,8-tetracarboxylic acid (H4AQTC): canted antiferromagnetism and slow magnetization relaxation in {[Co2(AQTC)(H2O)6]·6H2O}.

PubMed

Yan, Wei-Hong; Bao, Song-Song; Huang, Jian; Ren, Min; Sheng, Xiao-Li; Cai, Zhong-Sheng; Lu, Chang-Sheng; Meng, Qing-Jin; Zheng, Li-Min

2013-06-21

Three coordination polymers {[Co2(AQTC)(H2O)6]·6H2O}n (1), {[M2(AQTC)(bpym)(H2O)6]·6H2O}n (M = Co(2), Ni(3)) have been synthesized and structurally characterized, where H4AQTC is anthraquinone-1,4,5,8-tetracarboxylic acid and bpym is 2,2'-bipyrimidine. Complex 1 features a 3-D structure, where layers of Co2(AQTC) are cross-linked by Co-H2O chains. Complexes 2 and 3 are isostructural and display 1-D chain structures. The chains are connected through hydrogen-bonding interactions to form 3-D supramolecular structures. Magnetic properties of these complexes are investigated. Compound 1 shows canted antiferromagnetism and slow relaxation below 4.0 K. For complexes 2 and 3, dominant antiferromagnetic interactions are observed. The luminescent properties of the three complexes are investigated as well.

Crystal structure of the HA3 subcomponent of Clostridium botulinum type C progenitor toxin.

PubMed

Nakamura, Toshio; Kotani, Mao; Tonozuka, Takashi; Ide, Azusa; Oguma, Keiji; Nishikawa, Atsushi

2009-01-30

The Clostridium botulinum type C 16S progenitor toxin contains a neurotoxin and several nontoxic components, designated nontoxic nonhemagglutinin (HA), HA1 (HA-33), HA2 (HA-17), HA3a (HA-22-23), and HA3b (HA-53). The HA3b subcomponent seems to play an important role cooperatively with HA1 in the internalization of the toxin by gastrointestinal epithelial cells via binding of these subcomponents to specific oligosaccharides. In this study, we investigated the sugar-binding specificity of the HA3b subcomponent using recombinant protein fused to glutathione S-transferase and determined the three-dimensional structure of the HA3a-HA3b complex based on X-ray crystallography. The crystal structure was determined at a resolution of 2.6 A. HA3b contains three domains, domains I to III, and the structure of domain I resembles HA3a. In crystal packing, three HA3a-HA3b molecules are assembled to form a three-leaved propeller-like structure. The three HA3b domain I and three HA3a alternate, forming a trimer of dimers. In a database search, no proteins with high structural homology to any of the domains (Z score >10) were found. Especially, HA3a and HA3b domain I, mainly composed of beta-sheets, reveal a unique fold. In binding assays, HA3b bound sialic acid with high affinity, but did not bind galactose, N-acetylgalactosamine, or N-acetylglucosamine. The electron density of liganded N-acetylneuraminic acid was determined by crystal soaking. In the sugar-complex structure, the N-acetylneuraminic acid-binding site was located in the cleft formed between domains II and III of HA3b. This report provides the first determination of the three-dimensional structure of the HA3a-HA3b complex and its sialic acid binding site. Our results will provide useful information for elucidating the mechanism of assembly of the C16S toxin and for understanding the interactions with oligosaccharides on epithelial cells and internalization of the botulinum toxin complex.

Structural and functional features of formate hydrogen lyase, an enzyme of mixed-acid fermentation from Escherichia coli.

PubMed

Bagramyan, K; Trchounian, A

2003-11-01

Formate hydrogen lyase from Escherichia coli is a membrane-bound complex that oxidizes formic acid to carbon dioxide and molecular hydrogen. Under anaerobic growth conditions and fermentation of sugars (glucose), it exists in two forms. One form is constituted by formate dehydrogenase H and hydrogenase 3, and the other one is the same formate dehydrogenase and hydrogenase 4; the presence of small protein subunits, carriers of electrons, is also probable. Other proteins may also be involved in formation of the enzyme complex, which requires the presence of metal (nickel-cobalt). Its formation also depends on the external pH and the presence of formate. Activity of both forms requires F(0)F(1)-ATPase; this explains dependence of the complex functioning on proton-motive force. It is also possible that the formate hydrogen lyase complex will exhibit its own proton-translocating function.

Characterization of measurement errors using structure-from-motion and photogrammetry to measure marine habitat structural complexity.

PubMed

Bryson, Mitch; Ferrari, Renata; Figueira, Will; Pizarro, Oscar; Madin, Josh; Williams, Stefan; Byrne, Maria

2017-08-01

Habitat structural complexity is one of the most important factors in determining the makeup of biological communities. Recent advances in structure-from-motion and photogrammetry have resulted in a proliferation of 3D digital representations of habitats from which structural complexity can be measured. Little attention has been paid to quantifying the measurement errors associated with these techniques, including the variability of results under different surveying and environmental conditions. Such errors have the potential to confound studies that compare habitat complexity over space and time. This study evaluated the accuracy, precision, and bias in measurements of marine habitat structural complexity derived from structure-from-motion and photogrammetric measurements using repeated surveys of artificial reefs (with known structure) as well as natural coral reefs. We quantified measurement errors as a function of survey image coverage, actual surface rugosity, and the morphological community composition of the habitat-forming organisms (reef corals). Our results indicated that measurements could be biased by up to 7.5% of the total observed ranges of structural complexity based on the environmental conditions present during any particular survey. Positive relationships were found between measurement errors and actual complexity, and the strength of these relationships was increased when coral morphology and abundance were also used as predictors. The numerous advantages of structure-from-motion and photogrammetry techniques for quantifying and investigating marine habitats will mean that they are likely to replace traditional measurement techniques (e.g., chain-and-tape). To this end, our results have important implications for data collection and the interpretation of measurements when examining changes in habitat complexity using structure-from-motion and photogrammetry.

Article and method for making complex shaped preform and silicon carbide composite by melt infiltration

NASA Technical Reports Server (NTRS)

Corman, Gregory S. (Inventor); Steibel, James D. (Inventor); Schikner, Robert C. (Inventor); Szweda, Andrew (Inventor)

2001-01-01

Small diameter silicon carbide-containing fibers are provided in a bundle such as a fiber tow that can be formed into a structure where the radii of curvature is not limited to 10-20 inches. An aspect of this invention is directed to impregnating the bundles of fibers with the slurry composition to substantially coat the outside surface of an individual fiber within the bundle and to form a complex shaped preform with a mass of continuous fibers.

Article and method for making complex shaped preform and silicon carbide composite by melt infiltration

NASA Technical Reports Server (NTRS)

Szweda, Andrew (Inventor); Corman, Gregory S. (Inventor); Steibel, James D. (Inventor); Schikner, Robert C. (Inventor)

2000-01-01

Small diameter silicon carbide-containing fibers are provided in a bundle such as a fiber tow that can be formed into a structure where the radii of curvature is not limited to 10-20 inches. An aspect of this invention is directed to impregnating the bundles of fibers with the slurry composition to substantially coat the outside surface of an individual fiber within the bundle and to form a complex shaped preform with a mass of continuous fibers.

DOE Office of Scientific and Technical Information (OSTI.GOV)

AhYoung, Andrew P.; Lu, Brian; Cascio, Duilio

Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum – Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-vesicular exchange of essential phospholipids. Present in Fungi and Amoebas but not in Metazoans, ERMES is composed of five distinct subunits; among those, Mdm12, Mmm1 and Mdm34 each contain an SMP domain functioning as a lipid transfer module. We previously showed that the SMP domains of Mdm12 and Mmm1 form a hetero-tetramer. Here we describe our strategy to diversify the number of Mdm12/Mmm1 complexes suited formore » structural studies. We use sequence analysis of orthologues combined to protein engineering of disordered regions to guide the design of protein constructs and expand the repertoire of Mdm12/Mmm1 complexes more likely to crystallize. Using this combinatorial approach we report crystals of Mdm12/Mmm1 ERMES complexes currently diffracting to 4.5 Å resolution and a new structure of Mdm12 solved at 4.1 Å resolution. Our structure reveals a monomeric form of Mdm12 with a conformationally dynamic N-terminal β-strand; it differs from a previously reported homodimeric structure where the N-terminal β strands where swapped to promote dimerization. Based on our electron microscopy data, we propose a refined pseudo-atomic model of the Mdm12/Mmm1 complex that agrees with our crystallographic and small-angle X-ray scattering (SAXS) solution data.« less

Complexes of oxovanadium(IV), dioxovanadium(V) and dioxouranium(VI) with aminoacids in aqueous solution

NASA Astrophysics Data System (ADS)

Lagrange, P.; Schneider, M.; Lagrange, J.

1998-11-01

The equilibria between three oxocations (VO2+, VO2+ and UO22+) and several ?- aminoacids (glycine, serine, asparagine, lysine, aspartic acid and glutamic acid) are studied in aqueous solution. Stoichiometry and stability of the complexes formed are determined from a combination of potentiometric and spectroscopic measurements. Solution structures of the different complexes are proposed based on the thermodynamic results. The oxovanadium(IV) complexes appear less stable than the corresponding dioxouranium(VI) and dioxovanadium(V) complexes. VO2+ can be bound to only one ligand to form monodentate or chelate complexes. UO22+ and VO2+ cations may be chelated by one or two ligands. Les équilibres entre trois oxocations, VO2+, VO2+ et UO22+ et plusieurs α-aminoacides, glycine, sérine, asparagine, lysine et acides aspartique et glutamique, sont étudiés en solution aqueuse par potentiométrie couplée à la spectrophotométrie. Les complexes de VO2+ sont moins stables que les complexes de VO2+ et UO22+ de même stoechiométrie. VO2+ ne peut se lier qu'à un seul ligand pour former soit des complexes monodentés, soit des chélates. UO22+ et VO2+ peuvent être chélatés par un ou deux ligands. Des structures hypothétiques en solution sont proposées.

Enhancing oxidative stability in heated oils using core/shell structures of collagen and α-tocopherol complex.

PubMed

Gim, Seo Yeong; Hong, Seungmi; Kim, Jisu; Kwon, YongJun; Kim, Mi-Ja; Kim, GeunHyung; Lee, JaeHwan

2017-11-15

In this study, collagen mesh structure was prepared by carrying α-tocopherol in the form of core/shell complex. Antioxidant properties of α-tocopherol loaded carriers were tested in moisture added bulk oils at 140°C. From one gram of collagen core/shell complex, 138mg α-tocopherol was released in medium chain triacylglycerol (MCT). α-Tocopherol was substantially protected against heat treatment when α-tocopherol was complexed in collagen core/shell. Oxidative stability in bulk oil was significantly enhanced by added collagen mesh structure or collagen core/shell complex with α-tocopherol compared to that in control bulk oils (p<0.05), although no significant difference was observed between oils containing collagen mesh structure and collagen core/shell with α-tocopherol (p>0.05). Results of DPPH loss in methanol demonstrated that collagen core/shell with α-tocopherol had significantly (p<0.05) higher antioxidant properties than collagen mesh structure up to a certain period. Therefore, collagen core/shell complex is a promising way to enhance the stability of α-tocopherol and oxidative stability in oil-rich foods prepared at high temperature. Copyright © 2017 Elsevier Ltd. All rights reserved.

SVP-like MADS-box protein from Carya cathayensis forms higher-order complexes.

PubMed

Wang, Jingjing; Hou, Chuanming; Huang, Jianqin; Wang, Zhengjia; Xu, Yingwu

2015-03-01

To properly regulate plant flowering time and construct floral pattern, MADS-domain containing transcription factors must form multimers including homo- and hetero-dimers. They are also active in forming hetero-higher-order complexes with three to five different molecules. However, it is not well known if a MADS-box protein can also form homo-higher-order complex. In this study a biochemical approach is utilized to provide insight into the complex formation for an SVP-like MADS-box protein cloned from hickory. The results indicated that the protein is a heterogeneous higher-order complex with the peak population containing over 20 monomers. Y2H verified the protein to form homo-complex in yeast cells. Western blot of the hickory floral bud sample revealed that the protein exists in higher-order polymers in native. Deletion assays indicated that the flexible C-terminal residues are mainly responsible for the higher-order polymer formation and the heterogeneity. Current results provide direct biochemical evidences for an active MADS-box protein to be a high order complex, much higher than a quartermeric polymer. Analysis suggests that a MADS-box subset may be able to self-assemble into large complexes, and thereby differentiate one subfamily from the other in a higher-order structural manner. Present result is a valuable supplement to the action of mechanism for MADS-box proteins in plant development. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

[Spectrophotometric study of the interaction between rhenium complexes and phosphatidylcholine during liposome formation].

PubMed

Shtemenko, O V; Zeleniuk, M A; Shtemenko, N I; Verbyts'ka, Ia S

2002-01-01

The electron absorption spectra of halogenides and halogencarboxylate complex compounds of rhenium (III) having cluster structure with phosphatydilcholine and their lyposome forms were investigated. Some results which evidence for the interaction of these compounds with phosphatydilcholine were obtained. The possible mechanism of this interaction is discussed.

Metal-organic coordination architectures of tetrazole heterocycle ligands bearing acetate groups: Synthesis, characterization and magnetic properties

NASA Astrophysics Data System (ADS)

Hu, Bo-Wen; Zheng, Xiang-Yu; Ding, Cheng

2015-12-01

Two new coordination complexes with tetrazole heterocycle ligands bearing acetate groups, [Co(L)2]n (1) and [Co3(L)4(N3)2·2MeOH]n (2) (L=tetrazole-1-acetate) have been synthesized and structurally characterized. Single crystal structure analysis shows that the cobalt-complex 1 has the 3D 3,6-connected (42.6)2(44.62.88.10)-ant topology. By introducing azide in this system, complex 2 forms the 2D network containing the [Co3] units. And the magnetic properties of 1 and 2 have been studied.

Triangle network motifs predict complexes by complementing high-error interactomes with structural information.

PubMed

Andreopoulos, Bill; Winter, Christof; Labudde, Dirk; Schroeder, Michael

2009-06-27

A lot of high-throughput studies produce protein-protein interaction networks (PPINs) with many errors and missing information. Even for genome-wide approaches, there is often a low overlap between PPINs produced by different studies. Second-level neighbors separated by two protein-protein interactions (PPIs) were previously used for predicting protein function and finding complexes in high-error PPINs. We retrieve second level neighbors in PPINs, and complement these with structural domain-domain interactions (SDDIs) representing binding evidence on proteins, forming PPI-SDDI-PPI triangles. We find low overlap between PPINs, SDDIs and known complexes, all well below 10%. We evaluate the overlap of PPI-SDDI-PPI triangles with known complexes from Munich Information center for Protein Sequences (MIPS). PPI-SDDI-PPI triangles have ~20 times higher overlap with MIPS complexes than using second-level neighbors in PPINs without SDDIs. The biological interpretation for triangles is that a SDDI causes two proteins to be observed with common interaction partners in high-throughput experiments. The relatively few SDDIs overlapping with PPINs are part of highly connected SDDI components, and are more likely to be detected in experimental studies. We demonstrate the utility of PPI-SDDI-PPI triangles by reconstructing myosin-actin processes in the nucleus, cytoplasm, and cytoskeleton, which were not obvious in the original PPIN. Using other complementary datatypes in place of SDDIs to form triangles, such as PubMed co-occurrences or threading information, results in a similar ability to find protein complexes. Given high-error PPINs with missing information, triangles of mixed datatypes are a promising direction for finding protein complexes. Integrating PPINs with SDDIs improves finding complexes. Structural SDDIs partially explain the high functional similarity of second-level neighbors in PPINs. We estimate that relatively little structural information would be sufficient for finding complexes involving most of the proteins and interactions in a typical PPIN.

Triangle network motifs predict complexes by complementing high-error interactomes with structural information

PubMed Central

Andreopoulos, Bill; Winter, Christof; Labudde, Dirk; Schroeder, Michael

2009-01-01

Background A lot of high-throughput studies produce protein-protein interaction networks (PPINs) with many errors and missing information. Even for genome-wide approaches, there is often a low overlap between PPINs produced by different studies. Second-level neighbors separated by two protein-protein interactions (PPIs) were previously used for predicting protein function and finding complexes in high-error PPINs. We retrieve second level neighbors in PPINs, and complement these with structural domain-domain interactions (SDDIs) representing binding evidence on proteins, forming PPI-SDDI-PPI triangles. Results We find low overlap between PPINs, SDDIs and known complexes, all well below 10%. We evaluate the overlap of PPI-SDDI-PPI triangles with known complexes from Munich Information center for Protein Sequences (MIPS). PPI-SDDI-PPI triangles have ~20 times higher overlap with MIPS complexes than using second-level neighbors in PPINs without SDDIs. The biological interpretation for triangles is that a SDDI causes two proteins to be observed with common interaction partners in high-throughput experiments. The relatively few SDDIs overlapping with PPINs are part of highly connected SDDI components, and are more likely to be detected in experimental studies. We demonstrate the utility of PPI-SDDI-PPI triangles by reconstructing myosin-actin processes in the nucleus, cytoplasm, and cytoskeleton, which were not obvious in the original PPIN. Using other complementary datatypes in place of SDDIs to form triangles, such as PubMed co-occurrences or threading information, results in a similar ability to find protein complexes. Conclusion Given high-error PPINs with missing information, triangles of mixed datatypes are a promising direction for finding protein complexes. Integrating PPINs with SDDIs improves finding complexes. Structural SDDIs partially explain the high functional similarity of second-level neighbors in PPINs. We estimate that relatively little structural information would be sufficient for finding complexes involving most of the proteins and interactions in a typical PPIN. PMID:19558694

Complexity: the organizing principle at the interface of biological (dis)order.

PubMed

Bhat, Ramray; Pally, Dharma

2017-07-01

The term complexity means several things to biologists.When qualifying morphological phenotype, on the one hand, it is used to signify the sheer complicatedness of living systems, especially as a result of the multicomponent aspect of biological form. On the other hand, it has been used to represent the intricate nature of the connections between constituents that make up form: a more process-based explanation. In the context of evolutionary arguments, complexity has been defined, in a quantifiable fashion, as the amount of information, an informatic template such as a sequence of nucleotides or amino acids stores about its environment. In this perspective, we begin with a brief review of the history of complexity theory. We then introduce a developmental and an evolutionary understanding of what it means for biological systems to be complex.We propose that the complexity of living systems can be understood through two interdependent structural properties: multiscalarity of interconstituent mechanisms and excitability of the biological materials. The answer to whether a system becomes more or less complex over time depends on the potential for its constituents to interact in novel ways and combinations to give rise to new structures and functions, as well as on the evolution of excitable properties that would facilitate the exploration of interconstituent organization in the context of their microenvironments and macroenvironments.

Crystal structures of resorcin[4]arene and pyrogallol[4]arene complexes with proline: A model for proline recognition through Csbnd H···π interaction

NASA Astrophysics Data System (ADS)

Fujisawa, Ikuhide; Kitamura, Yuji; Kato, Ryo; Aoki, Katsuyuki

2018-07-01

Resorcin[4]arene (resorcinol cyclic tetramer, abbreviated as RCT) or pyrogallol[4]arene (pyrogallol cyclic tetramer, PCT) form host-guest 1:1 complexes with DL-proline (DL-Pro) or L-proline (L-Pro), [RCT·DL-Pro]·2MeOH·3.5H2O (1) and 2[PCT·L-Pro]·2EtOH·10H2O (2), whose crystal structures have been determined. In each complex, the proline ligand is incorporated into the bowl-shaped cavity of RCT or PCT host molecules through Csbnd H … π interactions between alkyl protons of the pyrrolidine ring of proline and π-rings of RCT or PCT, forming an [RCT/PCT·Pro] structural fragment. In the crystal lattice, two [RCT/PCT·Pro] fragments self-associate to form a ligand-mediated dimeric structure, [RCT·D-Pro·L-Pro·RCT] in 1 or [PCT·L-Pro·L-Pro·PCT] in 2. A 1H NMR solution study gave the host‒ligand binding constants of 10.0 ± 1.1 M-1 for the RCT-DL-Pro system and 17.3 ± 1.3 M-1 for the PCT-L-Pro system. These complexes provide a synthetic model for the recognition of the proline residue in proline-containing substrates or inhibitors by enzymes through Csbnd H … π interaction. The CSD survey revealed that the absolute value of the torsion angle N-Cα-Csbnd O1 (O1 is cis to N) about the carboxyl Cα-C bond of proline is significantly smaller than that of the Cβ-Cα-Csbnd O2 (O2 is cis to Cβ) torsion angle.

Structure of TatA Paralog, TatE, Suggests a Structurally Homogeneous Form of Tat Protein Translocase That Transports Folded Proteins of Differing Diameter

PubMed Central

Baglieri, Jacopo; Beck, Daniel; Vasisht, Nishi; Smith, Corinne J.; Robinson, Colin

2012-01-01

The twin-arginine translocation (Tat) system transports folded proteins across bacterial and plant thylakoid membranes. Most current models for the translocation mechanism propose the coalescence of a substrate-binding TatABC complex with a separate TatA complex. In Escherichia coli, TatA complexes are widely believed to form the translocation pore, and the size variation of TatA has been linked to the transport of differently sized substrates. Here, we show that the TatA paralog TatE can substitute for TatA and support translocation of Tat substrates including AmiA, AmiC, and TorA. However, TatE is found as much smaller, discrete complexes. Gel filtration and blue native electrophoresis suggest sizes between ∼50 and 110 kDa, and single-particle processing of electron micrographs gives size estimates of 70–90 kDa. Three-dimensional models of the two principal TatE complexes show estimated diameters of 6–8 nm and potential clefts or channels of up to 2.5 nm diameter. The ability of TatE to support translocation of the 90-kDa TorA protein suggests alternative translocation models in which single TatA/E complexes do not contribute the bulk of the translocation channel. The homogeneity of both the TatABC and the TatE complexes further suggests that a discrete Tat translocase can translocate a variety of substrates, presumably through the use of a flexible channel. The presence and possible significance of double- or triple-ring TatE forms is discussed. PMID:22190680

Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn(2+) and Zn(2+) ions.

PubMed

Drozdzal, Pawel; Gilski, Miroslaw; Kierzek, Ryszard; Lomozik, Lechoslaw; Jaskolski, Mariusz

2013-06-01

X-ray crystal structures of the spermine(4+) form of the Z-DNA duplex with the self-complementary d(CG)3 sequence in complexes with Mn(2+) and Zn(2+) cations have been determined at the ultrahigh resolutions of 0.75 and 0.85 Å, respectively. Stereochemical restraints were only used for the sperminium cation (in both structures) and for nucleotides with dual conformation in the Zn(2+) complex. The Mn(2+) and Zn(2+) cations at the major site, designated M(2+)(1), bind at the N7 position of G6 by direct coordination. The coordination geometry of this site was octahedral, with complete hydration shells. An additional Zn(2+)(2) cation was bis-coordinated in a tetrahedral fashion by the N7 atoms of G10 and G12 from a symmetry-related molecule. The coordination distances of Zn(2+)(1) and Zn(2+)(2) to the O6 atom of the guanine residues were 3.613 (6) and 3.258 (5) Å, respectively. Moreover, a chloride ion was also identified in the coordination sphere of Zn(2+)(2). Alternate conformations were observed in the Z-DNA-Zn(2+) structure not only at internucleotide linkages but also at the terminal C3'-OH group of G12. The conformation of the sperminium chain in the Z-DNA-Mn(2+) complex is similar to the spermine(4+) conformation in analogous Z-DNA-Mg(2+) structures. In the Z-DNA-Zn(2+) complex the sperminium cation is disordered and partially invisible in electron-density maps. In the Z-DNA-Zn(2+) complex the sperminium cation only interacts with the phosphate groups of the Z-DNA molecules, while in the Z-DNA-Mn(2+) structure it forms hydrogen bonds to both the phosphate groups and DNA bases.

[Botulism: structure and function of botulinum toxin and its clinical application].

PubMed

Oguma, Keiji; Yamamoto, Yumiko; Suzuki, Tomonori; Fatmawati, Ni Nengah Dwi; Fujita, Kumiko

2012-08-01

Clostridium botulinum produces seven immunological distinct poisonous neurotoxins, A to G, with molecular masses of approximately 150kDa. In acidic foods and culture fluid, the neurotoxins associate with non-toxic components, and form large complexes designated progenitor toxins. The progenitor toxins are found in three forms named LL, L, and M. These neurotoxins and progenitor toxins were purified, and whole nucleotide sequences of their structure genes were determined. In this manuscript, the structure and function of these toxins, and the application of these toxins to clinical usage have been described.

Quaternary structure of a G-protein-coupled receptor heterotetramer in complex with Gi and Gs.

PubMed

Navarro, Gemma; Cordomí, Arnau; Zelman-Femiak, Monika; Brugarolas, Marc; Moreno, Estefania; Aguinaga, David; Perez-Benito, Laura; Cortés, Antoni; Casadó, Vicent; Mallol, Josefa; Canela, Enric I; Lluís, Carme; Pardo, Leonardo; García-Sáez, Ana J; McCormick, Peter J; Franco, Rafael

2016-04-05

G-protein-coupled receptors (GPCRs), in the form of monomers or homodimers that bind heterotrimeric G proteins, are fundamental in the transfer of extracellular stimuli to intracellular signaling pathways. Different GPCRs may also interact to form heteromers that are novel signaling units. Despite the exponential growth in the number of solved GPCR crystal structures, the structural properties of heteromers remain unknown. We used single-particle tracking experiments in cells expressing functional adenosine A1-A2A receptors fused to fluorescent proteins to show the loss of Brownian movement of the A1 receptor in the presence of the A2A receptor, and a preponderance of cell surface 2:2 receptor heteromers (dimer of dimers). Using computer modeling, aided by bioluminescence resonance energy transfer assays to monitor receptor homomerization and heteromerization and G-protein coupling, we predict the interacting interfaces and propose a quaternary structure of the GPCR tetramer in complex with two G proteins. The combination of results points to a molecular architecture formed by a rhombus-shaped heterotetramer, which is bound to two different interacting heterotrimeric G proteins (Gi and Gs). These novel results constitute an important advance in understanding the molecular intricacies involved in GPCR function.

Syntheses and structural characterization of mercury (II) coordination polymers with neutral bidentate flexible pyrazole-based ligands

NASA Astrophysics Data System (ADS)

Lalegani, Arash; Khaledi Sardashti, Mohammad; Salavati, Hossein; Asadi, Amin; Gajda, Roman; Woźniak, Krzysztof

2016-03-01

Mercury(II) coordination compounds [Hg(μ-bbd)(μ-SCN)4]n(1) and [Hg(bpp)(SCN)2] (2) were synthesized by using the neutral flexible bidentate N-donor ligands 1,4-bis(3,5-dimethypyrazol-1-yl)butane (bbd) and 1,3-bis(3,5-dimethylpyrazolyl)propane (bpp), NCS- ligand and appropriate mercury(II) salts. Compound 1 forms a polymeric network with moieties which are connected by SCN groups and the mercury ions present as HgN3S2 trigonal bipyramides. The crystal structure of 2 is build of monomers and the mercury(II) ion adopts an HgN2S2 tetrahedral geometry. In the complex 1, each bbd acts as bridging ligand connecting Hg(μ-SCN)4 ions, while in the complex 2, the bpp ligand is coordinated to an mercury(II) ion in a cyclic-bidentate fashion forming an eight-membered metallocyclic ring. Moreover, in the tetrahedral structure of 2, the neutral molecules form a 1D chain structure through the C-H···N hydrogen bonds, whereas in 1 no hydrogen bonds are observed. Coordination compounds 1 and 2 have been characterized by infrared spectroscopy, elemental analyses and single-crystal X-ray diffraction.

A quantum chemical study of the structures, stability, and spectroscopy of halogen- and hydrogen-boned complexes between cyanoacetaldehyde and hypochlorous acids

NASA Astrophysics Data System (ADS)

Tang, Qingjie; Guo, Zhenfu; Li, Qingzhong

2014-03-01

The complexes of cyanoacetaldehyde and hypohalous acid (HOX, X = Cl, Br, and I) have been investigated. They can form six different structures (A, B, C, D, E, and F), the former three structures are mainly combined through a N(O)⋯X halogen bond and the latter three structures are maintained mainly by a N(O)⋯H hydrogen bond, although other weaker interactions are also present in most structures. The hydrogen-bonded structures are more stable than the respective halogen-bonded structures. The Osbnd H and Osbnd X bonds in the halogen- and hydrogen-bonded complexes are lengthened and show an observed red shift, while those in the weaker secondary interactions are contracted and display a small blue shift. The orbital interactions in NBO analysis and the electron densities in AIM analysis provide useful and reliable information for the strength of each type of interaction in different structures.

Caught in the Act: 1.5 Å Resolution Crystal Structures of the HIV-1 Protease and the I54V Mutant Reveal a Tetrahedral Reaction Intermediate

PubMed Central

Kovalevsky, Andrey Y.; Chumanevich, Alexander A.; Liu, Fengling; Louis, John M.; Weber, Irene T.

2008-01-01

HIV-1 protease (PR) is the target for several important antiviral drugs used in AIDS therapy. The drugs bind inside the active-site cavity of PR where normally the viral poly-protein substrate is bound and hydrolyzed. We report two high resolution crystal structures of wild-type PR (PRWT) and the multi-drug resistant variant with the I54V mutation (PRI54V) in complex with a peptide at 1.46 Å and 1.50 Å resolution, respectively. The peptide forms a gem-diol tetrahedral reaction intermediate (TI) in the crystal structures. Distinctive interactions are observed for the TI binding in the active site cavity of PRWT and PRI54V. The mutant PRI54V /TI complex has lost water-mediated hydrogen bond interactions with the amides of Ile 50 and 50′ in the flap. Hence, the structures provide insight into the mechanism of drug resistance arising from this mutation. The structures also illustrate an intermediate state in the hydrolysis reaction. One of the gem-diol hydroxide groups in the PRWT complex forms a very short (2.3 Å) hydrogen bond with the outer carboxylate oxygen of Asp25. Quantum chemical calculations based on this TI structure are consistent with protonation of the inner carboxylate oxygen of Asp25′, in contrast to several theoretical studies. These TI complexes and quantum calculations are discussed in relation to the chemical mechanism of the peptide bond hydrolysis catalyzed by PR. PMID:18052235

Analysis of interstellar cloud structure based on IRAS images

NASA Technical Reports Server (NTRS)

Scalo, John M.

1992-01-01

The goal of this project was to develop new tools for the analysis of the structure of densely sampled maps of interstellar star-forming regions. A particular emphasis was on the recognition and characterization of nested hierarchical structure and fractal irregularity, and their relation to the level of star formation activity. The panoramic IRAS images provided data with the required range in spatial scale, greater than a factor of 100, and in column density, greater than a factor of 50. In order to construct densely sampled column density maps of star-forming clouds, column density images of four nearby cloud complexes were constructed from IRAS data. The regions have various degrees of star formation activity, and most of them have probably not been affected much by the disruptive effects of young massive stars. The largest region, the Scorpius-Ophiuchus cloud complex, covers about 1000 square degrees (it was subdivided into a few smaller regions for analysis). Much of the work during the early part of the project focused on an 80 square degree region in the core of the Taurus complex, a well-studied region of low-mass star formation.

A study on an unusual SN2 mechanism in the methylation of benzyne through nickel-complexation.

PubMed

Hatakeyama, Makoto; Sakamoto, Yuki; Ogata, Koji; Sumida, Yuto; Sumida, Tomoe; Hosoya, Takamitsu; Nakamura, Shinichiro

2017-10-11

In this study, three reaction mechanisms of a benzyne-nickel (Ni) complex ([Ni(C 6 H 4 )(dcpe)]) with iodomethane during the methylation process were investigated, namely (a) S N 2 reaction of the benzyne-Ni complex with iodomethane, (b) concerted σ-bond metathesis during the bond breaking/forming processes, and (c) oxidative addition of iodomethane to the Ni-center and the subsequent reductive elimination process. DFT calculations revealed that the reaction barrier of the S N 2 reaction is slightly lower than those of the other mechanisms. The results of orbital analyses suggest that [Ni(C 6 H 4 )(dcpe)] forms a metallacycle structure between benzyne and the Ni II (3d 8 ) center instead of the η 2 -structure with the Ni 0 (3d 10 ) center. The metallacycle structures became inappropriate as the intermediates of oxidative addition in the formation of the Ni II -Me bond, avoiding further oxidation to the high-valent Ni IV . The high free energy along σ-bond metathesis was generated from the steric hindrance, thus invoking methylation and Ni-I bond formation concertedly.

Structural modulation of factor VIIa by full-length tissue factor (TF1-263): implication of novel interactions between EGF2 domain and TF.

PubMed

Prasad, Ramesh; Sen, Prosenjit

2018-02-01

Tissue factor (TF)-mediated factor VII (FVII) activation and a subsequent proteolytic TF-FVIIa binary complex formation is the key step initiating the coagulation cascade, with implications in various homeostatic and pathologic scenarios. TF binding allosterically modifies zymogen-like free FVIIa to its highly catalytically active form. As a result of unresolved crystal structure of the full-length TF 1-263 -FVIIa binary complex and free FVIIa, allosteric alterations in FVIIa following its binding to full-length TF and the consequences of these on function are not entirely clear. The present study aims to map and identify structural alterations in FVIIa and TF resulting from full-length TF binding to FVIIa and the key events responsible for enhanced FVIIa activity in coagulation. We constructed the full-length TF 1-263 -FVIIa membrane bound complex using computational modeling and subjected it to molecular dynamics (MD) simulations. MD simulations showed that TF alters the structure of each domain of FVIIa and these combined alterations contribute to enhanced TF-FVIIa activity. Detailed, domain-wise investigation revealed several new non-covalent interactions between TF and FVIIa that were not found in the truncated soluble TF-FVIIa crystal structure. The structural modulation of each FVIIa domain imparted by TF indicated that both inter and intra-domain communication is crucial for allosteric modulation of FVIIa. Our results suggest that these newly formed interactions can provide additional stability to the protease domain and regulate its activity profile by governing catalytic triad (CT) orientation and localization. The unexplored newly formed interactions between EGF2 and TF provides a possible explanation for TF-induced allosteric activation of FVIIa.

Recombinant production and solution structure of lipid transfer protein from lentil Lens culinaris

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gizatullina, Albina K.; Moscow Institute of Physics and Technology; Finkina, Ekaterina I.

2013-10-04

Highlights: •Lipid transfer protein from lentil seeds (Lc-LTP2) was overexpressed in E. coli. •Antimicrobial activity and spatial structure of the recombinant Lc-LTP2 were examined. •Internal tunnel-like lipid-binding cavity occupies ∼7% of the total Lc-LTP2 volume. •Binding of DMPG lipid induces moderate rearrangements in the Lc-LTP2 structure. •Lc-LTP2/DMPG complex has limited lifetime and dissociates within tens of hours. -- Abstract: Lipid transfer protein, designated as Lc-LTP2, was isolated from seeds of the lentil Lens culinaris. The protein has molecular mass 9282.7 Da, consists of 93 amino acid residues including 8 cysteines forming 4 disulfide bonds. Lc-LTP2 and its stable isotope labeledmore » analogues were overexpressed in Escherichia coli and purified. Antimicrobial activity of the recombinant protein was examined, and its spatial structure was studied by NMR spectroscopy. The polypeptide chain of Lc-LTP2 forms four α-helices (Cys4-Leu18, Pro26-Ala37, Thr42-Ala56, Thr64-Lys73) and a long C-terminal tail without regular secondary structure. Side chains of the hydrophobic residues form a relatively large internal tunnel-like lipid-binding cavity (van der Waals volume comes up to ∼600 Å{sup 3}). The side-chains of Arg45, Pro79, and Tyr80 are located near an assumed mouth of the cavity. Titration with dimyristoyl phosphatidylglycerol (DMPG) revealed formation of the Lc-LTP2/lipid non-covalent complex accompanied by rearrangements in the protein spatial structure and expansion of the internal cavity. The resultant Lc-LTP2/DMPG complex demonstrates limited lifetime and dissociates within tens of hours.« less

Oligomeric Properties of Survival Motor Neuron·Gemin2 Complexes*

PubMed Central

Gupta, Kushol; Martin, Renee; Sharp, Robert; Sarachan, Kathryn L.; Ninan, Nisha S.; Van Duyne, Gregory D.

2015-01-01

The survival motor neuron (SMN) protein forms the oligomeric core of a multiprotein complex required for the assembly of spliceosomal small nuclear ribonucleoproteins. Deletions and mutations in the SMN1 gene are associated with spinal muscular atrophy (SMA), a devastating neurodegenerative disease that is the leading heritable cause of infant mortality. Oligomerization of SMN is required for its function, and some SMA patient mutations disrupt the ability of SMN to self-associate. Here, we investigate the oligomeric nature of the SMN·Gemin2 complexes from humans and fission yeast (hSMN·Gemin2 and ySMN·Gemin2). We find that hSMN·Gemin2 forms oligomers spanning the dimer to octamer range. The YG box oligomerization domain of SMN is both necessary and sufficient to form these oligomers. ySMN·Gemin2 exists as a dimer-tetramer equilibrium with Kd = 1.0 ± 0.9 μm. A 1.9 Å crystal structure of the ySMN YG box confirms a high level of structural conservation with the human ortholog in this important region of SMN. Disulfide cross-linking experiments indicate that SMN tetramers are formed by self-association of stable, non-dissociating dimers. Thus, SMN tetramers do not form symmetric helical bundles such as those found in glycine zipper transmembrane oligomers. The dimer-tetramer nature of SMN complexes and the dimer of dimers organization of the SMN tetramer provide an important foundation for ongoing studies to understand the mechanism of SMN-assisted small nuclear ribonucleoprotein assembly and the underlying causes of SMA. PMID:26092730

High-level ab initio studies of the complex formed between CO and O2

NASA Astrophysics Data System (ADS)

Grein, Friedrich

2017-05-01

The explicitly correlated CCSD(T)-F12 method with VXZ-F12 basis sets was used to find the most stable structures of the van der Waals CO-O2 complexes. With geometry optimizations performed up to the quadruple-zeta level and basis set extrapolation, the calculated interaction energies for the triplet complexes are 123 cm-1 for the H complex in Cs symmetry (slipped near-parallel structure), 118 cm-1 for the X complex, also in Cs symmetry (perpendicular alignment) and 116 cm-1 for the CO-O2 T complex in C2v symmetry. The corresponding CCSD(T)-F12 results using the aug-cc-pVXZ basis sets are nearly the same. Similar calculations were performed for the CO-O2 singlet complexes, which are shown to have much higher stabilization energies, the highest being 206 cm-1 for the X complex.

Development of a novel biosensing system based on the structural change of a polymerized guanine-quadruplex DNA nanostructure.

PubMed

Morita, Yo; Yoshida, Wataru; Savory, Nasa; Han, Sung Woong; Tera, Masayuki; Nagasawa, Kazuo; Nakamura, Chikashi; Sode, Koji; Ikebukuro, Kazunori

2011-08-15

By inserting an adenosine aptamer into an aptamer that forms a G-quadruplex, we developed an adaptor molecule, named the Gq-switch, which links an electrode with flavin adenine dinucleotide-dependent glucose dehydrogenase (FADGDH) that is capable of transferring electron to a electrode directly. First, we selected an FADGDH-binding aptamer and identified that its sequence is composed of two blocks of consecutive six guanine bases and it forms a polymerized G-quadruplex structure. Then, we inserted a sequence of an adenosine aptamer between the two blocks of consecutive guanine bases, and we found it also bound to adenosine. Then we named it as Gq-switch. In the absence of adenosine, the Gq-switch-FADGDH complex forms a 30-nm high bulb-shaped structure that changes in the presence of adenosine to give an 8-nm high wire-shaped structure. This structural change brings the FADGDH sufficiently close to the electrode for electron transfer to occur, and the adenosine can be detected from the current produced by the FADGDH. Adenosine was successfully detected with a concentration dependency using the Gq-switch-FADGDH complex immobilized Au electrode by measuring response current to the addition of glucose. Copyright © 2011 Elsevier B.V. All rights reserved.

Kinetic analyses of vasculogenesis inform mechanistic studies

PubMed Central

Winfree, Seth; Chu, Chenghao; Tu, Wanzhu; Blue, Emily K.; Gohn, Cassandra R.; Dunn, Kenneth W.

2017-01-01

Vasculogenesis is a complex process by which endothelial stem and progenitor cells undergo de novo vessel formation. Quantitative assessment of vasculogenesis is a central readout of endothelial progenitor cell functionality. However, current assays lack kinetic measurements. To address this issue, new approaches were developed to quantitatively assess in vitro endothelial colony-forming cell (ECFC) network formation in real time. Eight parameters of network structure were quantified using novel Kinetic Analysis of Vasculogenesis (KAV) software. KAV assessment of structure complexity identified two phases of network formation. This observation guided the development of additional vasculogenic readouts. A tissue cytometry approach was established to quantify the frequency and localization of dividing ECFCs. Additionally, Fiji TrackMate was used to quantify ECFC displacement and speed at the single-cell level during network formation. These novel approaches were then implemented to identify how intrauterine exposure to maternal diabetes mellitus (DM) impairs fetal ECFC vasculogenesis. Fetal ECFCs exposed to maternal DM form fewer initial network structures, which are not stable over time. Correlation analyses demonstrated that ECFC samples with greater division in branches form fewer closed network structures. Additionally, reductions in average ECFC movement over time decrease structural connectivity. Identification of these novel phenotypes utilizing the newly established methodologies provides evidence for the cellular mechanisms contributing to aberrant ECFC vasculogenesis. PMID:28100488

Polycrystalline structures formed in evaporating droplets as a parameter to test the action of Zincum metallicum 30c in a wheat seed model.

PubMed

Kokornaczyk, Maria Olga; Baumgartner, Stephan; Betti, Lucietta

2016-05-01

Polycrystalline structures formed inside evaporating droplets of different biological fluids have been shown sensitive towards various influences, including ultra high dilutions (UHDs), representing so a new approach potentially useful for basic research in homeopathy. In the present study we tested on a wheat seed model Zincum metallicum 30c efficacy versus lactose 30c and water. Stressed and non-stressed wheat seeds were watered with the three treatments. Seed-leakage droplets were evaporated and the polycrystalline structures formed inside the droplet residues were analyzed for their local connected fractal dimensions (LCFDs) (measure of complexity) using the software ImageJ. We have found significant differences in LCFD values of polycrystalline structures obtained from stressed seeds following the treatments (p<0.0001); Zincum metallicum 30c lowered the structures' complexity compared to lactose 30c and water. In non-stressed seeds no significant differences were found. The droplet evaporation method (DEM) might represent a potentially useful tool in basic research in homeopathy. Furthermore our results suggest a sensitization of the stressed model towards the treatment action, which is conforming to previous findings. Copyright © 2015 The Faculty of Homeopathy. Published by Elsevier Ltd. All rights reserved.

Redefining the modular organization of the core Mediator complex.

PubMed

Wang, Xuejuan; Sun, Qianqian; Ding, Zhenrui; Ji, Jinhua; Wang, Jianye; Kong, Xiao; Yang, Jianghong; Cai, Gang

2014-07-01

The Mediator complex plays an essential role in the regulation of eukaryotic transcription. The Saccharomyces cerevisiae core Mediator comprises 21 subunits, which are organized into Head, Middle and Tail modules. Previously, the Head module was assigned to a distinct dense domain at the base, and the Middle and Tail modules were identified to form a tight structure above the Head module, which apparently contradicted findings from many biochemical and functional studies. Here, we compared the structures of the core Mediator and its subcomplexes, especially the first 3D structure of the Head + Middle modules, which permitted an unambiguous assignment of the three modules. Furthermore, nanogold labeling pinpointing four Mediator subunits from different modules conclusively validated the modular assignment, in which the Head and Middle modules fold back on one another and form the upper portion of the core Mediator, while the Tail module forms a distinct dense domain at the base. The new modular model of the core Mediator has reconciled the previous inconsistencies between the structurally and functionally defined Mediator modules. Collectively, these analyses completely redefine the modular organization of the core Mediator, which allow us to integrate the structural and functional information into a coherent mechanism for the Mediator's modularity and regulation in transcription initiation.

Redefining the modular organization of the core Mediator complex

PubMed Central

Wang, Xuejuan; Sun, Qianqian; Ding, Zhenrui; Ji, Jinhua; Wang, Jianye; Kong, Xiao; Yang, Jianghong; Cai, Gang

2014-01-01

The Mediator complex plays an essential role in the regulation of eukaryotic transcription. The Saccharomyces cerevisiae core Mediator comprises 21 subunits, which are organized into Head, Middle and Tail modules. Previously, the Head module was assigned to a distinct dense domain at the base, and the Middle and Tail modules were identified to form a tight structure above the Head module, which apparently contradicted findings from many biochemical and functional studies. Here, we compared the structures of the core Mediator and its subcomplexes, especially the first 3D structure of the Head + Middle modules, which permitted an unambiguous assignment of the three modules. Furthermore, nanogold labeling pinpointing four Mediator subunits from different modules conclusively validated the modular assignment, in which the Head and Middle modules fold back on one another and form the upper portion of the core Mediator, while the Tail module forms a distinct dense domain at the base. The new modular model of the core Mediator has reconciled the previous inconsistencies between the structurally and functionally defined Mediator modules. Collectively, these analyses completely redefine the modular organization of the core Mediator, which allow us to integrate the structural and functional information into a coherent mechanism for the Mediator's modularity and regulation in transcription initiation. PMID:24810298

The Effects of Focus on Forms and Focus on Form in Teaching Complex Grammatical Structures

ERIC Educational Resources Information Center

Pawlak, Miroslaw

2012-01-01

The classroom-based study reported in the present paper sought to compare the effectiveness of the focus on forms (FonFs) and focus on form (FonF) approach in teaching English third conditional to Polish high school students. It involved three intact classes, randomly designated as FonF (n = 34), FonFs (n = 36), and Control (n = 35) with a pretest…

New insights into the coordination chemistry of Schiff bases derived from amino acids: Planar [Ni4] complexes with tyrosine side-chains

NASA Astrophysics Data System (ADS)

Muche, Simon; Hołyńska, Małgorzata

2017-08-01

Structure and properties of a rare metal complex of the chiral Schiff base ligand derived from ortho-vanillin and L-tyrosine are presented. This study is a continuation of research on ligands containing biologically compatible moieties. The ligand is also fully characterized in form of a sodium salt, in particular in solution, for the first time. The metal complex contains a unique bowl-shaped [Ni4] core. Its structure is investigated both in solution (ESI-MS, NMR) and in solid state (X-ray diffraction studies). Under certain conditions the complex can be isolated as crystalline DMF solvate which is studied in solid state.

Red/near-infrared luminescence tuning of group-14 element complexes of dipyrrins based on a central atom.

PubMed

Yamamura, Masaki; Albrecht, Marcel; Albrecht, Markus; Nishimura, Yoshinobu; Arai, Tatsuo; Nabeshima, Tatsuya

2014-02-03

A dipyrrin complex has been one of the most utilized fluorescent dyes, and a variety of dipyrrin complexes show intriguing functions based on the various coordination structures of the central element. We now report the synthesis, structure, and photophysical properties of germanium and stannane complexes of the N2O2-type tetradentate dipyrrin, L·Ge and L·Sn, which are heavier analogues of the previously reported dipyrrin silicon complex, L·Si. The central group-14 atoms of the monomeric complexes have geometries close to trigonal bipyramidal (TBP), in which the contribution of the square-pyramidal (SP) character becomes higher as the central atom is heavier. Interestingly, L·Sn formed a dimeric structure in the crystal. All complexes L·Si, L·Ge, and L·Sn showed a fluorescence in the red/NIR region. Fluorescence quantum yields of L·Ge and L·Sn are higher than that of L·Si. These results indicated that the central atom on the dipyrrin complexes contributes not only to the geometry difference but also to tuning the fluorescence properties.

Self-assembly of InAs ring complexes on InP substrates by droplet epitaxy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noda, T.; Mano, T.; Jo, M.

We report the self-assembly of InAs ring complexes on InP (100) substrates by droplet epitaxy. Single-ring, ring-disk complex, and concentric double-ring structures were formed by controlling the As beam flux and substrate temperature. A clear photoluminescence signal was detected in a sample where InAs rings were embedded in InGaAs.

Structure of the human transcobalamin beta domain in four distinct states

PubMed Central

Bloch, Joël S.; Ruetz, Markus; Kräutler, Bernhard

2017-01-01

Vitamin B12 (cyanocobalamin, CNCbl) is an essential cofactor-precursor for two biochemical reactions in humans. When ingested, cobalamins (Cbl) are transported via a multistep transport system into the bloodstream, where the soluble protein transcobalamin (TC) binds Cbl and the complex is taken up into the cells via receptor mediated endocytosis. Crystal structures of TC in complex with CNCbl have been solved previously. However, the initial steps of holo-TC assembly have remained elusive. Here, we present four crystal structures of the beta domain of human TC (TC-beta) in different substrate-bound states. These include the apo and CNCbl-bound states, providing insight into the early steps of holo-TC assembly. We found that in vitro assembly of TC-alpha and TC-beta to a complex was Cbl-dependent. We also determined the structure of TC-beta in complex with cobinamide (Cbi), an alternative substrate, shedding light on the specificity of TC. We finally determined the structure of TC-beta in complex with an inhibitory antivitamin B12 (anti-B12). We used this structure to model the binding of anti-B12 into full-length holo-TC and could rule out that the inhibitory function of anti-B12 was based on an inability to form a functional complex with TC. PMID:28910388

Textures on Mars: evidences of a biogenic environment

NASA Astrophysics Data System (ADS)

Rizzo, V.; Cantasano, N.

Sediments on Mars could be explained as the result of simple coalescing structures having the ability to produce oriented concretions and more complex forms, as are intertwined filaments of microspherules, laminae and "blueberries", growing from a microscopic scale to a macroscopic one. Of which we have examples in some terrestrial microbial community, especially in regards to cyanobacteria and their organosedimentary products named stromatolites. This study aims to describe the most-often structural features that occur, showing their mutual relations in passing from simple to complex forms. These relationships could explain the genesis and the funny shapes of "blueberries" as the result of two different processes: by an enrolling sheet of microspherules or by an internal growing of minor spherule aggregates.

Peptidoglycan-associated lipoprotein (Pal) of Gram-negative bacteria: function, structure, role in pathogenesis and potential application in immunoprophylaxis.

PubMed

Godlewska, Renata; Wiśniewska, Katarzyna; Pietras, Zbigniew; Jagusztyn-Krynicka, Elzbieta Katarzyna

2009-09-01

The protein Pal (peptidoglycan-associated lipoprotein) is anchored in the outer membrane (OM) of Gram-negative bacteria and interacts with Tol proteins. Tol-Pal proteins form two complexes: the first is composed of three inner membrane Tol proteins (TolA, TolQ and TolR); the second consists of the TolB and Pal proteins linked to the cell's OM. These complexes interact with one another forming a multiprotein membrane-spanning system. It has recently been demonstrated that Pal is essential for bacterial survival and pathogenesis, although its role in virulence has not been clearly defined. This review summarizes the available data concerning the structure and function of Pal and its role in pathogenesis.

Structural and functional analysis of the human POT1-TPP1 telomeric complex

DOE PAGES

Rice, Cory; Shastrula, Prashanth Krishna; Kossenkov, Andrew V.; ...

2017-04-10

POT1 and TPP1 are part of the shelterin complex and are essential for telomere length regulation and maintenance. Naturally occurring mutations of the telomeric POT1–TPP1 complex are implicated in familial glioma, melanoma and chronic lymphocytic leukaemia. Here we report the atomic structure of the interacting portion of the human telomeric POT1–TPP1 complex and suggest how several of these mutations contribute to malignant cancer. The POT1 C-terminus (POT1C) forms a bilobal structure consisting of an OB-fold and a holiday junction resolvase domain. TPP1 consists of several loops and helices involved in extensive interactions with POT1C. Biochemical data shows that several ofmore » the cancer-associated mutations, partially disrupt the POT1–TPP1 complex, which affects its ability to bind telomeric DNA efficiently. A defective POT1–TPP1 complex leads to longer and fragile telomeres, which in turn promotes genomic instability and cancer.« less

Testing the effect of habitat structure and complexity on nekton assemblages using experimental oyster reefs

USGS Publications Warehouse

Humphries, Austin T.; LaPeyre, Megan K.; Kimball, Matthew E.; Rozas, Lawrence P.

2011-01-01

Structurally complex habitats are often associated with more diverse and abundant species assemblages in both aquatic and terrestrial ecosystems. Biogenic reefs formed by the eastern oyster (Crassostrea virginica) are complex in nature and are recognized for their potential habitat value in estuarine systems along the US Atlantic and Gulf of Mexico coasts. Few studies, however, have examined the response of nekton to structural complexity within oyster reefs. We used a quantitative sampling technique to examine how the presence and complexity of experimental oyster reefs influence the abundance, biomass, and distribution of nekton by sampling reefs 4 months and 16 months post-construction. Experimental oyster reefs were colonized immediately by resident fishes and decapod crustaceans, and reefs supported a distinct nekton assemblage compared to mud-bottom habitat. Neither increased reef complexity, nor age of the experimental reef resulted in further changes in nekton assemblages or increases in nekton abundance or diversity. The presence of oyster reefs per se was the most important factor determining nekton usage.

Structural and functional analysis of the human POT1-TPP1 telomeric complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rice, Cory; Shastrula, Prashanth Krishna; Kossenkov, Andrew V.

POT1 and TPP1 are part of the shelterin complex and are essential for telomere length regulation and maintenance. Naturally occurring mutations of the telomeric POT1–TPP1 complex are implicated in familial glioma, melanoma and chronic lymphocytic leukaemia. Here we report the atomic structure of the interacting portion of the human telomeric POT1–TPP1 complex and suggest how several of these mutations contribute to malignant cancer. The POT1 C-terminus (POT1C) forms a bilobal structure consisting of an OB-fold and a holiday junction resolvase domain. TPP1 consists of several loops and helices involved in extensive interactions with POT1C. Biochemical data shows that several ofmore » the cancer-associated mutations, partially disrupt the POT1–TPP1 complex, which affects its ability to bind telomeric DNA efficiently. A defective POT1–TPP1 complex leads to longer and fragile telomeres, which in turn promotes genomic instability and cancer.« less

Chiral SiO2 and Ag@SiO2 Materials Templated by Complexes Consisting of Comblike Polyethyleneimine and Tartaric Acid.

PubMed

Yao, Dong-Dong; Murata, Hiroki; Tsunega, Seiji; Jin, Ren-Hua

2015-10-26

A facile avenue to fabricate micrometer-sized chiral (L-, D-) and meso-like (dl-) SiO2 materials with unique structures by using crystalline complexes (cPEI/tart), composed of comblike polyethyleneimine (cPEI) and L-, D-, or dl-tartaric acid, respectively, as catalytic templates is reported. Interestingly, both chiral crystalline complexes appeared as regularly left- and right-twisted bundle structures about 10 μm in length and about 5 μm in diameter, whereas the dl-form occurred as circular structures with about 10 μm diameter. Subsequently, SiO2 @cPEI/tart hybrids with high silica content (>55.0 wt %) were prepared by stirring a mixture containing tetramethoxysilane (TMOS) and the aggregates of the crystalline complexes in water. The chiral SiO2 hybrids and calcined chiral SiO2 showed very strong CD signals and a nanofiber-based morphology on their surface, whereas dl-SiO2 showed no CD activity and a nanosheet-packed disklike shape. Furthermore, metallic silver nanoparticles (Ag NPs) were encapsulated in each silica hybrid to obtain chiral (D and L forms) and meso-like (dl form) Ag@SiO2 composites. Also, the reaction between L-cysteine (Lcys) and these Ag@SiO2 composites was preliminarily investigated. Only chiral L- and D-Ag@SiO2 composites promoted the reaction between Lcys and Ag NPs to produce a molecular [Ag-Lcys]n complex with remarkable exciton chirality, whereas the reaction hardly occurred in the case of meso-like (dl-) Ag@SiO2 composite. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure of thallium(III) chloride, bromide, and cyanide complexes in aqueous solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blixt, J.; Glaser, J.; Sandstroem, M.

1995-05-10

The structures of the hydrated thallium(III) halide and pseudohalide complexes, [TlX{sub n}(OH{sub 2}){sub m}]{sup (3-d)+}, X = Cl, Br, CN, in aqueous solution have been studied by a combination of X-ray absorption fine structure spectroscopy (XAFS), large-angle X-ray scattering (LAXS), and vibrational spectroscopic (Raman and IR) techniques including far-infrared studies of aqueous solutions and some solid phases with known structures. The vibrational Tl-X frequencies of all complexes are reported, force constants are calculated using normal coordinate analysis, and assignments are given. The structural results are consistent with octahedral six-coordination for the cationic complexes Tl(OH{sub 2}){sub 6}{sup 3$PLU}, TlX(OH{sub 2}){sub 5}{supmore » 2+}, and trans-TlX{sub 2}(OH{sub 2}){sub 4}{sup +}. The coordination geometry changes to trigonal bipyramidal for the neutral TlBr{sub 3}(OH{sub 2}){sub 2} complex and possibly also for TlCl{sub 3}(OH{sub 2}){sub 2}. The TlX{sub 4}{sup -} complexes are all tetrahedral. Higher chloride complexes, TlCl{sub 5}(OH{sub 2}){sup 2-} and TlCl{sub 6}{sup 3-}, are formed and have again octahedral coordination geometry. 65 refs., 7 figs., 5 tabs.« less

Cryo-EM Structure of the TOM Core Complex from Neurospora crassa.

PubMed

Bausewein, Thomas; Mills, Deryck J; Langer, Julian D; Nitschke, Beate; Nussberger, Stephan; Kühlbrandt, Werner

2017-08-10

The TOM complex is the main entry gate for protein precursors from the cytosol into mitochondria. We have determined the structure of the TOM core complex by cryoelectron microscopy (cryo-EM). The complex is a 148 kDa symmetrical dimer of ten membrane protein subunits that create a shallow funnel on the cytoplasmic membrane surface. In the core of the dimer, the β-barrels of the Tom40 pore form two identical preprotein conduits. Each Tom40 pore is surrounded by the transmembrane segments of the α-helical subunits Tom5, Tom6, and Tom7. Tom22, the central preprotein receptor, connects the two Tom40 pores at the dimer interface. Our structure offers detailed insights into the molecular architecture of the mitochondrial preprotein import machinery. Copyright © 2017 Elsevier Inc. All rights reserved.

Design and synthesis of binucleating macrocyclic clefts derived from Schiff-base calixpyrroles.

PubMed

Givaja, Gonzalo; Volpe, Manuel; Leeland, James W; Edwards, Michael A; Young, Thomas K; Darby, S Barnie; Reid, Stuart D; Blake, Alexander J; Wilson, Claire; Wolowska, Joanna; McInnes, Eric J L; Schröder, Martin; Love, Jason B

2007-01-01

The syntheses, characterisation and complexation reactions of a series of binucleating Schiff-base calixpyrrole macrocycles are described. The acid-templated [2+2] condensations between meso-disubstituted diformyldipyrromethanes and o-phenylenediamines generate the Schiff-base pyrrolic macrocycles H(4)L(1) to H(4)L(6) upon basic workup. The single-crystal X-ray structures of both H(4)L(3).2 EtOH and H(4)L(6).H2O confirm that [2+2] cyclisation has occurred, with either EtOH or H2O hydrogen-bonded within the macrocyclic cleft. A series of complexation reactions generate the dipalladium [Pd2(L)] (L=L(1) to L(5)), dinickel [Ni2(L(1))] and dicopper [Cu2(L)] (L=L(1) to L(3)) complexes. All of these complexes have been structurally characterised in the solid state and are found to adopt wedged structures that are enforced by the rigidity of the aryl backbone to give a cleft reminiscent of the structures of Pacman porphyrins. The binuclear nickel complexes [Ni2(mu-OMe)2Cl2(HOMe)2(H(4)L(1))] and [Ni2(mu-OH)2Cl2(HOMe)(H(4)L(5))] have also been prepared, although in these cases the solid-state structures show that the macrocyclic ligand remains protonated at the pyrrolic nitrogen atoms, and the Ni(II) cations are therefore co-ordinated by the imine nitrogen atoms only to give an open conformation for the complex. The dicopper complex [Cu2(L(3))] was crystallised in the presence of pyridine to form the adduct [Cu2(py)(L(3))], in which, in the solid state, the pyridine ligand is bound within the binuclear molecular cleft. Reaction between H(4)L(1) and [Mn(thf){N(SiMe(3))2}2] results in clean formation of the dimanganese complex [Mn2(L(1))], which, upon crystallisation, formed the mixed-valent complex [Mn2(mu-OH)(L(1))] in which the hydroxo ligand bridges the metal centres within the molecular cleft.

Structural diversity of benzil bis(benzoylhydrazone): Mononuclear, binuclear and trinuclear complexes.

PubMed

López-Torres, Elena; Mendiola, M Antonia

2009-10-07

The coordination behaviour of the Schiff-base, benzil bis(benzoylhydrazone), LH(2) towards divalent nickel, lead, cadmium, zinc and copper ions has been investigated. The complexes have been fully characterized by techniques including (113)Cd and (207)Pb NMR, as well as (13)C and (113)Cd CP/MAS NMR and by single crystal X-ray diffraction. All the complexes have the general formula [ML](n) (n = 1-3 depending on the metal ion), with the ligand doubly deprotonated. The nickel complex [NiL] is a monomeric compound, the lead complex [PbL](2) shows a binuclear structure, whereas zinc [ZnL](3) and copper [CuL](3) complexes are trinuclear helicates. The cadmium complex seems to be a dimer with a structure similar to that of . In the nickel and lead derivatives, the ligand behaves as a tetradentate N(2)O(2) chelate and in complex also as a bridge through one of the O atoms. In the crystal structures of Zn and Cu complexes [ML](3) each metal is in a pentadentate N(3)O(2) environment formed by two different ligands, one tridentate chelate and the other bidentate chelate, giving rise to trinuclear helicates. These results point out the versatility of benzil bis(benzoylhydrazone) on its coordination.

Structure of UreG/UreF/UreH Complex Reveals How Urease Accessory Proteins Facilitate Maturation of Helicobacter pylori Urease

PubMed Central

Fong, Yu Hang; Wong, Ho Chun; Yuen, Man Hon; Lau, Pak Ho; Chen, Yu Wai; Wong, Kam-Bo

2013-01-01

Urease is a metalloenzyme essential for the survival of Helicobacter pylori in acidic gastric environment. Maturation of urease involves carbamylation of Lys219 and insertion of two nickel ions at its active site. This process requires GTP hydrolysis and the formation of a preactivation complex consisting of apo-urease and urease accessory proteins UreF, UreH, and UreG. UreF and UreH form a complex to recruit UreG, which is a SIMIBI class GTPase, to the preactivation complex. We report here the crystal structure of the UreG/UreF/UreH complex, which illustrates how UreF and UreH facilitate dimerization of UreG, and assembles its metal binding site by juxtaposing two invariant Cys66-Pro67-His68 metal binding motif at the interface to form the (UreG/UreF/UreH)2 complex. Interaction studies revealed that addition of nickel and GTP to the UreG/UreF/UreH complex releases a UreG dimer that binds a nickel ion at the dimeric interface. Substitution of Cys66 and His68 with alanine abolishes the formation of the nickel-charged UreG dimer. This nickel-charged UreG dimer can activate urease in vitro in the presence of the UreF/UreH complex. Static light scattering and atomic absorption spectroscopy measurements demonstrated that the nickel-charged UreG dimer, upon GTP hydrolysis, reverts to its monomeric form and releases nickel to urease. Based on our results, we propose a mechanism on how urease accessory proteins facilitate maturation of urease. PMID:24115911

Structural basis for inhibition of TLR2 by staphylococcal superantigen-like protein 3 (SSL3)

PubMed Central

Koymans, Kirsten J.; Feitsma, Louris J.; Brondijk, T. Harma C.; Aerts, Piet C.; Lukkien, Eddie; Lössl, Philip; van Kessel, Kok P. M.; de Haas, Carla J. C.; van Strijp, Jos A. G.; Huizinga, Eric G.

2015-01-01

Toll-like receptors (TLRs) are crucial in innate recognition of invading micro-organisms and their subsequent clearance. Bacteria are not passive bystanders and have evolved complex evasion mechanisms. Staphylococcus aureus secretes a potent TLR2 antagonist, staphylococcal superantigen-like protein 3 (SSL3), which prevents receptor stimulation by pathogen-associated lipopeptides. Here, we present crystal structures of SSL3 and its complex with TLR2. The structure reveals that formation of the specific inhibitory complex is predominantly mediated by hydrophobic contacts between SSL3 and TLR2 and does not involve interaction of TLR2–glycans with the conserved LewisX binding site of SSL3. In the complex, SSL3 partially covers the entrance to the lipopeptide binding pocket in TLR2, reducing its size by ∼50%. We show that this is sufficient to inhibit binding of agonist Pam2CSK4 effectively, yet allows SSL3 to bind to an already formed TLR2–Pam2CSK4 complex. The binding site of SSL3 overlaps those of TLR2 dimerization partners TLR1 and TLR6 extensively. Combined, our data reveal a robust dual mechanism in which SSL3 interferes with TLR2 activation at two stages: by binding to TLR2, it blocks ligand binding and thus inhibits activation. Second, by interacting with an already formed TLR2–lipopeptide complex, it prevents TLR heterodimerization and downstream signaling. PMID:26283364

Structural model of the p14/SF3b155 · branch duplex complex.

PubMed

Schellenberg, Matthew J; Dul, Erin L; MacMillan, Andrew M

2011-01-01

Human p14 (SF3b14), a component of the spliceosomal U2 snRNP, interacts directly with the pre-mRNA branch adenosine within the context of the bulged duplex formed between the pre-mRNA branch region and U2 snRNA. This association occurs early in spliceosome assembly and persists within the fully assembled spliceosome. Analysis of the crystal structure of a complex containing p14 and a peptide derived from p14-associated SF3b155 combined with the results of cross-linking studies has suggested that the branch nucleotide interacts with a pocket on a non-canonical RNA binding surface formed by the complex. Here we report a structural model of the p14 · bulged duplex interaction based on a combination of X-ray crystallography of an adenine p14/SF3b155 peptide complex, biochemical comparison of a panel of disulfide cross-linked protein-RNA complexes, and small-angle X-ray scattering (SAXS). These studies reveal specific recognition of the branch adenosine within the p14 pocket and establish the orientation of the bulged duplex RNA bound on the protein surface. The intimate association of one surface of the bulged duplex with the p14/SF3b155 peptide complex described by this model buries the branch nucleotide at the interface and suggests that p14 · duplex interaction must be disrupted before the first step of splicing.

Structural model of the p14/SF3b155·branch duplex complex

PubMed Central

Schellenberg, Matthew J.; Dul, Erin L.; MacMillan, Andrew M.

2011-01-01

Human p14 (SF3b14), a component of the spliceosomal U2 snRNP, interacts directly with the pre-mRNA branch adenosine within the context of the bulged duplex formed between the pre-mRNA branch region and U2 snRNA. This association occurs early in spliceosome assembly and persists within the fully assembled spliceosome. Analysis of the crystal structure of a complex containing p14 and a peptide derived from p14-associated SF3b155 combined with the results of cross-linking studies has suggested that the branch nucleotide interacts with a pocket on a non-canonical RNA binding surface formed by the complex. Here we report a structural model of the p14•bulged duplex interaction based on a combination of X-ray crystallography of an adenine p14/SF3b155 peptide complex, biochemical comparison of a panel of disulfide cross-linked protein–RNA complexes, and small-angle X-ray scattering (SAXS). These studies reveal specific recognition of the branch adenosine within the p14 pocket and establish the orientation of the bulged duplex RNA bound on the protein surface. The intimate association of one surface of the bulged duplex with the p14/SF3b155 peptide complex described by this model buries the branch nucleotide at the interface and suggests that p14•duplex interaction must be disrupted before the first step of splicing. PMID:21062891

Synthesis, spectral and quantum chemical studies on NO-chelating sulfamonomethoxine-cyclophosph(V)azane and its Er(III) complex.

PubMed

Alaghaz, Abdel-Nasser M A; Ammar, Reda A A; Koehler, Gottfried; Wolschann, Karl Peter; El-Gogary, Tarek M

2014-07-15

Computational studies have been carried out at the DFT-B3LYP/6-31G(d) level of theory on the structural and spectroscopic properties of novel ethane-1,2-diol-dichlorocyclophosph(V)azane of sulfamonomethoxine (L), and its binuclear Er(III) complex. Different tautomers of the ligand were optimized at the ab initio DFT level. Keto-form structure is about 15.8 kcal/mol more stable than the enol form (taking zpe correction into account). Simulated IR frequencies were scaled and compared with that experimentally measured. TD-DFT method was used to compute the UV-VIS spectra which show good agreement with measured electronic spectra. The structures of the novel isolated products are proposed based on elemental analyses, IR, UV-VIS, (1)H NMR, (31)P NMR, SEM, XRD spectra, effective magnetic susceptibility measurements and thermogravimetric analysis (TGA). Copyright © 2014 Elsevier B.V. All rights reserved.

Optically active single-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Peng, Xiaobin; Komatsu, Naoki; Bhattacharya, Sumanta; Shimawaki, Takanori; Aonuma, Shuji; Kimura, Takahide; Osuka, Atsuhiro

2007-06-01

The optical, electrical and mechanical properties of single-walled carbon nanotubes (SWNTs) are largely determined by their structures, and bulk availability of uniform materials is vital for extending their technological applications. Since they were first prepared, much effort has been directed toward selective synthesis and separation of SWNTs with specific structures. As-prepared samples of chiral SWNTs contain equal amounts of left- and right-handed helical structures, but little attention has been paid to the separation of these non-superimposable mirror image forms, known as optical isomers. Here, we show that optically active SWNT samples can be obtained by preferentially extracting either right- or left-handed SWNTs from a commercial sample. Chiral `gable-type' diporphyrin molecules bind with different affinities to the left- and right-handed helical nanotube isomers to form complexes with unequal stabilities that can be readily separated. Significantly, the diporphyrins can be liberated from the complexes afterwards, to provide optically enriched SWNTs.

Emulating porphyrins with a rippled multivacancy graphene system

NASA Astrophysics Data System (ADS)

Mombrú, Dominique; Faccio, Ricardo; Mombrú, Alvaro W.

2018-04-01

The interaction between a complex porphyrin-like system formed by an iron atom and multivacant graphene layer and O2, CO and CO2 molecules is studied, using Density Functional Theory (DFT) calculations. The multivacancy graphene system used for this study, consists in the removal of a 1,4-dimethybenzene-like moiety, in a 6 × 6 supercell. This removal and the structural optimization subsequently performed, yield to a biaxial vacancy, where the location of an iron atom embedded in it, lead to a system with resemblance to iron-porphyrin systems. This similar structure could be used to form complexes where gas molecules are allowed to interact with these iron-octavacant graphene systems. The study focuses on the structure of the system and the net magnetic moment for different gas molecules: O2, CO2 and CO. Rippling in the vacant graphene is enhanced through this interaction.

Molecular complexes of alprazolam with carboxylic acids, boric acid, boronic acids, and phenols. Evaluation of supramolecular heterosynthons mediated by a triazole ring.

PubMed

Varughese, Sunil; Azim, Yasser; Desiraju, Gautam R

2010-09-01

A series of molecular complexes, both co-crystals and salts, of a triazole drug-alprazolam-with carboxylic acids, boric acid, boronic acids, and phenols have been analyzed with respect to heterosynthons present in the crystal structures. In all cases, the triazole ring behaves as an efficient hydrogen bond acceptor with the acidic coformers. The hydrogen bond patterns exhibited with aromatic carboxylic acids were found to depend on the nature and position of the substituents. Being a strong acid, 2,6-dihydroxybenzoic acid forms a salt with alprazolam. With aliphatic dicarboxylic acids alprazolam forms hydrates and the water molecules play a central role in synthon formation and crystal packing. The triazole ring makes two distinct heterosynthons in the molecular complex with boric acid. Boronic acids and phenols form consistent hydrogen bond patterns, and these are seemingly independent of the substitutional effects. Boronic acids form noncentrosymmetric cyclic synthons, while phenols form O--H...N hydrogen bonds with the triazole ring.

A bacterial hydrogen-dependent CO2 reductase forms filamentous structures.

PubMed

Schuchmann, Kai; Vonck, Janet; Müller, Volker

2016-04-01

Interconversion of CO2 and formic acid is an important reaction in bacteria. A novel enzyme complex that directly utilizes molecular hydrogen as electron donor for the reversible reduction of CO2 has recently been identified in the Wood-Ljungdahl pathway of an acetogenic bacterium. This pathway is utilized for carbon fixation as well as energy conservation. Here we describe the further characterization of the quaternary structure of this enzyme complex and the unexpected behavior of this enzyme in polymerizing into filamentous structures. Polymerization of metabolic enzymes into similar structures has been observed only in rare cases but the increasing number of examples point towards a more general characteristic of enzyme functioning. Polymerization of the purified enzyme into ordered filaments of more than 0.1 μm in length was only dependent on the presence of divalent cations. Polymerization was a reversible process and connected to the enzymatic activity of the oxygen-sensitive enzyme with the filamentous form being the most active state. © 2016 Federation of European Biochemical Societies.

Structural and molecular interrogation of intact biological systems

PubMed Central

Chung, Kwanghun; Wallace, Jenelle; Kim, Sung-Yon; Kalyanasundaram, Sandhiya; Andalman, Aaron S.; Davidson, Thomas J.; Mirzabekov, Julie J.; Zalocusky, Kelly A.; Mattis, Joanna; Denisin, Aleksandra K.; Pak, Sally; Bernstein, Hannah; Ramakrishnan, Charu; Grosenick, Logan; Gradinaru, Viviana; Deisseroth, Karl

2014-01-01

Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease. PMID:23575631

Generating "fragment-based virtual library" using pocket similarity search of ligand-receptor complexes.

PubMed

Khashan, Raed S

2015-01-01

As the number of available ligand-receptor complexes is increasing, researchers are becoming more dedicated to mine these complexes to aid in the drug design and development process. We present free software which is developed as a tool for performing similarity search across ligand-receptor complexes for identifying binding pockets which are similar to that of a target receptor. The search is based on 3D-geometric and chemical similarity of the atoms forming the binding pocket. For each match identified, the ligand's fragment(s) corresponding to that binding pocket are extracted, thus forming a virtual library of fragments (FragVLib) that is useful for structure-based drug design. The program provides a very useful tool to explore available databases.

Super-complexes of adhesion GPCRs and neural guidance receptors

NASA Astrophysics Data System (ADS)

Jackson, Verity A.; Mehmood, Shahid; Chavent, Matthieu; Roversi, Pietro; Carrasquero, Maria; Del Toro, Daniel; Seyit-Bremer, Goenuel; Ranaivoson, Fanomezana M.; Comoletti, Davide; Sansom, Mark S. P.; Robinson, Carol V.; Klein, Rüdiger; Seiradake, Elena

2016-04-01

Latrophilin adhesion-GPCRs (Lphn1-3 or ADGRL1-3) and Unc5 cell guidance receptors (Unc5A-D) interact with FLRT proteins (FLRT1-3), thereby promoting cell adhesion and repulsion, respectively. How the three proteins interact and function simultaneously is poorly understood. We show that Unc5D interacts with FLRT2 in cis, controlling cell adhesion in response to externally presented Lphn3. The ectodomains of the three proteins bind cooperatively. Crystal structures of the ternary complex formed by the extracellular domains reveal that Lphn3 dimerizes when bound to FLRT2:Unc5, resulting in a stoichiometry of 1:1:2 (FLRT2:Unc5D:Lphn3). This 1:1:2 complex further dimerizes to form a larger `super-complex' (2:2:4), using a previously undescribed binding motif in the Unc5D TSP1 domain. Molecular dynamics simulations, point-directed mutagenesis and mass spectrometry demonstrate the stability and molecular properties of these complexes. Our data exemplify how receptors increase their functional repertoire by forming different context-dependent higher-order complexes.

Characterizing the Structure and Oligomerization of Major Royal Jelly Protein 1 (MRJP1) by Mass Spectrometry and Complementary Biophysical Tools.

PubMed

Mandacaru, Samuel C; do Vale, Luis H F; Vahidi, Siavash; Xiao, Yiming; Skinner, Owen S; Ricart, Carlos A O; Kelleher, Neil L; de Sousa, Marcelo Valle; Konermann, Lars

2017-03-21

Royal jelly (RJ) triggers the development of female honeybee larvae into queens. This effect has been attributed to the presence of major royal jelly protein 1 (MRJP1) in RJ. MRJP1 isolated from royal jelly is tightly associated with apisimin, a 54-residue α-helical peptide that promotes the noncovalent assembly of MRJP1 into multimers. No high-resolution structural data are available for these complexes, and their binding stoichiometry remains uncertain. We examined MRJP1/apisimin using a range of biophysical techniques. We also investigated the behavior of deglycosylated samples, as well as samples with reduced apisimin content. Our mass spectrometry (MS) data demonstrate that the native complexes predominantly exist in a (MRJP1 4 apisimin 4 ) stoichiometry. Hydrogen/deuterium exchange MS reveals that MRJP1 within these complexes is extensively disordered in the range of residues 20-265. Marginally stable secondary structure (likely antiparallel β-sheet) exists around residues 266-432. These weakly structured regions interchange with conformers that are extensively unfolded, giving rise to bimodal (EX1) isotope distributions. We propose that the native complexes have a "dimer of dimers" quaternary structure in which MRJP1 chains are bridged by apisimin. Specifically, our data suggest that apisimin acts as a linker that forms hydrophobic contacts involving the MRJP1 segment 316 VLFFGLV 322 . Deglycosylation produces large soluble aggregates, highlighting the role of glycans as aggregation inhibitors. Samples with reduced apisimin content form dimeric complexes with a (MRJP1 2 apisimin 1 ) stoichiometry. The information uncovered in this work will help pave the way toward a better understanding of the unique physiological role played by MRJP1 during queen differentiation.

Structural insights into NHEJ: building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time

PubMed Central

Williams, Gareth J.; Hammel, Michal; Radhakrishnan, Sarvan Kumar; Ramsden, Dale; Lees-Miller, Susan P.; Tainer, John A.

2014-01-01

Non-homologous end joining (NHEJ) is the major pathway for repair of DNA double-strand breaks (DSBs) in human cells. NHEJ is also needed for V(D)J recombination and the development of T and B cells in vertebrate immune systems, and acts in both the generation and prevention of non-homologous chromosomal translocations, a hallmark of genomic instability and many human cancers. X-ray crystal structures, cryo-electron microscopy envelopes, and small angle X-ray scattering (SAXS) solution conformations and assemblies are defining most of the core protein components for NHEJ: Ku70/Ku80 heterodimer; the DNA dependent protein kinase catalytic subunit (DNA-PKcs); the structure-specific endonuclease Artemis along with polynucleotide kinase/phosphatase (PNKP), aprataxin and PNKP related protein (APLF); the scaffolding proteins XRCC4 and XLF (XRCC4-like factor); DNA polymerases, and DNA ligase IV (Lig IV). The dynamic assembly of multi-protein NHEJ complexes at DSBs is regulated in part by protein phosphorylation. The basic steps of NHEJ have been biochemically defined to require: 1) DSB detection by the Ku heterodimer with subsequent DNA-PKcs tethering to form the DNA-PKcs-Ku-DNA complex (termed DNA-PK), 2) lesion processing, and 3) DNA end ligation by Lig IV, which functions in complex with XRCC4 and XLF. The current integration of structures by combined methods is resolving puzzles regarding the mechanisms, coordination and regulation of these three basic steps. Overall, structural results suggest the NHEJ system forms a flexing scaffold with the DNA-PKcs HEAT repeats acting as compressible macromolecular springs suitable to store and release conformational energy to apply forces to regulate NHEJ complexes and the DNA substrate for DNA end protection, processing, and ligation. PMID:24656613

The structure of human tripeptidyl peptidase II as determined by a hybrid approach.

PubMed

Schönegge, Anne-Marie; Villa, Elizabeth; Förster, Friedrich; Hegerl, Reiner; Peters, Jürgen; Baumeister, Wolfgang; Rockel, Beate

2012-04-04

Tripeptidyl-peptidase II (TPPII) is a high molecular mass (∼5 MDa) serine protease, which is thought to act downstream of the 26S proteasome, cleaving peptides released by the latter. Here, the structure of human TPPII (HsTPPII) has been determined to subnanometer resolution by cryoelectron microscopy and single-particle analysis. The complex is built from two strands forming a quasihelical structure harboring a complex system of inner cavities. HsTPPII particles exhibit some polymorphism resulting in complexes consisting of nine or of eight dimers per strand. To obtain deeper insights into the architecture and function of HsTPPII, we have created a pseudoatomic structure of the HsTPPII spindle using a comparative model of HsTPPII dimers and molecular dynamics flexible fitting. Analyses of the resulting hybrid structure of the HsTPPII holocomplex provide new insights into the mechanism of maturation and activation. Copyright © 2012 Elsevier Ltd. All rights reserved.

The structure of plant photosystem I super-complex at 2.8 Å resolution

PubMed Central

Mazor, Yuval; Borovikova, Anna; Nelson, Nathan

2015-01-01

Most life forms on Earth are supported by solar energy harnessed by oxygenic photosynthesis. In eukaryotes, photosynthesis is achieved by large membrane-embedded super-complexes, containing reaction centers and connected antennae. Here, we report the structure of the higher plant PSI-LHCI super-complex determined at 2.8 Å resolution. The structure includes 16 subunits and more than 200 prosthetic groups, which are mostly light harvesting pigments. The complete structures of the four LhcA subunits of LHCI include 52 chlorophyll a and 9 chlorophyll b molecules, as well as 10 carotenoids and 4 lipids. The structure of PSI-LHCI includes detailed protein pigments and pigment–pigment interactions, essential for the mechanism of excitation energy transfer and its modulation in one of nature's most efficient photochemical machines. DOI: http://dx.doi.org/10.7554/eLife.07433.001 PMID:26076232

Topological Entropy Measure of Artificial Grammar Complexity for Use in Designing Experiments on Human Performance in Intelligence, Surveillance, and Reconnaissance (ISR) Tasks

DTIC Science & Technology

2015-04-02

grammar may be stated as AA 6→ AA, so not form AAA xB 6→ BB, so not form xBB xS 6→ SS, so not form xSS SA 6→ AB, so not form SAB BA 6→ AS, so not form BAS... 350 . Dienes, Z., & Scott, R. (2005). Measuring Unconscious Knowledge: Distinguishing Structural Knowledge and Judgment Knowledge. Psychological

Engaging with Molecular Form to Understand Function

ERIC Educational Resources Information Center

Barber, Nicola C.; Stark, Louisa A.

2014-01-01

Cells are bustling factories with diverse and prolific arrays of molecular machinery. Remarkably, this machinery self-organizes to carry out the complex biochemical activities characteristic of life. When Watson and Crick published the structure of DNA, they noted that DNA base pairing creates a double-stranded form that provides a means of…

Synthetic humic substances and their use for remediation of contaminated environments

NASA Astrophysics Data System (ADS)

Dudare, Diana; Klavins, Maris

2014-05-01

Soils are increasingly subjected to different chemical stresses, because of increasing industrialization process and other factors. Different anthropogenic compounds (organic or inorganic in nature) upon entering the soil, may not only influence its productivity potential, but may also affect the quality of groundwater and food chain. Consequently, soils of different environments contain a complex mixture of contaminants, such as oil products, metals, organic solvents, acids, bases and radionuclides. Thereby greater focus should be paid to risk assessment and evaluation of remedial techniques in order to restore the quality of the soil and groundwater. The treatment technologies presently used to remove contaminants are physical, chemical and biological technologies. Many functional groups in the structure of humic substances determine their ability to interact with metal ions forming stable complexes and influencing speciation of metal ions in the environment, as well mobility, behaviour and speciation forms in the environment. Humic substances are suggested for use in the remediation of environments contaminated with metals, owing to complex forming properties. Several efforts have been undertaken with respect to synthesize humic substances for their structural studies. At the same time the real number of methods suggested for synthesis of humic substances is highly limited and their synthesis in general has been used mostly for their structural analysis. The present study deals with development of approaches for synthesis of humic substances with increased complex forming ability in respect to metal ions. Industrially produced humic substances (TEHUM) were used for comparison and after their modification their properties were analyzed for their elemental composition; functional group content changes in spectral characteristics. Synthetic humic substances showed significant differences in the number of functional groups and in ability to interact with the metal ions, which were reflected in their complexation properties towards metal ions. FTIR spectra gave evidence of the presence of metal ions, strongly bound and protected in inner sphere complexes. Considering a large scale of production of humic substances, the obtained synthetic humic substances with modified properties are perspective and sustainable areas of use. The obtained results of this study showed that synthetic humic substances can be used for remediation of environments contaminated with heavy metal ions.

Chelating DTPA amphiphiles: ion-tunable self-assembly structures and gadolinium complexes.

PubMed

Moghaddam, Minoo J; de Campo, Liliana; Kirby, Nigel; Drummond, Calum J

2012-10-05

A series of chelating amphiphiles and their gadolinium (Gd(III)) metal complexes have been synthesized and studied with respect to their neat and lyotropic liquid crystalline phase behavior. These amphiphiles have the ability to form ion-tunable self-assembly nanostructures and their associated Gd(III) complexes have potential as magnetic resonance imaging (MRI) contrast enhancement agents. The amphiphiles are composed of diethylenetriaminepentaacetic acid (DTPA) chelates conjugated to one or two oleyl chain(s) (DTPA-MO and DTPA-BO), or isoprenoid-type chain(s) of phytanyl (DTPA-MP and DTPA-BP). The thermal phase behavior of the neat amphiphiles was examined by differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and cross polarizing optical microscopy (POM). Self-assembly of neat amphiphiles and their associated Gd complexes, as well as their lyotropic phase behavior in water and sodium acetate solutions of different ionic strengths, were examined by POM and small and wide angle X-ray scattering (SWAXS). All neat amphiphiles exhibited lamellar structures. The non-complexed amphiphiles showed a variety of lyotropic phases depending on the number and nature of the hydrophobic chain in addition to the ionic state of the hydration. Upon hydration with increased Na-acetate concentration and the subtle changes in the effective headgroup size, the interfacial curvature of the amphiphile increased, altering the lyotropic liquid crystalline structures towards higher order mesophases such as the gyroid (Ia3d) bicontinuous cubic phase. The chelation of Gd with the DTPA amphiphiles resulted in lamellar crystalline structures for all the neat amphiphiles. Upon hydration with water, the Gd-complexed mono-conjugates formed micellar or vesicular self-assemblies, whilst the bis-conjugates transformed only partially into lyotropic liquid crystalline mesophases.

Solution structure of a DNA complex with the fluorescent bis-intercalator TOTO determined by NMR spectroscopy.

PubMed

Spielmann, H P; Wemmer, D E; Jacobsen, J P

1995-07-11

We have used two-dimensional 1H NMR spectroscopy to determine the solution structure of the DNA oligonucleotide d(5'-CGCTAGCG-3')2 complexed with the bis-intercalating dye 1,1'-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)bis[4-(3-methyl -2,3- dihydrobenzo-1,3-thiazolyl-2-methylidene)qui nolinium] tetraiodide (TOTO). The determination of the structure was based on total relaxation matrix analysis of the NOESY cross-peak intensities using the program MARDIGRAS. Improved procedures to consider the experimental "noise" in NOESY spectra during these calculations have been employed. The NOE-derived distance restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for the TOTO complex from both A-form and B-form dsDNA starting structures. The root-mean-square (rms) deviation of the coordinates for the 40 structures of the complex was 1.45 A. The local DNA structure is distorted in the complex. The helix is unwound by 60 degrees and has an overall helical repeat of 12 base pairs, caused by bis-intercalation of TOTO. The poly(propylenamine) linker chain is located in the minor groove of dsDNA. Calculations indicate that the benzothiazole ring system is twisted relative to the quinoline in the uncomplexed TOTO molecule. The site selectivity of TOTO for the CTAG-CTAG site is explained by its ability to adapt to the base pair propeller twist of dsDNA to optimize stacking and the hydrophobic interaction between the thymidine methyl group and the benzothiazole ring. There is a 3000-fold fluorescence enhancement upon binding of TOTO to dsDNA. Rotation about the cyanine methine bonds is possible in free TOTO, allowing relaxation nonradiatively. When bound to dsDNA, the benzothiazole ring and the quinolinium ring are clamped by the nucleobases preventing this rotation, and the chromophore loses excitation energy by fluorescence instead.

Isolated glyoxylic acid-water 1:1 complexes in low temperature argon matrices.

PubMed

Lundell, Jan; Olbert-Majkut, Adriana

2015-02-05

The 1:1 hydrogen bonded complexes between glyoxylic acid (GA) and water are studied in low temperature argon matrices. Four different complex structures were found in deposited matrices. The lowest energy conformer (T1) of GA was found to form complex, where the water molecule was attached to the opposite side of the intramolecular hydrogen bond in the molecule (T1B). Interestingly, this complex was estimated to be+8.0 kJ mol(-1) higher in energy than the most stable structure (T1A), where the water is inserted into the internal hydrogen bond, and also found in solid argon but in smaller abundance. For the second-lowest energy conformer of GA (T2), the two lowest-energy complex structures were identified, with the most stable complex structure (T2A) also being the most abundant in the matrices. The difference between experiment and computational energetic order of the two complex structures of the same GA conformer is explained by contributions of deformation energy upon complexation and the effect of the environment. The computed BSSE-corrected interaction energies are for the two most stable complexes of the two GA conformers for T1A and T2A -42.11 and -45.03 kJ mol(-1), respectively, at the CCSD(T)/aug-cc-pVTZ//B3LYP/aug-cc-pVTZ level of theory. Copyright © 2013 Elsevier B.V. All rights reserved.

The molten glass sewing machine

PubMed Central

Inamura, Chikara; Lizardo, Daniel; Franchin, Giorgia; Stern, Michael; Houk, Peter; Oxman, Neri

2017-01-01

We present a fluid-instability-based approach for digitally fabricating geometrically complex uniformly sized structures in molten glass. Formed by mathematically defined and physically characterized instability patterns, such structures are produced via the additive manufacturing of optically transparent glass, and result from the coiling of an extruded glass thread. We propose a minimal geometrical model—and a methodology—to reliably control the morphology of patterns, so that these building blocks can be assembled into larger structures with tailored functionally and optically tunable properties. This article is part of the themed issue ‘Patterning through instabilities in complex media: theory and applications’. PMID:28373379

Pwp2 mediates UTP-B assembly via two structurally independent domains.

PubMed

Boissier, Fanny; Schmidt, Christina Maria; Linnemann, Jan; Fribourg, Sébastien; Perez-Fernandez, Jorge

2017-06-09

The SSU processome constitutes a large ribonucleoprotein complex involved in the early steps of ribosome biogenesis. UTP-B is one of the first multi-subunit protein complexes that associates with the pre-ribosomal RNA to form the SSU processome. To understand the molecular basis of the hierarchical assembly of the SSU-processome, we have undergone a structural and functional analysis of the UTP-B subunit Pwp2p. We show that Pwp2p is required for the proper assembly of UTP-B and for a productive association of UTP-B with pre-rRNA. These two functions are mediated by two distinct structural domains. The N-terminal domain of Pwp2p folds into a tandem WD-repeat (tWD) that associates with Utp21p, Utp18p, and Utp6p to form a core complex. The CTDs of Pwp2p and Utp21p mediate the assembly of the heterodimer Utp12p:Utp13p that is required for the stable incorporation of the UTP-B complex in the SSU processome. Finally, we provide evidence suggesting a role of UTP-B as a platform for the binding of assembly factors during the maturation of 20S rRNA precursors.

Structure of a HOIP/E2~ubiquitin complex reveals RBR E3 ligase mechanism and regulation

PubMed Central

Lechtenberg, Bernhard C.; Rajput, Akhil; Sanishvili, Ruslan; Dobaczewska, Małgorzata K.; Ware, Carl F.; Mace, Peter D.; Riedl, Stefan J.

2015-01-01

Ubiquitination is a central process affecting all facets of cellular signaling and function1. A critical step in ubiquitination is the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to a substrate or a growing ubiquitin chain, which is mediated by E3 ubiquitin ligases. RING-type E3 ligases typically facilitate the transfer of ubiquitin from the E2 directly to the substrate2,3. The RBR family of RING-type E3 ligases, however, breaks this paradigm by forming a covalent intermediate with ubiquitin similarly to HECT-type E3 ligases4–6. The RBR family includes Parkin4 and HOIP, the central catalytic factor of the linear ubiquitin chain assembly complex (LUBAC)7. While structural insights into the RBR E3 ligases Parkin and HHARI in their overall autoinhibited forms are available8–13, no structures exist of intact fully active RBR E3 ligases or any of their complexes. Thus, the RBR mechanism of action has remained largely enigmatic. Here we present the first structure of the fully active HOIP-RBR in its transfer complex with an E2~ubiquitin conjugate, which elucidates the intricate nature of RBR E3 ligases. The active HOIP-RBR adopts a conformation markedly different from that of autoinhibited RBRs. HOIP-RBR binds the E2~ubiquitin conjugate in an elongated fashion, with the E2 and E3 catalytic centers ideally aligned for ubiquitin transfer, which structurally both requires and enables a HECT-like mechanism. In addition, surprisingly, three distinct helix–IBR-fold motifs inherent to RBRs form ubiquitin-binding regions that engage the activated ubiquitin of the E2~Ub conjugate as well as an additional regulatory ubiquitin molecule. The features uncovered reveal critical states of the HOIP-RBR E3 ligase cycle, and comparison with Parkin and HHARI suggests a general mechanism for RBR E3 ligases. PMID:26789245

Ophthalmic drug dosage forms: characterisation and research methods.

PubMed

Baranowski, Przemysław; Karolewicz, Bożena; Gajda, Maciej; Pluta, Janusz

2014-01-01

This paper describes hitherto developed drug forms for topical ocular administration, that is, eye drops, ointments, in situ gels, inserts, multicompartment drug delivery systems, and ophthalmic drug forms with bioadhesive properties. Heretofore, many studies have demonstrated that new and more complex ophthalmic drug forms exhibit advantage over traditional ones and are able to increase the bioavailability of the active substance by, among others, reducing the susceptibility of drug forms to defense mechanisms of the human eye, extending contact time of drug with the cornea, increasing the penetration through the complex anatomical structure of the eye, and providing controlled release of drugs into the eye tissues, which allows reducing the drug application frequency. The rest of the paper describes recommended in vitro and in vivo studies to be performed for various ophthalmic drugs forms in order to assess whether the form is acceptable from the perspective of desired properties and patient's compliance.

Structure of Franciscan complex in the Stanley Mountain window, Southern Coast ranges, California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Korsch, R.J.

1982-11-01

Three sets of deformational events are recognized in the Franciscan Complex of the Stanley Mt. area, S. Coast ranges, California. First, in pre-melange time, shortening of the relatively cohesive sequence of interbedded graywacke and mudstone formed isoclinal folds and an axial-plane slaty cleavage. Second, fragmentation of the once cohesive sequence, probably over a considerable period of time, produced the configuration now considered a melange. Third, after the melange developed, the Franciscan Complex was deformed along with the surrounding upper Mesozoic Great Valley sequence into the Stanley Mt. antiform. In the cohesive Upper Cretaceous Carrie Creek Formation, macroscopic and mesoscopic foldsmore » have 2 predominant orientations. The less cohesive Franciscan Complex attempted to fold, as shown by the distribution of shear foliations on stereographic projections, but lack of lithologic continuity and slip along previously formed shear fractures prevents the recognition of macroscopic folds. Hence, in the Franciscan Complex of the Stanley Mt. window, several lines of evidence show that the melange structure is tectonic in origin, not just a tectonic imprint superimposed upon already chaotic rocks of sedimentary origin (olistostromes). 43 references.« less

Structure-Function Relationship of the Bik1-Bim1 Complex.

PubMed

Stangier, Marcel M; Kumar, Anil; Chen, Xiuzhen; Farcas, Ana-Maria; Barral, Yves; Steinmetz, Michel O

2018-04-03

In budding yeast, the microtubule plus-end tracking proteins Bik1 (CLIP-170) and Bim1 (EB1) form a complex that interacts with partners involved in spindle positioning, including Stu2 and Kar9. Here, we show that the CAP-Gly and coiled-coil domains of Bik1 interact with the C-terminal ETF peptide of Bim1 and the C-terminal tail region of Stu2, respectively. The crystal structures of the CAP-Gly domain of Bik1 (Bik1CG) alone and in complex with an ETF peptide revealed unique, functionally relevant CAP-Gly elements, establishing Bik1CG as a specific C-terminal phenylalanine recognition domain. Unlike the mammalian CLIP-170-EB1 complex, Bik1-Bim1 forms ternary complexes with the EB1-binding motifs SxIP and LxxPTPh, which are present in diverse proteins, including Kar9. Perturbation of the Bik1-Bim1 interaction in vivo affected Bik1 localization and astral microtubule length. Our results provide insight into the role of the Bik1-Bim1 interaction for cell division, and demonstrate that the CLIP-170-EB1 module is evolutionarily flexible. Copyright © 2018 Elsevier Ltd. All rights reserved.

Ophthalmic Drug Dosage Forms: Characterisation and Research Methods

PubMed Central

Baranowski, Przemysław; Karolewicz, Bożena; Gajda, Maciej; Pluta, Janusz

2014-01-01

This paper describes hitherto developed drug forms for topical ocular administration, that is, eye drops, ointments, in situ gels, inserts, multicompartment drug delivery systems, and ophthalmic drug forms with bioadhesive properties. Heretofore, many studies have demonstrated that new and more complex ophthalmic drug forms exhibit advantage over traditional ones and are able to increase the bioavailability of the active substance by, among others, reducing the susceptibility of drug forms to defense mechanisms of the human eye, extending contact time of drug with the cornea, increasing the penetration through the complex anatomical structure of the eye, and providing controlled release of drugs into the eye tissues, which allows reducing the drug application frequency. The rest of the paper describes recommended in vitro and in vivo studies to be performed for various ophthalmic drugs forms in order to assess whether the form is acceptable from the perspective of desired properties and patient's compliance. PMID:24772038

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Jing-Yun, E-mail: jyunwu@ncnu.edu.tw; Tsai, Chi-Jou; Chang, Ching-Yun

A Zn(II)−salicylaldimine complex [Zn(L{sup salpyca})(H{sub 2}O)]{sub n} (1, where H{sub 2}L{sup salpyca}=4-hydroxy-3-(((pyridin-2-yl)methylimino)methyl)benzoic acid), with a one-dimensional (1D) chain structure, has been successfully converted to a discrete Ni(II)−salicylaldimine complex [Ni(L{sup salpyca})(H{sub 2}O){sub 3}] (2) and an infinite Cu(II)−salicylaldimine complex ([Cu(L{sup salpyca})]·3H{sub 2}O){sub n} (3) through a metal-ion exchange induced structural transformation process. However, such processes do not worked by Mn(II) and Co(II) ions. Solid-state structure analyses reveal that complexes 1–3 form comparable coordinative or supramolecular zigzag chains running along the crystallographic [201] direction. In addition, replacing Zn(II) ion by Ni(II) and Cu(II) ions caused changes in coordination environment and sphere ofmore » metal centers, from a 5-coordinate intermediate geometry of square pyramidal and trigonal bipyramidal in 1 to a 6-coordinate octahedral geometry in 2, and to a 4-coordiante square planar geometry in 3. This study shows that metal-ion exchange serves as a very efficient way of forming new coordination complexes that may not be obtained through direct synthesis. - Graphical abstract: A Zn(II)−salicylaldimine zigzag chain has been successfully converted to a Ni(II)−salicylaldimine supramolecular zigzag chain and a Cu(II)−salicylaldimine coordinative zigzag chain through metal-ion exchange induced structural transformations, which is not achieved by Mn(II) and Co(II) ions.« less

Optimal Rating Procedures and Methodology for NAEP Open- Ended Items. Working Paper Series.

ERIC Educational Resources Information Center

Patz, Richard J.; Wilson, Mark; Hoskens, Machteld

The National Assessment of Educational Progress (NAEP) collects data in the form of repeated, discrete measures (test items) with hierarchical structure for both measures and subjects, that is complex by any standard. This complexity has been managed through a "divide and conquer" approach of isolating and evaluating sources of…

Immunostimulatory complexes containing Eimeria tenella antigens and low toxicity plant saponins induce antibody response and provide protection from challenge in broiler chickens

USDA-ARS?s Scientific Manuscript database

Immunostimulating complexes (ISCOMs) are unique multimolecular structures formed by encapsulating antigens, lipids and triterpene saponins and are one of the most successful antigen delivery systems for microbial antigens. In the current study, both the route of administration and the antigen conce...

Discovering Structure in High-Dimensional Data Through Correlation Explanation

DTIC Science & Technology

2014-12-08

transforming complex data into simpler, more meaningful forms goes under the rubric of representation learning [2] which shares many goals with...Zhivotovsky, and M.W. Feldman. Genetic structure of human populations. Science, 298(5602):2381–2385, 2002. [14] K. Bache and M. Lichman. UCI machine

Evolution Process and Structural Analysis of Precambrian Jirisan Metamorphic and Sancheong Anorthosite Complexes in the Jirisan Province, Yeongnam Massif, Korea

NASA Astrophysics Data System (ADS)

Kang, J. H.; Lee, D. S.

2016-12-01

The Jirisan metamorphic complex consists mainly of schist, blastoporphyritic granite gneiss, granitic gneiss, leucocratic gneiss, biotite gneiss, banded gneiss, migmatitic gneiss and granite gneiss. The Paleoproterozoic (1.87 1.79 Ga) Sancheong anorthosite complex, which intrude it, is classified into massive-type and foliation-type Sancheong anorthosite, Fe-Ti ore body, and mafic granulite which were formed from the multiple fractionation and polybaric crystallization of the coeval and cogenetic magma. These complexes went at least through three times of ductile deformation during Early Proterozoic Late Paleozoic. The D1 deformation formed sheath or "A" type folds and its characteristic orientation was uncertain due to the intensive multi-deformation superimposed after that. The D2 deformation occurred under the EW- or WNW-directed tectonic compression, and formed a regional NS or NNE trend of isoclinal and intrafolial folds and an extensive ductile shear zone accompanied by mylonitization. The D3 deformation occurred under the NS- or NNW-directed tectonic compression environment, and formed an EW or ENE trend of open and tight folds and a partial semibrittle shear zone accompanied by mylonitization, and rearranged the NS-trend pre-D3 structural elements into (E)NE or (W)NW direction. The D2 deformation generally increases from the center toward the margin of Sancheong anorthosite complex but is more intensive in the eastern than western parts of Sancheong anorthosite complex. While the D3 deformation is inversely more intensive in the its western than eastern parts. The D2 and D3 deformations are closely related to the distribution features of Sancheong anorthosite complex. These three tectonic events are expected to give important information in understanding and reconstructing the tectonic movement after the formation of Columbia Supercontinent as well as the present NS-trend tectonic frame of the Jirisan province of the Yeongnam massif, the Korean Peninsula.

Looping and clustering model for the organization of protein-DNA complexes on the bacterial genome

NASA Astrophysics Data System (ADS)

Walter, Jean-Charles; Walliser, Nils-Ole; David, Gabriel; Dorignac, Jérôme; Geniet, Frédéric; Palmeri, John; Parmeggiani, Andrea; Wingreen, Ned S.; Broedersz, Chase P.

2018-03-01

The bacterial genome is organized by a variety of associated proteins inside a structure called the nucleoid. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the looping and clustering model, which employs a statistical physics approach to describe protein-DNA complexes. The looping and clustering model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins that is organized around a single high-affinity binding site. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and loop closure entropy of this protein-DNA cluster on the one hand, and the positional entropy for placing loops within the cluster on the other. Indeed, we show that the protein interaction strength determines the ‘tightness’ of the loopy protein-DNA complex. Thus, our model provides a theoretical framework for quantitatively computing the binding profiles of ParB-like proteins around a cognate (parS) binding site.

Hydrothermal synthesis and crystal structure of alkaline earth metal (Mg, Ca) based on 2,5-Dimethylbenzene-1,4-diylbis(methylene) diphosphonic acid

NASA Astrophysics Data System (ADS)

Xie, Y. C.; Cheng, Q. R.; Pan, Z. Q.

2018-02-01

New magnesium phosphonates Mg(H2L)31 (H4L = 2,5-dimethylbenzene-1,4 -diylbis(methylene)diphosphonic acid) and Ca(H2L)·2H2O 2 have been hydrothermally synthesized from H4L and the corresponding metal salts. Complex 1 and 2 have been characterized by IR, powder and single-crystal X-ray diffraction methods. Complex 1 crystallizes in trigonal space group R-3c and complex 2 belongs to the triclinic space group. The complexes both form two-dimensional (2D) network structure and show three-dimensional (3D) network through hydrogen bonds. Thermal stability of complex 1 and 2 have also been investigated. CCDC: 1534599 for 1; 1536423 for 2.

Molecular structure of human KATP in complex with ATP and ADP

PubMed Central

Lee, Kenneth Pak Kin

2017-01-01

In many excitable cells, KATP channels respond to intracellular adenosine nucleotides: ATP inhibits while ADP activates. We present two structures of the human pancreatic KATP channel, containing the ABC transporter SUR1 and the inward-rectifier K+ channel Kir6.2, in the presence of Mg2+ and nucleotides. These structures, referred to as quatrefoil and propeller forms, were determined by single-particle cryo-EM at 3.9 Å and 5.6 Å, respectively. In both forms, ATP occupies the inhibitory site in Kir6.2. The nucleotide-binding domains of SUR1 are dimerized with Mg2+-ATP in the degenerate site and Mg2+-ADP in the consensus site. A lasso extension forms an interface between SUR1 and Kir6.2 adjacent to the ATP site in the propeller form and is disrupted in the quatrefoil form. These structures support the role of SUR1 as an ADP sensor and highlight the lasso extension as a key regulatory element in ADP’s ability to override ATP inhibition. PMID:29286281

THE BIOLOGICAL ACTIVITY OF SOLUBLE ANTIGEN-ANTIBODY COMPLEXES

PubMed Central

Ishizaka, Kimishige; Ishizaka, Teruko; Campbell, Dan H.

1959-01-01

Soluble BSA-anti-BSA complexes, formed in antigen excess, give immediate skin reactions in normal guinea pigs. The mechanism of the reaction is not that of passive or reversed passive anaphylaxis. The complex itself is toxic. Skin activity of the complex depends on its composition. It has become obvious that the complex composed of two antigen molecules and one antibody molecule, (Ag2Ab), does not have the activity, whereas, Ag3Ab2 and more complicated complexes do. The role of complement as well as speculation on the structural changes of antibody-antigen complexes is presented. PMID:13620844

[Lipoproteins as a specific circulatory transport system].

PubMed

Titov, V N

1998-01-01

In accordance with the systemic approach, each circulatory transport system is highly specific and transports an elementary substance from cell to cell in the hydrated medium. In the author's opinion, the lipoprotein system has also a functional specificity and carries the elementary substance fatty acid in the blood stream. A great variety of fatty acids, the individuality of their physicochemical properties, great stereochemic differences of saturated and polyenic fatty acids make their transport virtually impossible. The steric individuality of fatty acids can be reduced if the acids are covalently bonded by a matrix as complex lipids. For formation of complex lipids, nature prefers esterification of fatty acids with alcohols which have a varying hydrophoby, such as glycerol, sphingosine, cholesterol, cetyl alcohol. The steric differences of saturated and polyenic fatty acids form a basis for their being structurized in different lipids. Triacyl glycerides are a transport form of saturated, monounsaturated fatty acids and their transforms and give rise to a crystalline phase. Phospholipids and cholesterol esters are a transport form of mainly polyunsaturated fatty acids in the polar phase in the former case and in the crystalline phase in the latter one. The individual apolipoproteins structure complex lipids into individual lipoprotein particles and transport them in the hydrated medium of blood flow. Saturated fatty acids chiefly transport lipoprotein particles formed by apoB-48- and apoB-100-isoproteins. Polyenic acids transport mainly high-density apoA-1-lipoprotein particles, which makes up a main physiological function of the latter. Cholesterol is nothing more than a matrix; it reesterifies polyenic fatty acids from the polar transport form of phospholipids into the unpolar transport form of cholesterol esters. Cholesterol esterification of polyenic fatty acids may structure complex lipid in the unpolar phase and transport it to the cells via apoB-100-ligand-receptor interaction, which is considered to be a key stage in the multistage process of active transport to the cells of polyenic fatty acids. However, the significant differences of active and inactive transport of polyenic fatty acids in the blood stream await a separate consideration.

Structure of complex of N-methylpiperidine betaine with p-hydroxybenzoic acid studied by X-ray, FT-IR and DFT methods

NASA Astrophysics Data System (ADS)

Dega-Szafran, Z.; Dutkiewicz, G.; Kosturkiewicz, Z.; Szafran, M.

2008-03-01

Crystal structure of the complex of N-methylpiperidine betaine ( N-carboxymethyl- N-methylpiperidinium inner salt, MPB) with p-hydroxybenzoic acid (HBA) has been determined by X-ray diffraction. The crystals are triclinic, space group Pī, with a = 6.1156(5), b = 10.6869(10), c = 12.0320(10) Å, α = 109.55(1)°, β = 95.25(1)°, γ = 99.22(1)°, Z = 2, R = 0.034. Two molecules of p-hydroxybenzoic acid and two molecules of N-methylpiperidine betaine are linked together forming a centrosymmetric dimer, (MPB·HBA) 2, by four O-H···O hydrogen bonds of lengths 2.622(1) and 2.617(1) Å, between the carboxylic and hydroxy groups of HBA and both oxygen atoms of the carboxylate group of MPB, respectively. The piperidine ring has a chair conformation with the CH 2COO - substituent in the axial position and the CH 3 group in the equatorial one. Two parallel aromatic rings in (MPB·HBA) 2 are distanced by 3.457 Å. In the crystals the complexes form "islands" related to the neighboring complexes by the inversion centers, weak C-H···O bonds and van der Waals forces. A broad band in the 3100-2400 cm -1 region and two bands attributed to the νC dbnd O (1689 cm -1) and νasCOO (1607 cm -1) vibrations in the FT-IR spectrum confirm the structure of the title complex. The two structures of MPB·HBA, denoted as A and B, have been optimized by the B3LYP/6-31G(d,p) method. In A, MPB forms a O-H···O hydrogen bond (2.562 Å) with the carboxylic group of HBA shorter than in the crystals, while in B it interacts with the phenolic group of HBA by a longer O-H···O hydrogen bond (2.661 Å) than in the crystals. Complex A is slightly more stable than B (0.15 kcal/mol).

Breakdown of the balanced lethals in Rhoeo: the structure of the Alethal Renner complex of the homozygotic stock of Rhoeo.

PubMed

Golczyk, H

2011-01-01

Fluorescence in situ hybridization, base-specific fluorescence, C-banding and silver-staining were performed to reveal the cyto-molecular constitution of the karyotype in the bivalent-forming Rhoeo spathacea concolor. It was shown that the genome of this form is almost identical to the β-complex of the ring-forming rhoeos. In spite of some modifications in the arrangement of a few distal rDNA sites and in the amount of pericentromeric AT-rich heterochromatin, the alethal genome of the bivalent-forming Rhoeo seems segmentally unaltered. Thus, the breakdown of balanced lethals in Rhoeo is most likely uncoupled from creating new chromosome arm combinations. Copyright © 2011 S. Karger AG, Basel.

ESR, spectroscopic, and quantum-chemical studies on the electronic structures of complexes formed by Cu(I) with radicals (in Russian)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gritsan, N.P.; Usov, O.M.; Shokhirev, N.V.

1986-07-01

The optical and ESR spectra have been examined for complexes of Cu(I) with various radicals, which contain various numbers of Cl/sup -/ ions in the central-atom coordination sphere. The spin-Hamiltonian parameters have been determined for all these radical complexes, and the observed ESR spectra have been compared with those calculated with allowance for second-order effects. The observed values for the isotropic and anisotropic components of the HFI constant from the central ion have been used to estimate the contributions from the 4s and 3d/sup 2//sub z/ orbitals of the copper ion to the unpaired-electron MO. Quantum-chemical calculations have been performedmore » by the INDO method on the electronic structures and geometries of complexes formed by CH/sub 2/OH with Cu(I) for various Cl/sup -/ contents in the coordination sphere. The radical is coordinated by the ..pi.. orbital on the carbon atom, and the stabilities of the radical complexes decrease as the number of Cl/sup -/ ions in the coordination sphere increases. A geometry close to planar for the CuCl/sub 4//sup 3 -/ fragment in a complex containing four Cl/sup -/ ions.« less

Calorimetric studies of the interactions of metalloenzyme active site mimetics with zinc-binding inhibitors.

PubMed

Robinson, Sophia G; Burns, Philip T; Miceli, Amanda M; Grice, Kyle A; Karver, Caitlin E; Jin, Lihua

2016-07-19

The binding of drugs to metalloenzymes is an intricate process that involves several interactions, including binding of the drug to the enzyme active site metal, as well as multiple interactions between the drug and the enzyme residues. In order to determine the free energy contribution of Zn(2+) binding by known metalloenzyme inhibitors without the other interactions, valid active site zinc structural mimetics must be formed and binding studies need to be performed in biologically relevant conditions. The potential of each of five ligands to form a structural mimetic with Zn(2+) was investigated in buffer using Isothermal Titration Calorimetry (ITC). All five ligands formed strong 1 : 1 (ligand : Zn(2+)) binary complexes. The complexes were used in further ITC experiments to study their interaction with 8-hydroxyquinoline (8-HQ) and/or acetohydroxamic acid (AHA), two bidentate anionic zinc-chelating enzyme inhibitors. It was found that tetradentate ligands were not suitable for creating zinc structural mimetics for inhibitor binding in solution due to insufficient coordination sites remaining on Zn(2+). A stable binary complex, [Zn(BPA)](2+), which was formed by a tridentate ligand, bis(2-pyridylmethyl)amine (BPA), was found to bind one AHA in buffer or a methanol : buffer mixture (60 : 40 by volume) at pH 7.25 or one 8-HQ in the methanol : buffer mixture at pH 6.80, making it an effective structural mimetic for the active site of zinc metalloenzymes. These results are consistent with the observation that metalloenzyme active site zinc ions have three residues coordinated to them, leaving one or two sites open for inhibitors to bind. Our findings indicate that Zn(BPA)X2 can be used as an active site structural mimetic for zinc metalloenzymes for estimating the free energy contribution of zinc binding to the overall inhibitor active site interactions. Such use will help aid in the rational design of inhibitors to a variety of zinc metalloenzymes.

Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus vascular endothelial growth factor} protein complex by racemic crystallography

PubMed Central

Mandal, Kalyaneswar; Uppalapati, Maruti; Ault-Riché, Dana; Kenney, John; Lowitz, Joshua; Sidhu, Sachdev S.; Kent, Stephen B.H.

2012-01-01

Total chemical synthesis was used to prepare the mirror image (D-protein) form of the angiogenic protein vascular endothelial growth factor (VEGF-A). Phage display against D-VEGF-A was used to screen designed libraries based on a unique small protein scaffold in order to identify a high affinity ligand. Chemically synthesized D- and L- forms of the protein ligand showed reciprocal chiral specificity in surface plasmon resonance binding experiments: The L-protein ligand bound only to D-VEGF-A, whereas the D-protein ligand bound only to L-VEGF-A. The D-protein ligand, but not the L-protein ligand, inhibited the binding of natural VEGF165 to the VEGFR1 receptor. Racemic protein crystallography was used to determine the high resolution X-ray structure of the heterochiral complex consisting of {D-protein antagonist + L-protein form ofVEGF-A}. Crystallization of a racemic mixture of these synthetic proteins in appropriate stoichiometry gave a racemic protein complex of more than 73 kDa containing six synthetic protein molecules. The structure of the complex was determined to a resolution of 1.6 Å. Detailed analysis of the interaction between the D-protein antagonist and the VEGF-A protein molecule showed that the binding interface comprised a contact surface area of approximately 800 Å2 in accord with our design objectives, and that the D-protein antagonist binds to the same region of VEGF-A that interacts with VEGFR1-domain 2. PMID:22927390

Method for fabricating five-level microelectromechanical structures and microelectromechanical transmission formed

DOEpatents

Rodgers, M. Steven; Sniegowski, Jeffry J.; Miller, Samuel L.; McWhorter, Paul J.

2000-01-01

A process for forming complex microelectromechanical (MEM) devices having five layers or levels of polysilicon, including four structural polysilicon layers wherein mechanical elements can be formed, and an underlying polysilicon layer forming a voltage reference plane. A particular type of MEM device that can be formed with the five-level polysilicon process is a MEM transmission for controlling or interlocking mechanical power transfer between an electrostatic motor and a self-assembling structure (e.g. a hinged pop-up mirror for use with an incident laser beam). The MEM transmission is based on an incomplete gear train and a bridging set of gears that can be moved into place to complete the gear train to enable power transfer. The MEM transmission has particular applications as a safety component for surety, and for this purpose can incorporate a pin-in-maze discriminator responsive to a coded input signal.

Crystal structures of the CPAP/STIL complex reveal its role in centriole assembly and human microcephaly

PubMed Central

Cottee, Matthew A; Muschalik, Nadine; Wong, Yao Liang; Johnson, Christopher M; Johnson, Steven; Andreeva, Antonina; Oegema, Karen; Lea, Susan M; Raff, Jordan W; van Breugel, Mark

2013-01-01

Centrioles organise centrosomes and template cilia and flagella. Several centriole and centrosome proteins have been linked to microcephaly (MCPH), a neuro-developmental disease associated with small brain size. CPAP (MCPH6) and STIL (MCPH7) are required for centriole assembly, but it is unclear how mutations in them lead to microcephaly. We show that the TCP domain of CPAP constitutes a novel proline recognition domain that forms a 1:1 complex with a short, highly conserved target motif in STIL. Crystal structures of this complex reveal an unusual, all-β structure adopted by the TCP domain and explain how a microcephaly mutation in CPAP compromises complex formation. Through point mutations, we demonstrate that complex formation is essential for centriole duplication in vivo. Our studies provide the first structural insight into how the malfunction of centriole proteins results in human disease and also reveal that the CPAP–STIL interaction constitutes a conserved key step in centriole biogenesis. DOI: http://dx.doi.org/10.7554/eLife.01071.001 PMID:24052813

Structure of the cellulose synthase complex of Gluconacetobacter hansenii at 23.4 Å resolution

DOE PAGES

Du, Juan; Vepachedu, Venkata; Cho, Sung Hyun; ...

2016-05-23

Bacterial crystalline cellulose is used in biomedical and industrial applications, but the molecular mechanisms of synthesis are unclear. Unlike most bacteria, which make non-crystalline cellulose, Gluconacetobacter hansenii extrudes profuse amounts of crystalline cellulose. Its cellulose synthase (AcsA) exists as a complex with accessory protein AcsB, forming a 'terminal complex' (TC) that has been visualized by freeze-fracture TEM at the base of ribbons of crystalline cellulose. The catalytic AcsAB complex is embedded in the cytoplasmic membrane. The C-terminal portion of AcsC is predicted to form a translocation channel in the outer membrane, with the rest of AcsC possibly interacting with AcsDmore » in the periplasm. It is thus believed that synthesis from an organized array of TCs coordinated with extrusion by AcsC and AcsD enable this bacterium to make crystalline cellulose. The only structural data that exist for this system are the above mentioned freeze-fracture TEM images, fluorescence microscopy images revealing that TCs align in a row, a crystal structure of AcsD bound to cellopentaose, and a crystal structure of PilZ domain of AcsA. Here we advance our understanding of the structural basis for crystalline cellulose production by bacterial cellulose synthase by determining a negative stain structure resolved to 23.4 angstrom for highly purified AcsAB complex that catalyzed incorporation of UDP-glucose into β-1,4-glucan chains, and responded to the presence of allosteric activator cyclic diguanylate. Although the AcsAB complex was functional in vitro, the synthesized cellulose was not visible in TEM. The negative stain structure revealed that AcsAB is very similar to that of the BcsAB synthase of Rhodobacter sphaeroides, a non-crystalline cellulose producing bacterium. Furthermore, the results indicate that the crystalline cellulose producing and non-crystalline cellulose producing bacteria share conserved catalytic and membrane translocation components, and support the hypothesis that it is the extrusion mechanism and order in linearly arrayed TCs that enables production of crystalline cellulose.« less

Structure of the cellulose synthase complex of Gluconacetobacter hansenii at 23.4 Å resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Juan; Vepachedu, Venkata; Cho, Sung Hyun

Bacterial crystalline cellulose is used in biomedical and industrial applications, but the molecular mechanisms of synthesis are unclear. Unlike most bacteria, which make non-crystalline cellulose, Gluconacetobacter hansenii extrudes profuse amounts of crystalline cellulose. Its cellulose synthase (AcsA) exists as a complex with accessory protein AcsB, forming a 'terminal complex' (TC) that has been visualized by freeze-fracture TEM at the base of ribbons of crystalline cellulose. The catalytic AcsAB complex is embedded in the cytoplasmic membrane. The C-terminal portion of AcsC is predicted to form a translocation channel in the outer membrane, with the rest of AcsC possibly interacting with AcsDmore » in the periplasm. It is thus believed that synthesis from an organized array of TCs coordinated with extrusion by AcsC and AcsD enable this bacterium to make crystalline cellulose. The only structural data that exist for this system are the above mentioned freeze-fracture TEM images, fluorescence microscopy images revealing that TCs align in a row, a crystal structure of AcsD bound to cellopentaose, and a crystal structure of PilZ domain of AcsA. Here we advance our understanding of the structural basis for crystalline cellulose production by bacterial cellulose synthase by determining a negative stain structure resolved to 23.4 angstrom for highly purified AcsAB complex that catalyzed incorporation of UDP-glucose into β-1,4-glucan chains, and responded to the presence of allosteric activator cyclic diguanylate. Although the AcsAB complex was functional in vitro, the synthesized cellulose was not visible in TEM. The negative stain structure revealed that AcsAB is very similar to that of the BcsAB synthase of Rhodobacter sphaeroides, a non-crystalline cellulose producing bacterium. Furthermore, the results indicate that the crystalline cellulose producing and non-crystalline cellulose producing bacteria share conserved catalytic and membrane translocation components, and support the hypothesis that it is the extrusion mechanism and order in linearly arrayed TCs that enables production of crystalline cellulose.« less

Structure of the Cellulose Synthase Complex of Gluconacetobacter hansenii at 23.4 Å Resolution

PubMed Central

Du, Juan; Vepachedu, Venkata; Cho, Sung Hyun; Kumar, Manish; Nixon, B. Tracy

2016-01-01

Bacterial crystalline cellulose is used in biomedical and industrial applications, but the molecular mechanisms of synthesis are unclear. Unlike most bacteria, which make non-crystalline cellulose, Gluconacetobacter hansenii extrudes profuse amounts of crystalline cellulose. Its cellulose synthase (AcsA) exists as a complex with accessory protein AcsB, forming a 'terminal complex' (TC) that has been visualized by freeze-fracture TEM at the base of ribbons of crystalline cellulose. The catalytic AcsAB complex is embedded in the cytoplasmic membrane. The C-terminal portion of AcsC is predicted to form a translocation channel in the outer membrane, with the rest of AcsC possibly interacting with AcsD in the periplasm. It is thus believed that synthesis from an organized array of TCs coordinated with extrusion by AcsC and AcsD enable this bacterium to make crystalline cellulose. The only structural data that exist for this system are the above mentioned freeze-fracture TEM images, fluorescence microscopy images revealing that TCs align in a row, a crystal structure of AcsD bound to cellopentaose, and a crystal structure of PilZ domain of AcsA. Here we advance our understanding of the structural basis for crystalline cellulose production by bacterial cellulose synthase by determining a negative stain structure resolved to 23.4 Å for highly purified AcsAB complex that catalyzed incorporation of UDP-glucose into β-1,4-glucan chains, and responded to the presence of allosteric activator cyclic diguanylate. Although the AcsAB complex was functional in vitro, the synthesized cellulose was not visible in TEM. The negative stain structure revealed that AcsAB is very similar to that of the BcsAB synthase of Rhodobacter sphaeroides, a non-crystalline cellulose producing bacterium. The results indicate that the crystalline cellulose producing and non-crystalline cellulose producing bacteria share conserved catalytic and membrane translocation components, and support the hypothesis that it is the extrusion mechanism and order in linearly arrayed TCs that enables production of crystalline cellulose. PMID:27214134

Additive lattice kirigami

PubMed Central

Castle, Toen; Sussman, Daniel M.; Tanis, Michael; Kamien, Randall D.

2016-01-01

Kirigami uses bending, folding, cutting, and pasting to create complex three-dimensional (3D) structures from a flat sheet. In the case of lattice kirigami, this cutting and rejoining introduces defects into an underlying 2D lattice in the form of points of nonzero Gaussian curvature. A set of simple rules was previously used to generate a wide variety of stepped structures; we now pare back these rules to their minimum. This allows us to describe a set of techniques that unify a wide variety of cut-and-paste actions under the rubric of lattice kirigami, including adding new material and rejoining material across arbitrary cuts in the sheet. We also explore the use of more complex lattices and the different structures that consequently arise. Regardless of the choice of lattice, creating complex structures may require multiple overlapping kirigami cuts, where subsequent cuts are not performed on a locally flat lattice. Our additive kirigami method describes such cuts, providing a simple methodology and a set of techniques to build a huge variety of complex 3D shapes. PMID:27679822

Additive lattice kirigami.

PubMed

Castle, Toen; Sussman, Daniel M; Tanis, Michael; Kamien, Randall D

2016-09-01

Kirigami uses bending, folding, cutting, and pasting to create complex three-dimensional (3D) structures from a flat sheet. In the case of lattice kirigami, this cutting and rejoining introduces defects into an underlying 2D lattice in the form of points of nonzero Gaussian curvature. A set of simple rules was previously used to generate a wide variety of stepped structures; we now pare back these rules to their minimum. This allows us to describe a set of techniques that unify a wide variety of cut-and-paste actions under the rubric of lattice kirigami, including adding new material and rejoining material across arbitrary cuts in the sheet. We also explore the use of more complex lattices and the different structures that consequently arise. Regardless of the choice of lattice, creating complex structures may require multiple overlapping kirigami cuts, where subsequent cuts are not performed on a locally flat lattice. Our additive kirigami method describes such cuts, providing a simple methodology and a set of techniques to build a huge variety of complex 3D shapes.

Structure of the Deactive State of Mammalian Respiratory Complex I.

PubMed

Blaza, James N; Vinothkumar, Kutti R; Hirst, Judy

2018-02-06

Complex I (NADH:ubiquinone oxidoreductase) is central to energy metabolism in mammalian mitochondria. It couples NADH oxidation by ubiquinone to proton transport across the energy-conserving inner membrane, catalyzing respiration and driving ATP synthesis. In the absence of substrates, active complex I gradually enters a pronounced resting or deactive state. The active-deactive transition occurs during ischemia and is crucial for controlling how respiration recovers upon reperfusion. Here, we set a highly active preparation of Bos taurus complex I into the biochemically defined deactive state, and used single-particle electron cryomicroscopy to determine its structure to 4.1 Å resolution. We show that the deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding to the NADH-reduced enzyme templates their reordering. Our structure both rationalizes biochemical data on the deactive state and offers new insights into its physiological and cellular roles. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Flat and complex temperate reefs provide similar support for fish: Evidence for a unimodal species-habitat relationship.

PubMed

Paxton, Avery B; Pickering, Emily A; Adler, Alyssa M; Taylor, J Christopher; Peterson, Charles H

2017-01-01

Structural complexity, a form of habitat heterogeneity, influences the structure and function of ecological communities, generally supporting increased species density, richness, and diversity. Recent research, however, suggests the most complex habitats may not harbor the highest density of individuals and number of species, especially in areas with elevated human influence. Understanding nuances in relationships between habitat heterogeneity and ecological communities is warranted to guide habitat-focused conservation and management efforts. We conducted fish and structural habitat surveys of thirty warm-temperate reefs on the southeastern US continental shelf to quantify how structural complexity influences fish communities. We found that intermediate complexity maximizes fish abundance on natural and artificial reefs, as well as species richness on natural reefs, challenging the current paradigm that abundance and other fish community metrics increase with increasing complexity. Naturally occurring rocky reefs of flat and complex morphologies supported equivalent abundance, biomass, species richness, and community composition of fishes. For flat and complex morphologies of rocky reefs to receive equal consideration as essential fish habitat (EFH), special attention should be given to detecting pavement type rocky reefs because their ephemeral nature makes them difficult to detect with typical seafloor mapping methods. Artificial reefs of intermediate complexity also maximized fish abundance, but human-made structures composed of low-lying concrete and metal ships differed in community types, with less complex, concrete structures supporting lower numbers of fishes classified largely as demersal species and metal ships protruding into the water column harboring higher numbers of fishes, including more pelagic species. Results of this study are essential to the process of evaluating habitat function provided by different types and shapes of reefs on the seafloor so that all EFH across a wide range of habitat complexity may be accurately identified and properly managed.

Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abdur, Rob; Gerlits, Oksana O.; Gan, Jianhua

2014-02-01

Selenium-derivatized oligonucleotides may facilitate phase determination and high-resolution structure determination for protein–nucleic acid crystallography. The Se atom-specific mutagenesis (SAM) strategy may also enhance the study of nuclease catalysis. The crystal structures of protein–nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein–nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H–RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissilemore » phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.« less

Effects of deuteration of the methyl and phenyl hydrogens on the rotational spectrum of anisole-water

NASA Astrophysics Data System (ADS)

Giuliano, Barbara M.; Melandri, Sonia; Caminati, Walther

2017-07-01

The role of non-covalent interactions in determining the structure of the 1:1 anisole-water molecular complex has been investigated by the analysis of the rotational spectra of the complex formed by the C6H5OCD3 and C6D5OCH3 deuterated species of anisole recorded with pulsed jet Fourier transform microwave spectroscopy. The deuteration of the methyl and phenyl hydrogens does not affect the structure and the internal dynamics of the complex, differently from the deuteration of the water moiety, which leads to large isotopic effects (Giuliano et al., 2005).

Photopolymerization of complex emulsions with irregular shapes fabricated by multiplex coaxial flow focusing

NASA Astrophysics Data System (ADS)

Wu, Qiang; Yang, Chaoyu; Yang, Jianxin; Huang, Fangsheng; Liu, Guangli; Zhu, Zhiqiang; Si, Ting; Xu, Ronald X.

2018-02-01

We fabricate complex emulsions with irregular shapes in the microscale by a simple but effective multiplex coaxial flow focusing process. A multiphase cone-jet structure is steadily formed, and the compound liquid jet eventually breaks up into Janus microdroplets due to the perturbations propagating along the jet interfaces. The microdroplet shapes can be exclusively controlled by interfacial tensions of adjacent phases. Crescent-moon-shaped microparticles and microcapsules with designated structural characteristics are further produced under ultraviolet light of photopolymerization after removing one hemisphere of the Janus microdroplets. These complex emulsions have potential applications in bioscience, food, functional materials, and controlled drug delivery.

Hydrogen-bonded complexes between dimethyl sulfoxide and monoprotic acids: molecular properties and IR spectroscopy.

PubMed

Belarmino, Márcia K D L; Cruz, Vanessa F; Lima, Nathália B D

2014-11-01

MP2/6-31++G(d,p) and DFT B3LYP/6-31++G(d,p) calculations were performed of the structure, binding energies, and vibrational modes of complexes between dimethyl sulfoxide (DMSO) as a proton acceptor and monoprotic linear acids HX (X = F, Cl, CN) as well as monoprotic carboxylic acids HOOCR (R = -H, -CH3, -C6H5) in 1:1 and 1:2 stoichiometric ratios. The results show that two different structures are possible in the 1:2 ratio: in the first, the DMSO molecule interacts with both acid molecules (leading to a "Y" structure); in the second, the DMSO interacts with only one monoprotic acid. The second structure shows a lower stability per hydrogen bond. The spontaneities of the reactions to form the 1:1 and 1:2 complexes are greatly influenced by the X group of the linear acid. With the exception of HCN, all the reactions are spontaneous. In the 1:2 complexes with Y structure, we observed that the hydrogen atoms of the linear acid are coupled in symmetric and asymmetric modes, while this type of coupling is absent from the other 1:2 complexes.

The structure of the yeast NADH dehydrogenase (Ndi1) reveals overlapping binding sites for water- and lipid-soluble substrates.

PubMed

Iwata, Momi; Lee, Yang; Yamashita, Tetsuo; Yagi, Takao; Iwata, So; Cameron, Alexander D; Maher, Megan J

2012-09-18

Bioenergy is efficiently produced in the mitochondria by the respiratory system consisting of complexes I-V. In various organisms, complex I can be replaced by the alternative NADH-quinone oxidoreductase (NDH-2), which catalyzes the transfer of an electron from NADH via FAD to quinone, without proton pumping. The Ndi1 protein from Saccharomyces cerevisiae is a monotopic membrane protein, directed to the matrix. A number of studies have investigated the potential use of Ndi1 as a therapeutic agent against complex I disorders, and the NDH-2 enzymes have emerged as potential therapeutic targets for treatments against the causative agents of malaria and tuberculosis. Here we present the crystal structures of Ndi1 in its substrate-free, NAD(+)- and ubiquinone- (UQ2) complexed states. The structures reveal that Ndi1 is a peripheral membrane protein forming an intimate dimer, in which packing of the monomeric units within the dimer creates an amphiphilic membrane-anchor domain structure. Crucially, the structures of the Ndi1-NAD(+) and Ndi1-UQ2 complexes show overlapping binding sites for the NAD(+) and quinone substrates.

Synthesis and spectral characterization of mono- and binuclear copper(II) complexes derived from 2-benzoylpyridine-N4-methyl-3-thiosemicarbazone: Crystal structure of a novel sulfur bridged copper(II) box-dimer

NASA Astrophysics Data System (ADS)

Jayakumar, K.; Sithambaresan, M.; Aiswarya, N.; Kurup, M. R. Prathapachandra

2015-03-01

Mononuclear and binuclear copper(II) complexes of 2-benzoylpyridine-N4-methyl thiosemicarbazone (HL) were prepared and characterized by a variety of spectroscopic techniques. Structural evidence for the novel sulfur bridged copper(II) iodo binuclear complex is obtained by single crystal X-ray diffraction analysis. The complex [Cu2L2I2], a non-centrosymmetric box dimer, crystallizes in monoclinic C2/c space group and it was found to have distorted square pyramidal geometry (Addison parameter, τ = 0.238) with the square basal plane occupied by the thiosemicarbazone moiety and iodine atom whereas the sulfur atom from the other coordinated thiosemicarbazone moiety occupies the apical position. This is the first crystallographically studied system having non-centrosymmetrical entities bridged via thiolate S atoms with Cu(II)sbnd I bond. The tridentate thiosemicarbazone coordinates in mono deprotonated thionic tautomeric form in all complexes except in sulfato complex, [Cu(HL)(SO4)]·H2O (1) where it binds to the metal centre in neutral form. The magnetic moment values and the EPR spectral studies reflect the binuclearity of some of the complexes. The spin Hamiltonian and bonding parameters are calculated based on EPR studies. In all the complexes g|| > g⊥ > 2.0023 and the g values in frozen DMF are consistent with the dx2-y2 ground state. The thermal stabilities of some of the complexes were also determined.

Titan tholins formed from simuolated upper and lower atmosphere

NASA Astrophysics Data System (ADS)

Taniuchi, Toshinori; Hosogai, Tomohiro; Takano, Yoshinori; Kaneko, Takeo; Kobayashi, Kensei; Khare, Bishun; McKay, Chris

Titan, the biggest satellite of Saturn, has dense atmosphere that mainly consists of nitrogen and methane. In this study, we irradiated proton beams to the mixture of nitrogen and methane, and analyzed the structure, the chemical composition, and molecular weight of the resulting aerosols (named PI-tholins), in order to simulate possible reactions in the lower Titan atmosphere. On the other hand, magnetosphere electrons could be effective for the formation of organic molecules in the upper atmosphere of Titan. Thus we compared PI-tholin with the tholin formed by plasma discharge (named PD-tholins). A mixture of methane and nitrogen was irradiated with 3 MeV protons from a van de Graaff accelerator (Tokyo Institute of Technology). Many nitriles and nitrogen-containing heterocyclic compounds were detected by Py-GC/MS, showing that quite complex organics were formed from the simulated Titan atmosphere by proton irradiation. Microscopic observation showed that the complex organic aerosols had the structure bigger than 0.01 mm. G-value of Gly was 0.03. PD-tholins were produced by plasma discharge in 1 Torr of a mixture of methane and nitrogen by using plasma discharge facility RFX-600 (NASA Ames Research Center). Discharges were continued at 100 W for 72 hours. PD-tholins had similar chemical structures to PI-tholins. But the G-value of Gly in PD-tholins was 0.000091, which was much less thatn that in PI-tholins. It was implied that cosmic rays in the lower Titan atmosphere was much more effective to form complex organics yielding amino acids than other energies in the upper Titan atmosphere.

A novel cetyltrimethyl ammonium silver bromide complex and silver bromide nanoparticles obtained by the surfactant counterion.

PubMed

Liu, Xian-Hao; Luo, Xiao-Hong; Lu, Shu-Xia; Zhang, Jing-Chang; Cao, Wei-Liang

2007-03-01

A novel cetyltrimethyl ammonium silver bromide (CTASB) complex has been prepared simply through the reaction of silver nitrate with cetyltrimethyl ammonium bromide (CTAB) in aqueous solution at room temperature by controlling the concentration of CTAB and the molar ratio of CTAB to silver nitrate in the reaction solution, in which halogen in CTAB is used as surfactant counterion. The structure and thermal behavior of cetyltrimethyl ammonium silver bromide have been investigated by using X-ray diffraction (XRD), infrared spectroscopy (IR), X-ray photoelectron spectroscopy (XPS), UV/vis spectroscopy, thermal analysis (TG-DTA), transmission electron microscopy (TEM), and scanning electron microscopy (SEM). The results show that the complex possesses a metastable layered structure. Upon heating the CTASB aqueous dispersion to above 80 degrees C, the structure change of the complex took place and CTAB-capped nanosized silver bromide particles further formed.

Effector region of the translation elongation factor EF-Tu.GTP complex stabilizes an orthoester acid intermediate structure of aminoacyl-tRNA in a ternary complex.

PubMed Central

Förster, C; Limmer, S; Zeidler, W; Sprinzl, M

1994-01-01

tRNA(Val) from Escherichia coli was aminoacylated with [1-13C]valine and its complex with Thermus thermophilus elongation factor EF-Tu.GTP was analyzed by 13C NMR spectroscopy. The results suggest that the aminoacyl residue of the valyl-tRNA in ternary complex with bacterial EF-Tu and GTP is not attached to tRNA by a regular ester bond to either a 2'- or 3'-hydroxyl group; instead, an intermediate orthoester acid structure with covalent linkage to both vicinal hydroxyls of the terminal adenosine-76 is formed. Mutation of arginine-59 located in the effector region of EF-Tu, a conserved residue in protein elongation factors and the alpha subunits of heterotrimeric guanine nucleotide-binding regulatory proteins (G proteins), abolishes the stabilization of the orthoester acid structure of aminoacyl-tRNA. PMID:8183898

When is an imine not an imine? Unusual reactivity of a series of Cu(II) imine-pyridine complexes and their exploitation for the Henry reaction.

PubMed

Cooper, Christine J; Jones, Matthew D; Brayshaw, Simon K; Sonnex, Benjamin; Russell, Mark L; Mahon, Mary F; Allan, David R

2011-04-14

In this paper we report the synthesis and solid-state structures for a series of pyridine based Cu(II) complexes and preliminary data for the asymmetric Henry reaction. Interestingly, the solid-state structures indicate the incorporation of an alcohol into one of the imine groups of the ligand, forming a rare α-amino ether group. The complexes have been studied via single crystal X-ray diffraction, EPR spectroscopy and mass spectrometry. Intriguingly, it has been observed that the alcohol only adds to one of the imine moieties. Density functional theory (DFT) calculations have also been employed to rationalise the observed structures. The Cu(II) complexes have been tested in the asymmetric Henry reaction (benzaldehyde + nitromethane or nitroethane) with ee's up to 84% being achieved as well as high conversions and modest diastereoselectivities. © The Royal Society of Chemistry 2011

Insights into cellulosome assembly and dynamics: from dissection to reconstruction of the supramolecular enzyme complex.

PubMed

Smith, Steven P; Bayer, Edward A

2013-10-01

Cellulosomes are multi-enzyme complexes produced by anaerobic bacteria for the efficient deconstruction of plant cell wall polysaccharides. The assembly of enzymatic subunits onto a central non-catalytic scaffoldin subunit is mediated by a highly specific interaction between the enzyme-bearing dockerin modules and the resident cohesin modules of the scaffoldin, which affords their catalytic activities to work synergistically. The scaffoldin also imparts substrate-binding and bacterial-anchoring properties, the latter of which involves a second cohesin-dockerin interaction. Recent structure-function studies reveal an ever-growing array of unique and increasingly complex cohesin-dockerin complexes and cellulosomal enzymes with novel activities. A 'build' approach involving multimodular cellulosomal segments has provided a structural model of an organized yet conformationally dynamic supramolecular assembly with the potential to form higher order structures. Copyright © 2013. Published by Elsevier Ltd.

High-pressure metamorphism and uplift of the Olympic subduction complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brandon, M.T.; Calderwood, A.R.

1990-12-01

The discovery of the critical assemblage lawsonite + quartz + calcite indicates that a significant part of the Cenozoic Olympic subduction complex of northwestern Washington State formed by underplating at a depth of about 11 km. The deep structural level exposed in this area is attributed to the presence of a 10-km-high arch in the underlying Juan de Fuca plate. The authors postulate that this arch was formed when the southern Cordilleran coastline swung westward as a result of middle Miocene to recent extension in the Basin and Range province.

Influence of ionic liquids on the syntheses and structures of Mn(II) coordination polymers based on multidentate N-heterocyclic aromatic ligands and bridging carboxylate ligands.

PubMed

Qin, Jian-Hua; Wang, Hua-Rui; Pan, Qi; Zang, Shuang-Quan; Hou, Hongwei; Fan, Yaoting

2015-10-28

Seven Mn(ii) coordination polymers, namely {[Mn2(ptptp)Cl2(H2O)3]·H2O}n (1), {[Mn(μ-ptptp)3]2[Mn3(μ3-Cl)]2}·2Cl·16H2O (2), {[Mn2(ptptp)(ip)2(H2O)3]·H2O}n (3), {[Mn2(ptptp)(5-CH3-ip)2(H2O)3]·H2O}n (4), {[Mn4(ptptp)(5-Br-ip)3(H2O)3]·4H2O}n (5), {[Mn2(ptptp)(Hbtc)(H2O)2]·2H2O}n (6) and {[Mn2(ptptp)(tdc)(H2O)2]·1.5H2O}n (7), have been prepared based on multidentate N-heterocyclic aromatic ligands and bridging carboxylate ligands (H2ptptp = 2-(5-{6-[5-(pyrazin-2-yl)-1H-1,2,4-triazol-3-yl]pyridin-2-yl}-1H-1,2,4-triazol-3-yl)pyrazine; R-isophthalic acids, H2ip-R: R = -H (3), -CH3 (4), -Br (5); H3btc = trimesic acid (6); H2tdc = thiophene-2,5-dicarboxylic acid (7)), in order to further probe the multiple roles of [RMI]Br ionic liquids in the hydro/solvothermal synthesis (RMI = 1-alkyl-3-methylimidazolium, R = ethyl, or propyl, or butyl). The successful syntheses of complexes 2-6 suggest that in hydro/solvothermal synthesis the addition of a small amount of [RMI]Br plays a crucial role. Complex 1 exhibits single right-handed helices constructed by ptptp ligands and Mn(ii) ions. Complex 2 possesses octanuclear helicate structures in which two propeller-shaped [Mn(μ-ptptp)3](4-) units embrace two [Mn3(μ3-Cl)](5+) cluster cores inside. Complexes 3 and 4 are isostructural and display a 1D double chain formed by two kinds of pseudo meso-helices: (Mn-ptptp)n and (Mn-5-R-ip)n. Complex 5 has a 2D structure containing 1D Mn(ii) ion chains formed through carboxylates and [ptptp](2-)-N,N bridges. Complex 6 shows a 2D structure formed by a meso-helix (Mn-ptptp)n and the partly deprotonated Hbtc ligands. Complex 7 features a heterochiral [2 + 2] coaxially nested double-helical column formed by using the outer double-helices (Mn-ptptp)n as a template to encapsulate the inner double-helices (Mn-tdc)n with opposite orientation. All complexes were characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, single-crystal X-ray crystallography and powder X-ray diffraction. The magnetic properties of 1-7 were also investigated.

Structure of isocitrate dehydrogenase with alpha-ketoglutarate at 2.7-A resolution: conformational changes induced by decarboxylation of isocitrate.

PubMed

Stoddard, B L; Koshland, D E

1993-09-14

The structure of the isocitrate dehydrogenase (IDH) complex with bound alpha-ketoglutarate, Ca2+, and NADPH was solved at 2.7-A resolution. The alpha-ketoglutarate binds in the active site at the same position and orientation as isocitrate, with a difference between the two bound molecules of about 0.8 A. The Ca2+ metal is coordinated by alpha-ketoglutarate, three conserved aspartate residues, and a pair of water molecules. The largest motion in the active site relative to the isocitrate enzyme complex is observed for tyrosine 160, which originally forms a hydrogen bond to the labile carboxyl group of isocitrate and moves to form a new hydrogen bond to Asp 307 in the complex with alpha-ketoglutarate. This triggers a number of significant movements among several short loops and adjoining secondary structural elements in the enzyme, most of which participate in dimer stabilization and formation of the active-site cleft. These rearrangements are similar to the ligand-binding-induced movements observed in globins and insulin and serve as a model for an enzymatic mechanism which involves local shifts of secondary structural elements during turnover, rather than large-scale domain closures or loop transitions induced by substrate binding such as those observed in hexokinase or triosephosphate isomerase.

Conformational Changes and Substrate Recognition in Pseudomonas aeruginosa d-Arginine Dehydrogenase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Guoxing; Yuan, Hongling; Li, Congran

2010-11-15

DADH catalyzes the flavin-dependent oxidative deamination of D-amino acids to the corresponding {alpha}-keto acids and ammonia. Here we report the first X-ray crystal structures of DADH at 1.06 {angstrom} resolution and its complexes with iminoarginine (DADH{sub red}/iminoarginine) and iminohistidine (DADH{sub red}/iminohistidine) at 1.30 {angstrom} resolution. The DADH crystal structure comprises an unliganded conformation and a product-bound conformation, which is almost identical to the DADH{sub red}/iminoarginine crystal structure. The active site of DADH was partially occupied with iminoarginine product (30% occupancy) that interacts with Tyr53 in the minor conformation of a surface loop. This flexible loop forms an 'active site lid',more » similar to those seen in other enzymes, and may play an essential role in substrate recognition. The guanidinium side chain of iminoarginine forms a hydrogen bond interaction with the hydroxyl of Thr50 and an ionic interaction with Glu87. In the structure of DADH in complex with iminohistidine, two alternate conformations were observed for iminohistidine where the imidazole groups formed hydrogen bond interactions with the side chains of His48 and Thr50 and either Glu87 or Gln336. The different interactions and very distinct binding modes observed for iminoarginine and iminohistidine are consistent with the 1000-fold difference in k{sub cat}/K{sub m} values for D-arginine and D-histidine. Comparison of the kinetic data for the activity of DADH on different D-amino acids and the crystal structures in complex with iminoarginine and iminohistidine establishes that this enzyme is characterized by relatively broad substrate specificity, being able to oxidize positively charged and large hydrophobic D-amino acids bound within a flask-like cavity.« less

Germline-specific H1 variants: the "sexy" linker histones.

PubMed

Pérez-Montero, Salvador; Carbonell, Albert; Azorín, Fernando

2016-03-01

The eukaryotic genome is packed into chromatin, a nucleoprotein complex mainly formed by the interaction of DNA with the abundant basic histone proteins. The fundamental structural and functional subunit of chromatin is the nucleosome core particle, which is composed by 146 bp of DNA wrapped around an octameric protein complex formed by two copies of each core histone H2A, H2B, H3, and H4. In addition, although not an intrinsic component of the nucleosome core particle, linker histone H1 directly interacts with it in a monomeric form. Histone H1 binds nucleosomes near the exit/entry sites of linker DNA, determines nucleosome repeat length and stabilizes higher-order organization of nucleosomes into the ∼30 nm chromatin fiber. In comparison to core histones, histone H1 is less well conserved through evolution. Furthermore, histone H1 composition in metazoans is generally complex with most species containing multiple variants that play redundant as well as specific functions. In this regard, a characteristic feature is the presence of specific H1 variants that replace somatic H1s in the germline and during early embryogenesis. In this review, we summarize our current knowledge about their structural and functional properties.

Structural Context of Disease-Associated Mutations and Putative Mechanism of Autoinhibition Revealed by X-Ray Crystallographic Analysis of the EZH2-SET Domain

PubMed Central

Antonysamy, Stephen; Condon, Bradley; Druzina, Zhanna; Bonanno, Jeffrey B.; Gheyi, Tarun; Zhang, Feiyu; MacEwan, Iain; Zhang, Aiping; Ashok, Sheela; Rodgers, Logan; Russell, Marijane; Gately Luz, John

2013-01-01

The enhancer-of-zeste homolog 2 (EZH2) gene product is an 87 kDa polycomb group (PcG) protein containing a C-terminal methyltransferase SET domain. EZH2, along with binding partners, i.e., EED and SUZ12, upon which it is dependent for activity forms the core of the polycomb repressive complex 2 (PRC2). PRC2 regulates gene silencing by catalyzing the methylation of histone H3 at lysine 27. Both overexpression and mutation of EZH2 are associated with the incidence and aggressiveness of various cancers. The novel crystal structure of the SET domain was determined in order to understand disease-associated EZH2 mutations and derive an explanation for its inactivity independent of complex formation. The 2.00 Å crystal structure reveals that, in its uncomplexed form, the EZH2 C-terminus folds back into the active site blocking engagement with substrate. Furthermore, the S-adenosyl-L-methionine (SAM) binding pocket observed in the crystal structure of homologous SET domains is notably absent. This suggests that a conformational change in the EZH2 SET domain, dependent upon complex formation, must take place for cofactor and substrate binding activities to be recapitulated. In addition, the data provide a structural context for clinically significant mutations found in the EZH2 SET domain. PMID:24367637

Liquid-crystalline dendrimer Cu(II) complexes and Cu(0) nanoclusters based on the Cu(II) complexes: An electron paramagnetic resonance investigation

NASA Astrophysics Data System (ADS)

Domracheva, N. E.; Mirea, A.; Schwoerer, M.; Torre-Lorente, L.; Lattermann, G.

2007-07-01

New nanostructured materials, namely, the liquid-crystalline copper(II) complexes that contain poly(propylene imine) dendrimer ligands of the first (ligand 1) and second (ligand 2) generations and which have a columnar mesophase and different copper contents (x = Cu/L), are investigated by EPR spectroscopy. The influence of water molecules and nitrate counterions on the magnetic properties of complex 2 (x = 7.3) is studied. It is demonstrated that water molecules can extract some of the copper ions from dendrimer complexes and form hexaaqua copper complexes with free ions. The dimer spectra of fully hydrated complex 2 (x = 7.3) are observed at temperatures T < 10 K. For this complex, the structure is identified and the distance between the copper ions is determined. It is shown that the nitrate counterion plays the role of a bridge between the hexaaqua copper(II) complex and the dendrimer copper(II) complex. The temperature-induced valence tautomerism attended by electron transport is revealed for the first time in blue dendrimer complexes 1 (x = 1.9) with a dimer structure. The activation energy for electron transport is estimated to be 0.35 meV. The coordination of the copper ion site (NO4) and the structural arrangement of green complexes 1 (x = 1.9) in the columnar mesophase are determined. Complexes of this type form linear chains in which nitrate counterions serve as bridges between copper centers. It is revealed that green complexes 1 (x = 1.9) dissolved in isotropic inert solvents can be oriented in the magnetic field (B 0 = 8000 G). The degree of orientation of these complexes is rather high (S z = 0.76) and close to that of systems with a complete ordering (S z = 1) in the magnetic field. Copper(0) nanoclusters prepared by reduction of complex 2 (x = 7.3) in two reducing agents (NaBH4, N2H4 · H2O) are examined. A model is proposed for a possible location of Cu(0) nanoclusters in a dendrimer matrix.

Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Duckhoe; Sahin, Ozgur

2015-03-01

Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

Synthesis, structural characterization, and thermal stability studies of heteroleptic cadmium(II) dithiocarbamate with different pyridyl groups

NASA Astrophysics Data System (ADS)

Onwudiwe, Damian C.; Hosten, Eric C.

2018-01-01

The synthesis, characterization and crystal structures of three chloroform solvated adducts of cadmium with mixed ligands of N-alkyl-N-phenyldithiocarbamate and pyridine, 2,2-bipyridine and 1, 10 phenanthroline represented as [CdL1L2 (py)2]·CHCl3(1), [CdL1L2bpy]•CHCl3(2), and [CdL1L2phen]•CHCl3(3) (LI = N-methyl-N-phenyldithiocarbamate, L2 = N-ethyl-N-phenyldithiocarbamate, py = pyridine, bpy = 2,2-bipyridine and phen = 1,10-phenanthroline) respectively are reported. Complex 1, which crystallized in the monoclinic space group P-1, is a centrosymmetric dimeric structure where each Cd center is bonded to two monodentate pyridine, a bidentate terminal dithiocarbamate, and another bidentate bridging dithiocarbamate to form a four-membered ring. Complex 2 crystallized in the monoclinic space group P21/c, with four discrete monomeric molecules in the asymmetric unit. The structure presents a cadmium atom coordinated by two sulphur atoms of a dithiocarbamate ligand and two nitrogen atoms of the 2,2‧-bipyridine to form a CdS4N2 fragment, thus giving the structure around the Cd atom a distorted trigonal prism geometry. Complex 3 contains two discrete monomeric molecules of (phenanthroline) (N, N-methyl phenyl-N, N-ethyl phenyl dithiocarbamato)cadmium (II) per unit cell, and the complex crystallized in the triclinic space group P-1. The structure showed that the Cd atom is bonded to two bidentate dithiocarbamate ligands and to one bidentate phenanthroline ligand in a distorted trigonal prism geometry. All the compounds resulted in CdS as residue upon thermal decomposition process conducted under inert atmosphere.

Amphibolite boudins in marble on Naxos, Greece: 3D analysis of multiphase deformation on a retrograde P-T path

NASA Astrophysics Data System (ADS)

Virgo, Simon; von Hagke, Christoph; Urai, Janos L.

2017-04-01

Boudins are periodic structures that form by layer parallel extension in mechanically layered rocks. The characteristics of boudins such as orientation and geometry provide constraints on the paleo stress field as well as the rheology of the rocks during deformation. However, most characterizations of boudinage are based on 2D observations and do not consider the 3-dimensional complexity and potentially non-coaxial polyphase genesis of boudinage structures. In marble quarries in the high grade complex on Naxos, Greece, we studied spectacular outcrops of amphibolite and pegmatite boudins, in combination with serial slicing of quarried blocks to reconstruct the 3D boudin structures. We identified five boudin generations with two distinct generations of early, high grade pinch-and-swell followed by two generations of brittle shearband and torn boudins formed along the retrograde path under greenschist facies conditions. The five generations of boudinage indicate that E-W compression is the main mode of deformation in the marbles. The axis of extension changes from subvertical during pinch-and swell deformation to subhorizontal N-S extension at later stages of deformation. Later phases of boudinage are influenced by existing boudin geometries, producing complex structures in 3D. In 2D section the complexity is not directly apparent and reveals itself only after statistical analysis of long continuous sections. Apart from implications for the regional geology, our findings highlight the importance of 3D characterization of boudinage structures for boudin classification. The insights we gain from the analysis of multiphase boudinage structures on Naxos are the basis for quantitative boudin analysis to infer rheology, effective stress, vorticity and strain, and establish a boudin classification scheme with appeal to a complete mechanics.

Five-coordinate Co(II) complexes with nitrilotriacetic acid: Crystal structures of Ca[Co(Nta)X] . nH{sub 2}O (X{sup -} = Cl, Br, or NCS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polyakova, I. N.; Poznyak, A. L.; Sergienko, V. S.

2006-07-15

The synthesis and X-ray diffraction study of three Ca[Co(Nta)X] . nH{sub 2}O complexes [X{sup -} = Cl, n = 2.3 (I); X{sup -} = Br, n = 2 (II); and X{sup -} = NCS, n = 2 (III)] are performed. The main structural units of crystals I-III are the [CoX(Nta)]{sup 2-} anionic complexes and hydrated Ca{sup 2+} cations. The anionic complexes have similar structures. The coordination of the Co{sup 2+} atom in the shape of a trigonal bipyramid is formed by N + 3O atoms of the Nta{sup 3-} ligand and the X{sup -} anion in the trans position withmore » respect to N. In structures I-III, the Co-O and Co-N bond lengths lie in the ranges 1.998-2.032 and 2.186-2.201 A, respectively. The Co-X bond lengths are 2.294 (I), 2.436 and 2.445 (II), and 1.982 A (III). The environments of the Ca{sup 2+} cations include oxygen atoms of one or two water molecules and six or seven O(Nta) atoms with the coordination number of 9 in I or 8 in II and III. The Ca-O(Nta) bonds form a three-dimensional framework in I or layers in II and III. Water molecules are involved in the hydrogen bonds O(w)-H...O(Nta), O(w)-H...X, and O(w)-H...O(w). Structural data for crystals I-III are deposited with the Cambridge Structural Database (CCDC nos. 287 814-287 816)« less

Probabilistic Fatigue Damage Prognosis Using a Surrogate Model Trained Via 3D Finite Element Analysis

NASA Technical Reports Server (NTRS)

Leser, Patrick E.; Hochhalter, Jacob D.; Newman, John A.; Leser, William P.; Warner, James E.; Wawrzynek, Paul A.; Yuan, Fuh-Gwo

2015-01-01

Utilizing inverse uncertainty quantification techniques, structural health monitoring can be integrated with damage progression models to form probabilistic predictions of a structure's remaining useful life. However, damage evolution in realistic structures is physically complex. Accurately representing this behavior requires high-fidelity models which are typically computationally prohibitive. In the present work, a high-fidelity finite element model is represented by a surrogate model, reducing computation times. The new approach is used with damage diagnosis data to form a probabilistic prediction of remaining useful life for a test specimen under mixed-mode conditions.

Structural Studies of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Tetramer in Complex with Its Receptor, Sialyllactose

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuan, Ping; Thompson, Thomas B.; Wurzburg, Beth A.

2010-03-08

The paramyxovirus hemagglutinin-neuraminidase (HN) functions in virus attachment to cells, cleavage of sialic acid from oligosaccharides, and stimulating membrane fusion during virus entry into cells. The structural basis for these diverse functions remains to be fully understood. We report the crystal structures of the parainfluenza virus 5 (SV5) HN and its complexes with sialic acid, the inhibitor DANA, and the receptor sialyllactose. SV5 HN shares common structural features with HN of Newcastle disease virus (NDV) and human parainfluenza 3 (HPIV3), but unlike the previously determined HN structures, the SV5 HN forms a tetramer in solution, which is thought to bemore » the physiological oligomer. The sialyllactose complex reveals intact receptor within the active site, but no major conformational changes in the protein. The SV5 HN structures do not support previously proposed models for HN action in membrane fusion and suggest alternative mechanisms by which HN may promote virus entry into cells.« less

The Tom Core Complex

PubMed Central

Ahting, Uwe; Thun, Clemens; Hegerl, Reiner; Typke, Dieter; Nargang, Frank E.; Neupert, Walter; Nussberger, Stephan

1999-01-01

Translocation of nuclear-encoded preproteins across the outer membrane of mitochondria is mediated by the multicomponent transmembrane TOM complex. We have isolated the TOM core complex of Neurospora crassa by removing the receptors Tom70 and Tom20 from the isolated TOM holo complex by treatment with the detergent dodecyl maltoside. It consists of Tom40, Tom22, and the small Tom components, Tom6 and Tom7. This core complex was also purified directly from mitochondria after solubilization with dodecyl maltoside. The TOM core complex has the characteristics of the general insertion pore; it contains high-conductance channels and binds preprotein in a targeting sequence-dependent manner. It forms a double ring structure that, in contrast to the holo complex, lacks the third density seen in the latter particles. Three-dimensional reconstruction by electron tomography exhibits two open pores traversing the complex with a diameter of ∼2.1 nm and a height of ∼7 nm. Tom40 is the key structural element of the TOM core complex. PMID:10579717

Metal–organic coordination architectures of tetrazole heterocycle ligands bearing acetate groups: Synthesis, characterization and magnetic properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Bo-Wen, E-mail: bowenhu@hit.edu.cn; Zheng, Xiang-Yu; Ding, Cheng

2015-12-15

Two new coordination complexes with tetrazole heterocycle ligands bearing acetate groups, [Co(L){sub 2}]{sub n} (1) and [Co{sub 3}(L){sub 4}(N{sub 3}){sub 2}·2MeOH]{sub n} (2) (L=tetrazole-1-acetate) have been synthesized and structurally characterized. Single crystal structure analysis shows that the cobalt-complex 1 has the 3D 3,6-connected (4{sup 2}.6){sub 2}(4{sup 4}.6{sup 2}.8{sup 8}.10)-ant topology. By introducing azide in this system, complex 2 forms the 2D network containing the [Co{sub 3}] units. And the magnetic properties of 1 and 2 have been studied. - Graphical abstract: The synthesis, crystal structure, and magnetic properties of the new coordination complexes with tetrazole heterocycle ligands bearing acetate groupsmore » are reported. - Highlights: • Two novel Cobalt(II) complexes with tetrazole acetate ligands were synthesized. • The magnetic properties of two complexes were studied. • Azide as co-ligand resulted in different structures and magnetic properties. • The new coordination mode of tetrazole acetate ligand was obtained.« less

Cohesin-interacting protein WAPL-1 regulates meiotic chromosome structure and cohesion by antagonizing specific cohesin complexes

PubMed Central

Crawley, Oliver; Barroso, Consuelo; Testori, Sarah; Ferrandiz, Nuria; Silva, Nicola; Castellano-Pozo, Maikel; Jaso-Tamame, Angel Luis; Martinez-Perez, Enrique

2016-01-01

Wapl induces cohesin dissociation from DNA throughout the mitotic cell cycle, modulating sister chromatid cohesion and higher-order chromatin structure. Cohesin complexes containing meiosis-specific kleisin subunits govern most aspects of meiotic chromosome function, but whether Wapl regulates these complexes remains unknown. We show that during C. elegans oogenesis WAPL-1 antagonizes binding of cohesin containing COH-3/4 kleisins, but not REC-8, demonstrating that sensitivity to WAPL-1 is dictated by kleisin identity. By restricting the amount of chromosome-associated COH-3/4 cohesin, WAPL-1 controls chromosome structure throughout meiotic prophase. In the absence of REC-8, WAPL-1 inhibits COH-3/4-mediated cohesion, which requires crossover-fated events formed during meiotic recombination. Thus, WAPL-1 promotes functional specialization of meiotic cohesin: WAPL-1-sensitive COH-3/4 complexes modulate higher-order chromosome structure, while WAPL-1-refractory REC-8 complexes provide stable cohesion. Surprisingly, a WAPL-1-independent mechanism removes cohesin before metaphase I. Our studies provide insight into how meiosis-specific cohesin complexes are regulated to ensure formation of euploid gametes. DOI: http://dx.doi.org/10.7554/eLife.10851.001 PMID:26841696

Structures and unimolecular chemistry of M(Pro2-H)(+) (M = Mg, Ca, Sr, Ba, Mn, Fe, Co, Ni, Cu, Zn) by IRMPD spectroscopy, SORI-CID, and theoretical studies.

PubMed

Jami-Alahmadi, Yasaman; Fridgen, Travis D

2016-01-21

M(Pro2-H)(+) complexes were electrosprayed and isolated in an FTICR cell where their unimolecular chemistries and structures were explored using SORI-CID and IRMPD spectroscopy. These experiments were augmented by computational methods such as electronic structure, simulated annealing, and atoms in molecules (AIM) calculations. The unimolecular chemistries of the larger metal cation (Ca(2+), Sr(2+) and Ba(2+)) complexes predominantly involve loss of neutral proline whereas the complexes involving the smaller Mg(2+) and transition metal dications tend to lose small neutral molecules such as water and carbon dioxide. Interestingly, all complexes involving transition metal dications except for Cu(Pro2-H)(+) lose H2 upon collisional or IRMPD activation. IRMPD spectroscopy shows that the intact proline in the transition metal complexes and Cu(Pro2-H)(+) is predominantly canonical (charge solvated) while for the Ca(2+), Sr(2+), and Ba(2+) complexes, proline is in its zwitterionic form. The IRMPD spectra for both Mg(Pro2-H)(+) and Mn(Pro2-H)(+) are concluded to have contributions from both charge-solvated and canonical structures.

Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound to a Partner by Combined ESI-IM-MS and Modeling

NASA Astrophysics Data System (ADS)

D'Urzo, Annalisa; Konijnenberg, Albert; Rossetti, Giulia; Habchi, Johnny; Li, Jinyu; Carloni, Paolo; Sobott, Frank; Longhi, Sonia; Grandori, Rita

2015-03-01

Intrinsically disordered proteins (IDPs) form biologically active complexes that can retain a high degree of conformational disorder, escaping structural characterization by conventional approaches. An example is offered by the complex between the intrinsically disordered NTAIL domain and the phosphoprotein X domain (PXD) from measles virus (MeV). Here, distinct conformers of the complex are detected by electrospray ionization-mass spectrometry (ESI-MS) and ion mobility (IM) techniques yielding estimates for the solvent-accessible surface area (SASA) in solution and the average collision cross-section (CCS) in the gas phase. Computational modeling of the complex in solution, based on experimental constraints, provides atomic-resolution structural models featuring different levels of compactness. The resulting models indicate high structural heterogeneity. The intermolecular interactions are predominantly hydrophobic, not only in the ordered core of the complex, but also in the dynamic, disordered regions. Electrostatic interactions become involved in the more compact states. This system represents an illustrative example of a hydrophobic complex that could be directly detected in the gas phase by native mass spectrometry. This work represents the first attempt to modeling the entire NTAIL domain bound to PXD at atomic resolution.

Cells and cell biochemistry.

PubMed

Farley, Alistair; Hendry, Charles; McLafferty, Ella

This article, which forms part of the life sciences series, aims to promote understanding of the basic structure and function of cells. It assists healthcare professionals to appreciate the complex anatomy and physiology underpinning the functioning of the human body. Several introductory chemical concepts and terms are outlined. The basic building blocks of all matter, atoms, are examined and the way in which they may interact to form new compounds within the body is discussed. The basic structures and components that make up a typical cell are considered.

CryoEM structure of yeast cytoplasmic exosome complex.

PubMed

Liu, Jun-Jie; Niu, Chu-Ya; Wu, Yao; Tan, Dan; Wang, Yang; Ye, Ming-Da; Liu, Yang; Zhao, Wenwei; Zhou, Ke; Liu, Quan-Sheng; Dai, Junbiao; Yang, Xuerui; Dong, Meng-Qiu; Huang, Niu; Wang, Hong-Wei

2016-07-01

The eukaryotic multi-subunit RNA exosome complex plays crucial roles in 3'-to-5' RNA processing and decay. Rrp6 and Ski7 are the major cofactors for the nuclear and cytoplasmic exosomes, respectively. In the cytoplasm, Ski7 helps the exosome to target mRNAs for degradation and turnover via a through-core pathway. However, the interaction between Ski7 and the exosome complex has remained unclear. The transaction of RNA substrates within the exosome is also elusive. In this work, we used single-particle cryo-electron microscopy to solve the structures of the Ski7-exosome complex in RNA-free and RNA-bound forms at resolutions of 4.2 Å and 5.8 Å, respectively. These structures reveal that the N-terminal domain of Ski7 adopts a structural arrangement and interacts with the exosome in a similar fashion to the C-terminal domain of nuclear Rrp6. Further structural analysis of exosomes with RNA substrates harboring 3' overhangs of different length suggests a switch mechanism of RNA-induced exosome activation in the through-core pathway of RNA processing.

The Human Polycomb Group Complex Associates with Pericentromeric Heterochromatin to Form a Novel Nuclear Domain

PubMed Central

Saurin, Andrew J.; Shiels, Carol; Williamson, Jill; Satijn, David P.E.; Otte, Arie P.; Sheer, Denise; Freemont, Paul S.

1998-01-01

The Polycomb group (PcG) complex is a chromatin-associated multiprotein complex, involved in the stable repression of homeotic gene activity in Drosophila. Recently, a mammalian PcG complex has been identified with several PcG proteins implicated in the regulation of Hox gene expression. Although the mammalian PcG complex appears analogous to the complex in Drosophila, the molecular mechanisms and functions for the mammalian PcG complex remain unknown. Here we describe a detailed characterization of the human PcG complex in terms of cellular localization and chromosomal association. By using antibodies that specifically recognize three human PcG proteins— RING1, BMI1, and hPc2—we demonstrate in a number of human cell lines that the PcG complex forms a unique discrete nuclear structure that we term PcG bodies. PcG bodies are prominent novel nuclear structures with the larger PcG foci generally localized near the centromeres, as visualized with a kinetochore antibody marker. In both normal fetal and adult fibroblasts, PcG bodies are not randomly dispersed, but appear clustered into defined areas within the nucleus. We show in three different human cell lines that the PcG complex can tightly associate with large pericentromeric heterochromatin regions (1q12) on chromosome 1, and with related pericentromeric sequences on different chromosomes, providing evidence for a mammalian PcG–heterochromatin association. Furthermore, these heterochromatin-bound PcG complexes remain stably associated throughout mitosis, thereby allowing the potential inheritance of the PcG complex through successive cell divisions. We discuss these results in terms of the known function of the PcG complex as a transcriptional repression complex. PMID:9722603

Oxidation of municipal wastewater by free radicals mechanism. A UV/Vis spectroscopy study.

PubMed

Giannakopoulos, E; Isari, E; Bourikas, K; Karapanagioti, H K; Psarras, G; Oron, G; Kalavrouziotis, I K

2017-06-15

This study investigates the oxidation of municipal wastewater (WW) by complexation with natural polyphenols having radical scavenging activity, such as (3,4,5 tri-hydroxy-benzoic acid) gallic acid (GA) in alkaline pH (>7), under ambient O 2 and temperature. Physicochemical and structural characteristics of GA-WW complex-forming are evaluated by UV/Vis spectroscopy. The comparative analysis among UV/Vis spectra of GA monomer, GA-GA polymer, WW compounds, and GA-WW complex reveals significant differences within 350-450 and 500-900 nm. According to attenuated total reflectance (ATR) spectroscopy and thermogravimetric analysis (TGA), these spectra differences correspond to distinct complexes formed. This study suggests a novel role of natural polyphenols on the degradation and humification of wastes. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Postsynaptic Density Proteins Homer and Shank Form a Polymeric Network Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayashi, M.; Tang, C; Verpelli, C

2009-01-01

The postsynaptic density (PSD) is crucial for synaptic functions, but the molecular architecture retaining its structure and components remains elusive. Homer and Shank are among the most abundant scaffolding proteins in the PSD, working synergistically for maturation of dendritic spines. Here, we demonstrate that Homer and Shank, together, form a mesh-like matrix structure. Crystallographic analysis of this region revealed a pair of parallel dimeric coiled coils intercalated in a tail-to-tail fashion to form a tetramer, giving rise to the unique configuration of a pair of N-terminal EVH1 domains at each end of the coiled coil. In neurons, the tetramerization ismore » required for structural integrity of the dendritic spines and recruitment of proteins to synapses. We propose that the Homer-Shank complex serves as a structural framework and as an assembly platform for other PSD proteins.« less

Structures of Staphylococcus aureus D-tagatose-6-phosphate kinase implicate domain motions in specificity and mechanism.

PubMed

Miallau, Linda; Hunter, William N; McSweeney, Sean M; Leonard, Gordon A

2007-07-06

High resolution structures of Staphylococcus aureus d-tagatose-6-phosphate kinase (LacC) in two crystal forms are herein reported. The structures define LacC in apoform, in binary complexes with ADP or the co-factor analogue AMP-PNP, and in a ternary complex with AMP-PNP and D-tagatose-6-phosphate. The tertiary structure of the LacC monomer, which is closely related to other members of the pfkB subfamily of carbohydrate kinases, is composed of a large alpha/beta core domain and a smaller, largely beta "lid." Four extended polypeptide segments connect these two domains. Dimerization of LacC occurs via interactions between lid domains, which come together to form a beta-clasp structure. Residues from both subunits contribute to substrate binding. LacC adopts a closed structure required for phosphoryl transfer only when both substrate and co-factor are bound. A reaction mechanism similar to that used by other phosphoryl transferases is proposed, although unusually, when both substrate and co-factor are bound to the enzyme two Mg(2+) ions are observed in the active site. A new motif of amino acid sequence conservation common to the pfkB subfamily of carbohydrate kinases is identified.

Biomineralization of unicellular organisms: an unusual membrane biochemistry for the production of inorganic nano- and microstructures.

PubMed

Bäuerlein, Edmund

2003-02-10

With evolution, Nature has ingeniously succeeded in giving rise to an impressive variety of inorganic structures. Every organism that synthesizes biogenic minerals does so in a form that is unique to that species. This biomineralization is apparently biologically controlled. It is thus expected that both the synthesis and the form of every specific biogenic mineral is genetically determined and controlled. An investigation of the mechanism of biomineralization has only become possible with the development of modern methods in molecular biology. Unicellular organisms such as magnetic bacteria, calcareous algae, and diatoms, all of which are amongst the simplest forms of life, are particularly suited to be investigated by these methods. Crystals and composites of proteins and amorphous inorganic polymers are formed as complex structures within these organisms; these structures are not known in conventional inorganic chemistry.

Street as Sustainable City Structural Element

NASA Astrophysics Data System (ADS)

Leyzerova, A. V.; Bagina, E. J.

2017-11-01

Sustainability in architecture is nowadays of particular significance in the course of globalization and information density. The technospehere spontaneous development poses a threat to the sustainability of traditional urban forms where a street is one of the essential forming elements in the urban structure. The article proposes to consider formally compositional street features in relation to one of the traditional streets in the historic center of Ekaterinburg. The study examines the street-planning structure, the development of its skeleton elements, silhouette and fabric elevation characteristics as well as the scale characteristics and visual complexity of objects. The study provided architectural and artistic aspects of street sustainability, and limits of the appropriate scale and composition consistency under which the compatibility of alternative compositional forms existing at different times is possible.

Structural Insight into Nucleoprotein Conformation Change Chaperoned by VP35 Peptide in Marburg Virus.

PubMed

Liu, Baocheng; Dong, Shishang; Li, Guobang; Wang, Wenming; Liu, Xiang; Wang, Yantong; Yang, Cheng; Rao, Zihe; Guo, Yu

2017-08-15

Marburg virus (MARV) encodes a nucleoprotein (NP) to encapsidate its genome by oligomerization and form a ribonucleoprotein complex (RNP). According to previous investigation on nonsegmented negative-sense RNA viruses (nsNSV), the newly synthesized NPs must be prevented from indiscriminately binding to noncognate RNAs. During the viral RNA synthesis process, the RNPs undergo a transition from an RNA-bound form to a template-free form, to open access for the interaction between the viral polymerase and the RNA template. In filoviruses, this transition is regulated by VP35 peptide and other viral components. To further understand the dynamic process of filovirus RNP formation, we report here the structure of MARV NP core , both in the apo form and in the VP35 peptide-chaperoned form. These structures reveal a typical bilobed structure, with a positive-charged RNA binding groove between two lobes. In the apo form, the MARV NP exists in an interesting hexameric state formed by the hydrophobic interaction within the long helix of the NP core C-terminal region, which shows high structural flexibility among filoviruses and may imply critical function during RNP formation. Moreover, the VP35 peptide-chaperoned NP core remains in a monomeric state and completely loses its affinity for single-stranded RNA (ssRNA). The structural comparison reveals that the RNA binding groove undergoes a transition from closed state to open state, chaperoned by VP35 peptide, thus preventing the interaction for viral RNA. Our investigation provides considerable structural insight into the filovirus RNP working mechanism and may support the development of antiviral therapies targeting the RNP formation of filovirus. IMPORTANCE Marburg virus is one of the most dangerous viruses, with high morbidity and mortality. A recent outbreak in Angola in 2005 caused the deaths of 272 persons. NP is one of the most essential proteins, as it encapsidates and protects the whole virus genome simultaneously with self-assembly oligomerization. Here we report the structures of MARV NP core in two different forms. In the MARV NP apo form, we identify an interesting hexamer formed by hydrophobic interaction within a long helix, which is highly conserved and flexible among filoviruses and may indicate its critical function during the virus RNP formation. Moreover, the structural comparison with the NP-VP35 peptide complex reveals a structural transition chaperoned by VP35, in which the RNA binding groove undergoes a transition from closed state to open state. Finally, we discussed the high conservation and critical role of the VP35 binding pocket and its potential use for therapeutic development. Copyright © 2017 American Society for Microbiology.

First Principles Based Simulation of Reaction-Induced Phase Transition in Hydrogen Storage and Other Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ge, Qingfeng

2014-08-31

This major part of this proposal is simulating hydrogen interactions in the complex metal hydrides. Over the period of DOE BES support, key achievements include (i) Predicted TiAl 3Hx as a precursor state for forming TiAl 3 through analyzing the Ti-doped NaAlH 4 and demonstrated its catalytic role for hydrogen release; (ii) Explored the possibility of forming similar complex structures with other 3d transition metals in NaAlH 4 as well as the impact of such complex structures on hydrogen release/uptake; (iii) Demonstrated the role of TiAl 3 in hydriding process; (iv) Predicted a new phase of NaAlH 4 that linksmore » to Na3AlH6 using first-principles metadynamics; (v) Examined support effect on hydrogen release from supported/encapsulated NaAlH 4; and (vi) Expanded research scope beyond hydrogen storage. The success of our research is documented by the peer-reviewed publications.« less

Angioarchitecture of the bovine tunica albuginea vascular complex--a corrosive and histological study.

PubMed

Polguj, Michał; Sopiński, Marek; Jędrzejewski, Kazimierz; Bolanowski, Wojciech; Topol, Mirosław

2011-10-01

Histological and corrosive studies of 75 bovine testes were focused on the vascular complex of the tunica albuginea. Thanks to used MultiScanBase v.14.02 software arterial and venous vessels and also vascular anastomoses were analyzed preciously. The studies revealed the superficial layer containing vessels of smaller diameter and reduced wall structure and the deeper layer with wider, winding vessels and complete wall structure. The branches of the testicular artery and intra-tunical veins formed a vascular complex of the tunica albuginea. The intra-tunical veins were divided into two types. Type I veins ran parallel, drained intra-parenchymal veins and formed the origin of pampiniform plexus. Type II veins drained into type I intra-tunical veins. Indirect anastomoses among intra-tunical veins and arteries and venovenous connections were observed. The results of the study could contribute fuller description of the regulatory mechanism for testicular blood supply and optimization of the testicular biopsy to minimize bleeding risk. Copyright © 2010 Elsevier Ltd. All rights reserved.

Dynamic clustering of dynamin-amphiphysin helices regulates membrane constriction and fission coupled with GTP hydrolysis

PubMed Central

Kozai, Toshiya; Yang, Huiran; Ishikuro, Daiki; Seyama, Kaho; Kumagai, Yusuke; Abe, Tadashi; Yamada, Hiroshi; Uchihashi, Takayuki

2018-01-01

Dynamin is a mechanochemical GTPase essential for membrane fission during clathrin-mediated endocytosis. Dynamin forms helical complexes at the neck of clathrin-coated pits and their structural changes coupled with GTP hydrolysis drive membrane fission. Dynamin and its binding protein amphiphysin cooperatively regulate membrane remodeling during the fission, but its precise mechanism remains elusive. In this study, we analyzed structural changes of dynamin-amphiphysin complexes during the membrane fission using electron microscopy (EM) and high-speed atomic force microscopy (HS-AFM). Interestingly, HS-AFM analyses show that the dynamin-amphiphysin helices are rearranged to form clusters upon GTP hydrolysis and membrane constriction occurs at protein-uncoated regions flanking the clusters. We also show a novel function of amphiphysin in size control of the clusters to enhance biogenesis of endocytic vesicles. Our approaches using combination of EM and HS-AFM clearly demonstrate new mechanistic insights into the dynamics of dynamin-amphiphysin complexes during membrane fission. PMID:29357276

Construction and Structural Analysis of Tethered Lipid Bilayer Containing Photosynthetic Antenna Proteins for Functional Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sumino, Ayumi; Dewa, Takehisa; Takeuchi, Toshikazu

2011-07-11

The construction and structural analysis of a tethered planar lipid bilayer containing bacterial photosynthetic membrane proteins, light-harvesting complex 2 (LH2), and light-harvesting core complex (LH1-RC) is described and establishes this system as an experimental platform for their functional analysis. The planar lipid bilayer containing LH2 and/or LH1-RC complexes was successfully formed on an avidin-immobilized coverglass via an avidin-biotin linkage. Atomic force microscopy (AFM) showed that a smooth continuous membrane was formed there. Lateral diffusion of these membrane proteins, observed by a fluorescence recovery after photobleaching (FRAY), is discussed in terms of the membrane architecture. Energy transfer from LH2 to LH1-RCmore » within the tethered membrane architecture. Energy transfer from LH2 to LH1-RC within the tethered membrane was observed by steady-state fluorescence spectroscopy, indicating that the tethered membrane can mimic the natural situation.« less

X-ray structures of the Pseudomonas cichorii D-tagatose 3-epimerase mutant form C66S recognizing deoxy sugars as substrates.

PubMed

Yoshida, Hiromi; Yoshihara, Akihide; Ishii, Tomohiko; Izumori, Ken; Kamitori, Shigehiro

2016-12-01

Pseudomonas cichorii D-tagatose 3-epimerase (PcDTE), which has a broad substrate specificity, efficiently catalyzes the epimerization of not only D-tagatose to D-sorbose but also D-fructose to D-psicose (D-allulose) and also recognizes the deoxy sugars as substrates. In an attempt to elucidate the substrate recognition and catalytic reaction mechanisms of PcDTE for deoxy sugars, the X-ray structures of the PcDTE mutant form with the replacement of Cys66 by Ser (PcDTE_C66S) in complexes with deoxy sugars were determined. These X-ray structures showed that substrate recognition by the enzyme at the 1-, 2-, and 3-positions is responsible for enzymatic activity and that substrate-enzyme interactions at the 4-, 5-, and 6-positions are not essential for the catalytic reaction of the enzyme leading to the broad substrate specificity of PcDTE. They also showed that the epimerization site of 1-deoxy 3-keto D-galactitol is shifted from C3 to C4 and that 1-deoxy sugars may bind to the catalytic site in the inhibitor-binding mode. The hydrophobic groove that acts as an accessible surface for substrate binding is formed through the dimerization of PcDTE. In PcDTE_C66S/deoxy sugar complex structures, bound ligand molecules in both the linear and ring forms were detected in the hydrophobic groove, while bound ligand molecules in the catalytic site were in the linear form. This result suggests that the sugar-ring opening of a substrate may occur in the hydrophobic groove and also that the narrow channel of the passageway to the catalytic site allows a substrate in the linear form to pass through.