The structure of complex Lie groups

CERN Document Server

Lee, Dong Hoon

2001-01-01

Complex Lie groups have often been used as auxiliaries in the study of real Lie groups in areas such as differential geometry and representation theory. To date, however, no book has fully explored and developed their structural aspects.The Structure of Complex Lie Groups addresses this need. Self-contained, it begins with general concepts introduced via an almost complex structure on a real Lie group. It then moves to the theory of representative functions of Lie groups- used as a primary tool in subsequent chapters-and discusses the extension problem of representations that is essential for studying the structure of complex Lie groups. This is followed by a discourse on complex analytic groups that carry the structure of affine algebraic groups compatible with their analytic group structure. The author then uses the results of his earlier discussions to determine the observability of subgroups of complex Lie groups.The differences between complex algebraic groups and complex Lie groups are sometimes subtle ...

Oleic acid is a key cytotoxic component of HAMLET-like complexes.

Science.gov (United States)

Permyakov, Sergei E; Knyazeva, Ekaterina L; Khasanova, Leysan M; Fadeev, Roman S; Zhadan, Andrei P; Roche-Hakansson, Hazeline; Håkansson, Anders P; Akatov, Vladimir S; Permyakov, Eugene A

2012-01-01

HAMLET is a complex of α-lactalbumin (α-LA) with oleic acid (OA) that selectively kills tumor cells and Streptococcus pneumoniae. To assess the contribution of the proteinaceous component to cytotoxicity of HAMLET, OA complexes with proteins structurally and functionally distinct from α-LA were prepared. Similar to HAMLET, the OA complexes with bovine β-lactoglobulin (bLG) and pike parvalbumin (pPA) (bLG-OA-45 and pPA-OA-45, respectively) induced S. pneumoniae D39 cell death. The activation mechanisms of S. pneumoniae death for these complexes were analogous to those for HAMLET, and the cytotoxicity of the complexes increased with OA content in the preparations. The half-maximal inhibitory concentration for HEp-2 cells linearly decreased with rise in OA content in the preparations, and OA concentration in the preparations causing HEp-2 cell death was close to the cytotoxicity of OA alone. Hence, the cytotoxic action of these complexes against HEp-2 cells is induced mostly by OA. Thermal stabilization of bLG upon association with OA implies that cytotoxicity of bLG-OA-45 complex cannot be ascribed to molten globule-like conformation of the protein component. Overall, the proteinaceous component of HAMLET-like complexes studied is not a prerequisite for their activity; the cytotoxicity of these complexes is mostly due to the action of OA.

Complex DNA structures and structures of DNA complexes

International Nuclear Information System (INIS)

Chazin, W.J.; Carlstroem, G.; Shiow-Meei Chen; Miick, S.; Gomez-Paloma, L.; Smith, J.; Rydzewski, J.

1994-01-01

Complex DNA structures (for example, triplexes, quadruplexes, junctions) and DNA-ligand complexes are more difficult to study by NMR than standard DNA duplexes are because they have high molecular weights, show nonstandard or distorted local conformations, and exhibit large resonance linewidths and severe 1 H spectral overlap. These systems also tend to have limited solubility and may require specialized solution conditions to maintain favorable spectral characteristics, which adds to the spectroscopic difficulties. Furthermore, with more atoms in the system, both assignment and structure calculation become more challenging. In this article, we focus on demonstrating the current status of NMR studies of such systems and the limitations to further progress; we also indicate in what ways isotopic enrichment can be useful

Complex DNA structures and structures of DNA complexes

Energy Technology Data Exchange (ETDEWEB)

Chazin, W.J.; Carlstroem, G.; Shiow-Meei Chen; Miick, S.; Gomez-Paloma, L.; Smith, J.; Rydzewski, J. [Scripps Research Institute, La Jolla, CA (United States)

1994-12-01

Complex DNA structures (for example, triplexes, quadruplexes, junctions) and DNA-ligand complexes are more difficult to study by NMR than standard DNA duplexes are because they have high molecular weights, show nonstandard or distorted local conformations, and exhibit large resonance linewidths and severe {sup 1}H spectral overlap. These systems also tend to have limited solubility and may require specialized solution conditions to maintain favorable spectral characteristics, which adds to the spectroscopic difficulties. Furthermore, with more atoms in the system, both assignment and structure calculation become more challenging. In this article, we focus on demonstrating the current status of NMR studies of such systems and the limitations to further progress; we also indicate in what ways isotopic enrichment can be useful.

Tissue Factor-Factor VII Complex As a Key Regulator of Ovarian Cancer Phenotypes.

Science.gov (United States)

Koizume, Shiro; Miyagi, Yohei

2015-01-01

Tissue factor (TF) is an integral membrane protein widely expressed in normal human cells. Blood coagulation factor VII (fVII) is a key enzyme in the extrinsic coagulation cascade that is predominantly secreted by hepatocytes and released into the bloodstream. The TF-fVII complex is aberrantly expressed on the surface of cancer cells, including ovarian cancer cells. This procoagulant complex can initiate intracellular signaling mechanisms, resulting in malignant phenotypes. Cancer tissues are chronically exposed to hypoxia. TF and fVII can be induced in response to hypoxia in ovarian cancer cells at the gene expression level, leading to the autonomous production of the TF-fVII complex. Here, we discuss the roles of the TF-fVII complex in the induction of malignant phenotypes in ovarian cancer cells. The hypoxic nature of ovarian cancer tissues and the roles of TF expression in endometriosis are discussed. Arguments will be extended to potential strategies to treat ovarian cancers based on our current knowledge of TF-fVII function.

Linking structural features of protein complexes and biological function.

Science.gov (United States)

Sowmya, Gopichandran; Breen, Edmond J; Ranganathan, Shoba

2015-09-01

Protein-protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure-function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions. © 2015 The Protein Society.

Structural complexity and land-surface energy exchange along a gradient from arctic tundra to boreal forest

Science.gov (United States)

Thompson, C.; Beringer, J.; Chapin, F. S.; McGuire, A.D.

2004-01-01

Question: Current climate changes in the Alaskan Arctic, which are characterized by increases in temperature and length of growing season, could alter vegetation structure, especially through increases in shrub cover or the movement of treeline. These changes in vegetation structure have consequences for the climate system. What is the relationship between structural complexity and partitioning of surface energy along a gradient from tundra through shrub tundra to closed canopy forest? Location: Arctic tundra-boreal forest transition in the Alaskan Arctic. Methods: Along this gradient of increasing canopy complexity, we measured key vegetation characteristics, including community composition, biomass, cover, height, leaf area index and stem area index. We relate these vegetation characteristics to albedo and the partitioning of net radiation into ground, latent, and sensible heating fluxes. Results: Canopy complexity increased along the sequence from tundra to forest due to the addition of new plant functional types. This led to non-linear changes in biomass, cover, and height in the understory. The increased canopy complexity resulted in reduced ground heat fluxes, relatively conserved latent heat fluxes and increased sensible heat fluxes. The localized warming associated with increased sensible heating over more complex canopies may amplify regional warming, causing further vegetation change in the Alaskan Arctic.

Magneto-structural correlations in trinuclear Cu(II) complexes: a density functional study

CERN Document Server

Rodríguez-Forteá, A; Alvarez, S; Centre-De Recera-En-Quimica-Teorica; Alemany, P A; Centre-De Recera-En-Quimica-Teorica

2003-01-01

Density functional theoretical methods have been used to study magneto-structural correlations for linear trinuclear hydroxo-bridged copper(II) complexes. The nearest-neighbor exchange coupling constant shows very similar trends to those found earlier for dinuclear compounds for which the Cu-O-Cu angle and the out of plane displacement of the hydrogen atoms at the bridge are the two key structural factors that determine the nature of their magnetic behavior. Changes in these two parameters can induce variations of over 1000 cm sup - sup 1 in the value of the nearest-neighbor coupling constant. On the contrary, coupling between next-nearest neighbors is found to be practically independent of structural changes with a value for the coupling constant of about -60 cm sup - sup 1. The magnitude calculated for this coupling constant indicates that considering its value to be negligible, as usually done in experimental studies, can lead to considerable errors, especially for compounds in which the nearest-neighbor c...

Transcription initiation complex structures elucidate DNA opening.

Science.gov (United States)

Plaschka, C; Hantsche, M; Dienemann, C; Burzinski, C; Plitzko, J; Cramer, P

2016-05-19

Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts.

Tissue Factor–Factor VII Complex as a Key Regulator of Ovarian Cancer Phenotypes

Directory of Open Access Journals (Sweden)

Shiro Koizume

2015-01-01

Full Text Available Tissue factor (TF is an integral membrane protein widely expressed in normal human cells. Blood coagulation factor VII (fVII is a key enzyme in the extrinsic coagulation cascade that is predominantly secreted by hepatocytes and released into the bloodstream. The TF–fVII complex is aberrantly expressed on the surface of cancer cells, including ovarian cancer cells. This procoagulant complex can initiate intracellular signaling mechanisms, resulting in malignant phenotypes. Cancer tissues are chronically exposed to hypoxia. TF and fVII can be induced in response to hypoxia in ovarian cancer cells at the gene expression level, leading to the autonomous production of the TF–fVII complex. Here, we discuss the roles of the TF–fVII complex in the induction of malignant phenotypes in ovarian cancer cells. The hypoxic nature of ovarian cancer tissues and the roles of TF expression in endometriosis are discussed. Arguments will be extended to potential strategies to treat ovarian cancers based on our current knowledge of TF–fVII function.

Integrative structure and functional anatomy of a nuclear pore complex

Science.gov (United States)

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D.; Hogan, Joanna A.; Upla, Paula; Chemmama, Ilan E.; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S.; Wang, Junjie; Williams, Rosemary; Unruh, Jay R.; Greenberg, Charles H.; Jacobs, Erica Y.; Yu, Zhiheng; de La Cruz, M. Jason; Mironska, Roxana; Stokes, David L.; Aitchison, John D.; Jarrold, Martin F.; Gerton, Jennifer L.; Ludtke, Steven J.; Akey, Christopher W.; Chait, Brian T.; Sali, Andrej; Rout, Michael P.

2018-03-01

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Integrative structure and functional anatomy of a nuclear pore complex.

Science.gov (United States)

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael P

2018-03-22

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

A strategy study on the technology development for key nuclear structural materials

International Nuclear Information System (INIS)

Hong, Jun Hwa; Jeong, Youg Hwan; Kim, Tae Kyu

2012-01-01

In order to realize the advanced long-life PWRs and new Generation-IV nuclear systems, it is pre-requisite to establish or ensure the several key materials technology. In this study, we proposed the several key needs and directions for the key materials issues. Each issue is envisioned and described below. 1) Development of innovative nuclear structural materials with extreme environment-resistance for advanced G-IV systems 2) Improvement/development of key reactor materials for advanced and long -life PWRs. 3) Development of technologies against nuclear materials aging degradation

Designing complex systems - a structured activity

NARCIS (Netherlands)

van der Veer, Gerrit C.; van Vliet, Johannes C.; Lenting, Bert; Olson, Gary M.; Schuon, Sue

1995-01-01

This paper concerns the development of complex systems from the point of view of design as a structure of activities, related both to the clients and the users. Several modeling approaches will be adopted for different aspects of design, and several views on design will be integrated. The proposed

Benchmarking in pathology: development of a benchmarking complexity unit and associated key performance indicators.

Science.gov (United States)

Neil, Amanda; Pfeffer, Sally; Burnett, Leslie

2013-01-01

This paper details the development of a new type of pathology laboratory productivity unit, the benchmarking complexity unit (BCU). The BCU provides a comparative index of laboratory efficiency, regardless of test mix. It also enables estimation of a measure of how much complex pathology a laboratory performs, and the identification of peer organisations for the purposes of comparison and benchmarking. The BCU is based on the theory that wage rates reflect productivity at the margin. A weighting factor for the ratio of medical to technical staff time was dynamically calculated based on actual participant site data. Given this weighting, a complexity value for each test, at each site, was calculated. The median complexity value (number of BCUs) for that test across all participating sites was taken as its complexity value for the Benchmarking in Pathology Program. The BCU allowed implementation of an unbiased comparison unit and test listing that was found to be a robust indicator of the relative complexity for each test. Employing the BCU data, a number of Key Performance Indicators (KPIs) were developed, including three that address comparative organisational complexity, analytical depth and performance efficiency, respectively. Peer groups were also established using the BCU combined with simple organisational and environmental metrics. The BCU has enabled productivity statistics to be compared between organisations. The BCU corrects for differences in test mix and workload complexity of different organisations and also allows for objective stratification into peer groups.

Influence of processing parameters on pore structure of 3D porous chitosan-alginate polyelectrolyte complex scaffolds.

Science.gov (United States)

Florczyk, Stephen J; Kim, Dae-Joon; Wood, David L; Zhang, Miqin

2011-09-15

Fabrication of porous polymeric scaffolds with controlled structure can be challenging. In this study, we investigated the influence of key experimental parameters on the structures and mechanical properties of resultant porous chitosan-alginate (CA) polyelectrolyte complex (PEC) scaffolds, and on proliferation of MG-63 osteoblast-like cells, targeted at bone tissue engineering. We demonstrated that the porous structure is largely affected by the solution viscosity, which can be regulated by the acetic acid and alginate concentrations. We found that the CA PEC solutions with viscosity below 300 Pa.s yielded scaffolds of uniform pore structure and that more neutral pH promoted more complete complexation of chitosan and alginate, yielding stiffer scaffolds. CA PEC scaffolds produced from solutions with viscosities below 300 Pa.s also showed enhanced cell proliferation compared with other samples. By controlling the key experimental parameters identified in this study, CA PEC scaffolds of different structures can be made to suit various tissue engineering applications. Copyright © 2011 Wiley Periodicals, Inc.

Structure of a stacked anthraquinone–DNA complex

Science.gov (United States)

De Luchi, Daniela; Usón, Isabel; Wright, Glenford; Gouyette, Catherine; Subirana, Juan A.

2010-01-01

The crystal structure of the telomeric sequence d(UBrAGG) interacting with an anthraquinone derivative has been solved by MAD. In all previously studied complexes of intercalating drugs, the drug is usually sandwiched between two DNA base pairs. Instead, the present structure looks like a crystal of stacked anthraquinone molecules in which isolated base pairs are intercalated. Unusual base pairs are present in the structure, such as G·G and A·UBr reverse Watson–Crick base pairs. PMID:20823516

Structure-based characterization of multiprotein complexes.

Science.gov (United States)

Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J

2014-07-08

Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Crystal structure of the complex of carboxypeptidase A with a strongly bound phosphonate in a new crystalline form: comparison with structures of other complexes.

Science.gov (United States)

Kim, H; Lipscomb, W N

1990-06-12

O-[[(1R)-[[N-(Phenylmethoxycarbonyl)-L-alanyl]amino]ethyl] hydroxyphosphinyl]-L-3-phenyllacetate [ZAAP(O)F], an analogue of (benzyloxycarbonyl)-Ala-Ala-Phe or (benzyloxycarbonyl)-Ala-Ala-phenyllactate, binds to carboxypeptidase A with great affinity (Ki = 3 pM). Similar phosphonates have been shown to be transition-state analogues of the CPA-catalyzed hydrolysis [Hanson, J. E., Kaplan, A. P., & Bartlett, P. A. (1989) Biochemistry 28, 6294-6305]. In the present study, the structure of the complex of this phosphonate with carboxypeptidase A has been determined by X-ray crystallography to a resolution of 2.0 A. The complex crystallizes in the space group P2(1)2(1)2(1) with cell dimensions a = 61.9 A, b = 67.2 A, and c = 76.2 A. The structure of the complex was solved by molecular replacement. Refinement of the structure against 20,776 unique reflections between 10.0 and 2.0 A yields a crystallographic residual of 0.193, including 140 water molecules. The two phosphinyl oxygens of the inhibitor bind to the active-site zinc at 2.2 A on the electrophilic (Arg-127) side and 3.1 A on the nucleophilic (Glu-270) side. Various features of the binding mode of this phosphonate inhibitor are consistent with the hypothesis that carboxypeptidase A catalyzed hydrolysis proceeds through a general-base mechanism in which the carbonyl carbon of the substrate is attacked by Zn-hydroxyl (or Zn-water). An unexpected feature of the bound inhibitor, the cis carbamoyl ester bond at the benzyloxycarbonyl linkage to alanine, allows the benzyloxycarbonyl phenyl ring of the inhibitor to interact favorably with Tyr-198. This complex structure is compared with previous structures of carboxypeptidase A, including the complexes with the potato inhibitor, a hydrated keto methylene substrate analogue, and a phosphonamidate inhibitor. Comparisons are also made with the complexes of thermolysin with some phosphonamidate inhibitors.

Coral reef structural complexity provides important coastal protection from waves under rising sea levels

Science.gov (United States)

Harris, Daniel L.; Rovere, Alessio; Casella, Elisa; Power, Hannah; Canavesio, Remy; Collin, Antoine; Pomeroy, Andrew; Webster, Jody M.; Parravicini, Valeriano

2018-01-01

Coral reefs are diverse ecosystems that support millions of people worldwide by providing coastal protection from waves. Climate change and human impacts are leading to degraded coral reefs and to rising sea levels, posing concerns for the protection of tropical coastal regions in the near future. We use a wave dissipation model calibrated with empirical wave data to calculate the future increase of back-reef wave height. We show that, in the near future, the structural complexity of coral reefs is more important than sea-level rise in determining the coastal protection provided by coral reefs from average waves. We also show that a significant increase in average wave heights could occur at present sea level if there is sustained degradation of benthic structural complexity. Our results highlight that maintaining the structural complexity of coral reefs is key to ensure coastal protection on tropical coastlines in the future. PMID:29503866

One-time pad, complexity of verification of keys, and practical security of quantum cryptography

Energy Technology Data Exchange (ETDEWEB)

Molotkov, S. N., E-mail: sergei.molotkov@gmail.com [Russian Academy of Sciences, Institute of Solid State Physics (Russian Federation)

2016-11-15

A direct relation between the complexity of the complete verification of keys, which is one of the main criteria of security in classical systems, and a trace distance used in quantum cryptography is demonstrated. Bounds for the minimum and maximum numbers of verification steps required to determine the actual key are obtained.

One-time pad, complexity of verification of keys, and practical security of quantum cryptography

International Nuclear Information System (INIS)

Molotkov, S. N.

2016-01-01

A direct relation between the complexity of the complete verification of keys, which is one of the main criteria of security in classical systems, and a trace distance used in quantum cryptography is demonstrated. Bounds for the minimum and maximum numbers of verification steps required to determine the actual key are obtained.

Key Players in I-DmoI Endonuclease Catalysis Revealed from Structure and Dynamics

DEFF Research Database (Denmark)

Molina, Rafael; Besker, Neva; Marcaida, Maria Jose

2016-01-01

. The cleavage mechanism was related both to key structural effects, such as the position of water molecules and ions participating in the cleavage reaction, and to dynamical effects related to protein behavior. In particular, we found that the protein perturbation pattern significantly changes between cleaved......Homing endonucleases, such as I-DmoI, specifically recognize and cleave long DNA target sequences (∼20 bp) and are potentially powerful tools for genome manipulation. However, inefficient and off-target DNA cleavage seriously limits specific editing in complex genomes. One approach to overcome...

Three-dimensional structure of a pre-catalytic human spliceosomal complex B.

Science.gov (United States)

Boehringer, Daniel; Makarov, Evgeny M; Sander, Bjoern; Makarova, Olga V; Kastner, Berthold; Lührmann, Reinhard; Stark, Holger

2004-05-01

Major structural changes occur in the spliceosome during its transition from the fully assembled complex B to the catalytically activated spliceosome. To understand the rearrangement, it is necessary to know the detailed three-dimensional structures of these complexes. Here, we have immunoaffinity-purified human spliceosomes (designated B Delta U1) at a stage after U4/U6.U5 tri-snRNP integration but before activation, and have determined the three-dimensional structure of B Delta U1 by single-particle electron cryomicroscopy at a resolution of approximately 40 A. The overall size of the complex is about 370 x 270 x 170 A. The three-dimensional structure features a roughly triangular body linked to a head domain in variable orientations. The body is very similar in size and shape to the isolated U4/U6.U5 tri-snRNP. This provides initial insight into the structural organization of complex B.

The Structure of the Human Centrin 2-Xeroderma Pigmentosum Group C Protein Complex

Energy Technology Data Exchange (ETDEWEB)

Thompson,J.; Ryan, Z.; Salisbury, J.; Kumar, R.

2006-01-01

Human centrin-2 plays a key role in centrosome function and stimulates nucleotide excision repair by binding to the xeroderma pigmentosum group C protein. To determine the structure of human centrin-2 and to develop an understanding of molecular interactions between centrin and xeroderma pigmentosum group C protein, we characterized the crystal structure of calcium-loaded full-length centrin-2 complexed with a xeroderma pigmentosum group C peptide. Our structure shows that the carboxyl-terminal domain of centrin-2 binds this peptide and two calcium atoms, whereas the amino-terminal lobe is in a closed conformation positioned distantly by an ordered {alpha}-helical linker. A stretch of the amino-terminal domain unique to centrins appears disordered. Two xeroderma pigmentosum group C peptides both bound to centrin-2 also interact to form an {alpha}-helical coiled-coil. The interface between centrin-2 and each peptide is predominantly nonpolar, and key hydrophobic residues of XPC have been identified that lead us to propose a novel binding motif for centrin.

The Structure of the Human Centrin 2-Xeroderma Pigmentosum Group C Protein Complex

International Nuclear Information System (INIS)

Thompson, J.; Ryan, Z.; Salisbury, J.; Kumar, R.

2006-01-01

Human centrin-2 plays a key role in centrosome function and stimulates nucleotide excision repair by binding to the xeroderma pigmentosum group C protein. To determine the structure of human centrin-2 and to develop an understanding of molecular interactions between centrin and xeroderma pigmentosum group C protein, we characterized the crystal structure of calcium-loaded full-length centrin-2 complexed with a xeroderma pigmentosum group C peptide. Our structure shows that the carboxyl-terminal domain of centrin-2 binds this peptide and two calcium atoms, whereas the amino-terminal lobe is in a closed conformation positioned distantly by an ordered α-helical linker. A stretch of the amino-terminal domain unique to centrins appears disordered. Two xeroderma pigmentosum group C peptides both bound to centrin-2 also interact to form an α-helical coiled-coil. The interface between centrin-2 and each peptide is predominantly nonpolar, and key hydrophobic residues of XPC have been identified that lead us to propose a novel binding motif for centrin

Vulnerability of coral reef fisheries to a loss of structural complexity.

Science.gov (United States)

Rogers, Alice; Blanchard, Julia L; Mumby, Peter J

2014-05-05

Coral reefs face a diverse array of threats, from eutrophication and overfishing to climate change. As live corals are lost and their skeletons eroded, the structural complexity of reefs declines. This may have important consequences for the survival and growth of reef fish because complex habitats mediate predator-prey interactions [1, 2] and influence competition [3-5] through the provision of prey refugia. A positive correlation exists between structural complexity and reef fish abundance and diversity in both temperate and tropical ecosystems [6-10]. However, it is not clear how the diversity of available refugia interacts with individual predator-prey relationships to explain emergent properties at the community scale. Furthermore, we do not yet have the ability to predict how habitat loss might affect the productivity of whole reef communities and the fisheries they support. Using data from an unfished reserve in The Bahamas, we find that structural complexity is associated not only with increased fish biomass and abundance, but also with nonlinearities in the size spectra of fish, implying disproportionately high abundances of certain size classes. By developing a size spectrum food web model that links the vulnerability of prey to predation with the structural complexity of a reef, we show that these nonlinearities can be explained by size-structured prey refugia that reduce mortality rates and alter growth rates in different parts of the size spectrum. Fitting the model with data from a structurally complex habitat, we predict that a loss of complexity could cause more than a 3-fold reduction in fishery productivity. Copyright © 2014 Elsevier Ltd. All rights reserved.

Complexity of Curved Glass Structures

Science.gov (United States)

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.

Medicines counterfeiting is a complex problem: a review of key challenges across the supply chain.

Science.gov (United States)

Tremblay, Michael

2013-02-01

The paper begins by asking why there is a market for counterfeit medicines, which in effect creates the problem of counterfeiting itself. Contributing factors include supply chain complexity and the lack of whole-systems thinking. These two underpin the author's view that counterfeiting is a complex (i.e. wicked) problem, and that corporate, public policy and regulatory actions need to be mindful of how their actions may be causal. The paper offers a problem-based review of key components of this complexity, viz., the knowledge end-users/consumers have of medicines; whether restrictive information policies may hamper information provision to patients; the internet's direct access to consumers; internet-enabled distribution of unsafe and counterfeit medicines; whether the internet is a parallel and competitive supply chain to legitimate routes; organised crime as an emerging medicines manufacturer and supplier and whether substandard medicines is really the bigger problem. Solutions respect the perceived complexity of the supply chain challenges. The paper identifies the need to avoid technologically-driven solutions, calling for 'technological agnosticism'. Both regulation and public policy need to reflect the dynamic nature of the problem and avoid creating perverse incentives; it may be, for instance, that medicines pricing and reimbursement policies, which affect consumer/patient access may act as market signals to counterfeiters, since this creates a cash market in cheaper drugs.

A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding.

Science.gov (United States)

Lin, Ying-Ting

2013-04-30

A tandem technique of hard equipment is often used for the chemical analysis of a single cell to first isolate and then detect the wanted identities. The first part is the separation of wanted chemicals from the bulk of a cell; the second part is the actual detection of the important identities. To identify the key structural modifications around ligand binding, the present study aims to develop a counterpart of tandem technique for cheminformatics. A statistical regression and its outliers act as a computational technique for separation. A PPARγ (peroxisome proliferator-activated receptor gamma) agonist cellular system was subjected to such an investigation. Results show that this tandem regression-outlier analysis, or the prioritization of the context equations tagged with features of the outliers, is an effective regression technique of cheminformatics to detect key structural modifications, as well as their tendency of impact to ligand binding. The key structural modifications around ligand binding are effectively extracted or characterized out of cellular reactions. This is because molecular binding is the paramount factor in such ligand cellular system and key structural modifications around ligand binding are expected to create outliers. Therefore, such outliers can be captured by this tandem regression-outlier analysis.

Effects of demographic structure on key properties of stochastic density-independent population dynamics.

Science.gov (United States)

Vindenes, Yngvild; Sæther, Bernt-Erik; Engen, Steinar

2012-12-01

The development of stochastic demography has largely been based on age structured populations, although other types of demographic structure, especially permanent and dynamic heterogeneity, are likely common in natural populations. The combination of stochasticity and demographic structure is a challenge for analyses of population dynamics and extinction risk, because the population structure will fluctuate around the stable structure and the population size shows transient fluctuations. However, by using a diffusion approximation for the total reproductive value, density-independent dynamics of structured populations can be described with only three population parameters: the expected population growth rate, the environmental variance and the demographic variance. These parameters depend on population structure via the state-specific vital rates and transition rates. Once they are found, the diffusion approximation represents a substantial reduction in model complexity. Here, we review and compare the key population parameters across a wide range of demographic structure, from the case of no structure to the most general case of dynamic heterogeneity, and for both discrete and continuous types. We focus on the demographic variance, but also show how environmental stochasticity can be included. This study brings together results from recent models, each considering a specific type of population structure, and places them in a general framework for structured populations. Comparison across different types of demographic structure reveals that the reproductive value is an essential concept for understanding how population structure affects stochastic dynamics and extinction risk. Copyright © 2011 Elsevier Inc. All rights reserved.

A new entropy based method for computing software structural complexity

CERN Document Server

Roca, J L

2002-01-01

In this paper a new methodology for the evaluation of software structural complexity is described. It is based on the entropy evaluation of the random uniform response function associated with the so called software characteristic function SCF. The behavior of the SCF with the different software structures and their relationship with the number of inherent errors is investigated. It is also investigated how the entropy concept can be used to evaluate the complexity of a software structure considering the SCF as a canonical representation of the graph associated with the control flow diagram. The functions, parameters and algorithms that allow to carry out this evaluation are also introduced. After this analytic phase follows the experimental phase, verifying the consistency of the proposed metric and their boundary conditions. The conclusion is that the degree of software structural complexity can be measured as the entropy of the random uniform response function of the SCF. That entropy is in direct relation...

Weak Links The Universal Key to the Stability of Networks and Complex Systems

CERN Document Server

Csermely, Peter

2009-01-01

How can our societies be stabilized in a crisis? Why can we enjoy and understand Shakespeare? Why are fruitflies uniform? How do omnivorous eating habits aid our survival? What makes the Mona Lisa’s smile beautiful? How do women keep our social structures intact? – Could there possibly be a single answer to all these questions? This book shows that the statement: "weak links stabilize complex systems" provides the key to understanding each of these intriguing puzzles, and many others too. The author (recipient of several distinguished science communication prizes) uses weak (low affinity, low probability) interactions as a thread to introduce a vast variety of networks from proteins to economics and ecosystems. Many people, from Nobel Laureates to high-school students have helped to make the book understandable to all interested readers. This unique book and the ideas it develops will have a significant impact on many, seemingly diverse, fields of study. A very personal, engaging, and unique book that wil...

Nitrosonium complexes of organic compounds. Structure and reactivity

International Nuclear Information System (INIS)

Borodkin, Gennady I; Shubin, Vyacheslav G

2001-01-01

Data on the structures and reactivities of nitrosonium complexes of organic compounds are systematised and generalised. The characteristic features of the electronic structure of the NO + cation are responsible for a wide structural variety of nitrosonium complexes. Reactions of nitrosonium complexes are described. The bibliography includes 172 references.

Deciphering the structure of isomeric oligosaccharides in a complex mixture by tandem mass spectrometry: Photon activation with vacuum ultra-violet brings unique information and enables definitive structure assignment

Energy Technology Data Exchange (ETDEWEB)

Ropartz, David, E-mail: David.Ropartz@nantes.inra.fr [INRA, UR1268 Biopolymers Interactions Assemblies, F-44316 Nantes (France); Lemoine, Jérôme [Institut des Sciences Analytiques, UMR 5280, Université Lyon 1-CNRS, Université de Lyon, F-69622 Villeurbanne cedex (France); Giuliani, Alexandre [Synchrotron SOLEIL, L’Orme des Merisiers, F-91190 Gif-sur-Yvette (France); UAR 1008 CEPIA, INRA, F-44316 Nantes (France); Bittebière, Yann [INRA, UR1268 Biopolymers Interactions Assemblies, F-44316 Nantes (France); Enjalbert, Quentin [Institut des Sciences Analytiques, UMR 5280, Université Lyon 1-CNRS, Université de Lyon, F-69622 Villeurbanne cedex (France); Institut Lumière Matière, UMR5306, Université Lyon 1-CNRS, Université de Lyon, F-69622 Villeurbanne cedex (France); Antoine, Rodolphe; Dugourd, Philippe [Institut Lumière Matière, UMR5306, Université Lyon 1-CNRS, Université de Lyon, F-69622 Villeurbanne cedex (France); Ralet, Marie-Christine; Rogniaux, Hélène [INRA, UR1268 Biopolymers Interactions Assemblies, F-44316 Nantes (France)

2014-01-07

Graphical abstract: -- Highlights: •A complex mixture of methylated oligogalacturonans was fractionated by IP-RP-UHPLC. •Synchrotron-radiation in VUV range was used as an activation process for tandem MS. •VUV activation brought rich structural information compared to LE-CAD. •Resolution of more than 35 structures, including isomers, was successfully completed. -- Abstract: Carbohydrates have a wide variety of structures whose complexity and heterogeneity challenge the field of analytical chemistry. Tandem mass spectrometry, with its remarkable sensitivity and high information content, provides key advantages to addressing the structural elucidation of polysaccharides. Yet, classical fragmentation by collision-activated dissociation (CAD) in many cases fails to reach a comprehensive structural determination, especially when isomers have to be differentiated. In this work, for the first time, vacuum ultra-violet (VUV) synchrotron radiation is used as the activation process in tandem mass spectrometry of large oligosaccharides. Compared to low energy CAD (LE-CAD), photon activated dissociation brought more straightforward and valuable structural information. The outstanding feature was that complete series of informative ions were produced, with only minor neutral losses. Moreover, systematic fragmentation rules could be drawn thus facilitating the definitive assignments of fragment identities. As a result, most of the structures present in a complex mixture of oligogalacturonans could be comprehensively resolved, including many isomers differing in the position of methyl groups along the galacturonic acid backbone.

Structural Basis of Semaphorin-Plexin Recognition and Viral Mimicry from Sema7A and A39R Complexes with PlexinC1

Energy Technology Data Exchange (ETDEWEB)

Liu, Heli; Juo, Z. Sean; Shim, Ann Hye-Ryong; Focia, Pamela J.; Chen, Xiaoyan; Garcia, K. Christopher; He, Xiaolin (Stanford-MED); (NWU)

2010-10-18

Repulsive signaling by Semaphorins and Plexins is crucial for the development and homeostasis of the nervous, immune, and cardiovascular systems. Sema7A acts as both an immune and a neural Semaphorin through PlexinC1, and A39R is a Sema7A mimic secreted by smallpox virus. We report the structures of Sema7A and A39R complexed with the Semaphorin-binding module of PlexinC1. Both structures show two PlexinC1 molecules symmetrically bridged by Semaphorin dimers, in which the Semaphorin and PlexinC1 {beta} propellers interact in an edge-on, orthogonal orientation. Both binding interfaces are dominated by the insertion of the Semaphorin's 4c-4d loop into a deep groove in blade 3 of the PlexinC1 propeller. A39R appears to achieve Sema7A mimicry by preserving key Plexin-binding determinants seen in the mammalian Sema7A complex that have evolved to achieve higher affinity binding to the host-derived PlexinC1. The complex structures support a conserved Semaphorin-Plexin recognition mode and suggest that Plexins are activated by dimerization.

Structural and Biochemical Characterization of BdsA from Bacillus subtilis WU-S2B, a Key Enzyme in the “4S” Desulfurization Pathway

Directory of Open Access Journals (Sweden)

Tiantian Su

2018-02-01

Full Text Available Dibenzothiophene (DBT and their derivatives, accounting for the major part of the sulfur components in crude oil, make one of the most significant pollution sources. The DBT sulfone monooxygenase BdsA, one of the key enzymes in the “4S” desulfurization pathway, catalyzes the oxidation of DBT sulfone to 2′-hydroxybiphenyl 2-sulfonic acid (HBPSi. Here, we determined the crystal structure of BdsA from Bacillus subtilis WU-S2B, at the resolution of 2.2 Å, and the structure of the BdsA-FMN complex at 2.4 Å. BdsA and the BdsA-FMN complex exist as tetramers. DBT sulfone was placed into the active site by molecular docking. Seven residues (Phe12, His20, Phe56, Phe246, Val248, His316, and Val372 are found to be involved in the binding of DBT sulfone. The importance of these residues is supported by the study of the catalytic activity of the active site variants. Structural analysis and enzyme activity assay confirmed the importance of the right position and orientation of FMN and DBT sulfone, as well as the involvement of Ser139 as a nucleophile in catalysis. This work combined with our previous structure of DszC provides a systematic structural basis for the development of engineered desulfurization enzymes with higher efficiency and stability.

Does competitive entry structurally change key marketing metrics?

NARCIS (Netherlands)

Kornelis, Marcel; Dekimpe, Marnik G.; Leeflang, Peter S. H.

To what extent does competitive entry create a structural change in key marketing metrics? New players mayjust be a temporal nuisance to incumbents, but could also fundamentally change the latter's performance evolution, or induce them to permanently alter their spending levels and/or pricing

Crystal structures of the CPAP/STIL complex reveal its role in centriole assembly and human microcephaly

Science.gov (United States)

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

Methodology for Simulation and Analysis of Complex Adaptive Supply Network Structure and Dynamics Using Information Theory

Directory of Open Access Journals (Sweden)

Joshua Rodewald

2016-10-01

Full Text Available Supply networks existing today in many industries can behave as complex adaptive systems making them more difficult to analyze and assess. Being able to fully understand both the complex static and dynamic structures of a complex adaptive supply network (CASN are key to being able to make more informed management decisions and prioritize resources and production throughout the network. Previous efforts to model and analyze CASN have been impeded by the complex, dynamic nature of the systems. However, drawing from other complex adaptive systems sciences, information theory provides a model-free methodology removing many of those barriers, especially concerning complex network structure and dynamics. With minimal information about the network nodes, transfer entropy can be used to reverse engineer the network structure while local transfer entropy can be used to analyze the network structure’s dynamics. Both simulated and real-world networks were analyzed using this methodology. Applying the methodology to CASNs allows the practitioner to capitalize on observations from the highly multidisciplinary field of information theory which provides insights into CASN’s self-organization, emergence, stability/instability, and distributed computation. This not only provides managers with a more thorough understanding of a system’s structure and dynamics for management purposes, but also opens up research opportunities into eventual strategies to monitor and manage emergence and adaption within the environment.

Structure of 1-deoxy-d-xylulose 5-phosphate reductoisomerase in a quaternary complex with a magnesium ion, NADPH and the antimalarial drug fosmidomycin

International Nuclear Information System (INIS)

Yajima, Shunsuke; Hara, Kodai; Iino, Daisuke; Sasaki, Yasuyuki; Kuzuyama, Tomohisa; Ohsawa, Kanju; Seto, Haruo

2007-01-01

The crystal structure of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) from Escherichia coli complexed with Mg 2+ , NADPH and fosmidomycin was determined at 2.2 Å resolution. The structure showed a well defined loop conformation at the active site of DXR. The crystal structure of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) from Escherichia coli complexed with Mg 2+ , NADPH and fosmidomycin was solved at 2.2 Å resolution. DXR is the key enzyme in the 2-C-methyl-d-erythritol 4-phosphate pathway and is an effective target of antimalarial drugs such as fosmidomycin. In the crystal structure, electron density for the flexible loop covering the active site was clearly observed, indicating the well ordered conformation of DXR upon substrate binding. On the other hand, no electron density was observed for the nicotinamide-ribose portion of NADPH and the position of Asp149 anchoring Mg 2+ was shifted by NADPH in the active site

Crystal structure of CotA laccase complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) at a novel binding site

International Nuclear Information System (INIS)

Liu, Zhongchuan; Xie, Tian; Zhong, Qiuping; Wang, Ganggang

2016-01-01

The crystal structure of CotA complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) in a hole motif has been solved; this novel binding site could be a potential structure-based target for protein engineering of CotA laccase. The CotA laccase from Bacillus subtilis is an abundant component of the spore outer coat and has been characterized as a typical laccase. The crystal structure of CotA complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) in a hole motif has been solved. The novel binding site was about 26 Å away from the T1 binding pocket. Comparison with known structures of other laccases revealed that the hole is a specific feature of CotA. The key residues Arg476 and Ser360 were directly bound to ABTS. Site-directed mutagenesis studies revealed that the residues Arg146, Arg429 and Arg476, which are located at the bottom of the novel binding site, are essential for the oxidation of ABTS and syringaldazine. Specially, a Thr480Phe variant was identified to be almost 3.5 times more specific for ABTS than for syringaldazine compared with the wild type. These results suggest this novel binding site for ABTS could be a potential target for protein engineering of CotA laccases

Crystal structure of CotA laccase complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) at a novel binding site

Energy Technology Data Exchange (ETDEWEB)

Liu, Zhongchuan; Xie, Tian [Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of (China); Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu 610041, People’s Republic of (China); Zhong, Qiuping [Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of (China); Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu 610041, People’s Republic of (China); University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of (China); Wang, Ganggang, E-mail: wanggg@cib.ac.cn [Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of (China); Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu 610041, People’s Republic of (China)

2016-03-24

The crystal structure of CotA complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) in a hole motif has been solved; this novel binding site could be a potential structure-based target for protein engineering of CotA laccase. The CotA laccase from Bacillus subtilis is an abundant component of the spore outer coat and has been characterized as a typical laccase. The crystal structure of CotA complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) in a hole motif has been solved. The novel binding site was about 26 Å away from the T1 binding pocket. Comparison with known structures of other laccases revealed that the hole is a specific feature of CotA. The key residues Arg476 and Ser360 were directly bound to ABTS. Site-directed mutagenesis studies revealed that the residues Arg146, Arg429 and Arg476, which are located at the bottom of the novel binding site, are essential for the oxidation of ABTS and syringaldazine. Specially, a Thr480Phe variant was identified to be almost 3.5 times more specific for ABTS than for syringaldazine compared with the wild type. These results suggest this novel binding site for ABTS could be a potential target for protein engineering of CotA laccases.

Complex band structure and electronic transmission eigenchannels

DEFF Research Database (Denmark)

Jensen, Anders; Strange, Mikkel; Smidstrup, Soren

2017-01-01

and complex band structure, in this case individual eigenchannel transmissions and different complex bands. We present calculations of decay constants for the two most conductive states as determined by complex band structure and standard DFT Landauer transport calculations for one semi-conductor and two...

Probing the chemistry, electronic structure and redox energetics in pentavalent organometallic actinide complexes

Energy Technology Data Exchange (ETDEWEB)

Graves, Christopher R [Los Alamos National Laboratory; Vaughn, Anthony E [Los Alamos National Laboratory; Morris, David E [Los Alamos National Laboratory; Kiplinger, Jaqueline L [Los Alamos National Laboratory

2008-01-01

Complexes of the early actinides (Th-Pu) have gained considerable prominence in organometallic chemistry as they have been shown to undergo chemistries not observed with their transition- or lanthanide metal counterparts. Further, while bonding in f-element complexes has historically been considered to be ionic, the issue of covalence remains a subject of debate in the area of actinide science, and studies aimed at elucidating key bonding interactions with 5f-orbitals continue to garner attention. Towards this end, our interests have focused on the role that metal oxidation state plays in the structure, reactivity and spectral properties of organouranium complexes. We report our progress in the synthesis of substituted U{sup V}-imido complexes using various routes: (1) Direct oxidation of U{sup IV}-imido complexes with copper(I) salts; (2) Salt metathesis with U{sup V}-imido halides; (3) Protonolysis and insertion of an U{sup V}-imido alkyl or aryl complex with H-N{double_bond}CPh{sub 2} or N{triple_bond}C-Ph, respectively, to form a U{sup V}-imido ketimide complex. Further, we report and compare the crystallographic, electrochemical, spectroscopic and magnetic characterization of the pentavalent uranium (C{sub 5}Me{sub 5}){sub 2}U({double_bond}N-Ar)(Y) series (Y = OTf, SPh, C{triple_bond}C-Ph, NPh{sub 2}, OPh, N{double_bond}CPh{sub 2}) to further interrogate the molecular, electronic, and magnetic structures of this new class of uranium complexes.

Limitations and Extensions of the Lock-and-Key Principle: Differences between Gas State, Solution and Solid State Structures

Directory of Open Access Journals (Sweden)

Hans-Jörg Schneider

2015-03-01

Full Text Available The lock-and-key concept is discussed with respect to necessary extensions. Formation of supramolecular complexes depends not only, and often not even primarily on an optimal geometric fit between host and guest. Induced fit and allosteric interactions have long been known as important modifications. Different binding mechanisms, the medium used and pH effects can exert a major influence on the affinity. Stereoelectronic effects due to lone pair orientation can lead to variation of binding constants by orders of magnitude. Hydrophobic interactions due to high-energy water inside cavities modify the mechanical lock-and-key picture. That optimal affinities are observed if the cavity is only partially filled by the ligand can be in conflict with the lock-and-key principle. In crystals other forces than those between host and guest often dominate, leading to differences between solid state and solution structures. This is exemplified in particular with calixarene complexes, which by X-ray analysis more often than other hosts show guest molecules outside their cavity. In view of this the particular problems with the identification of weak interactions in crystals is discussed.

Robustness and structure of complex networks

Science.gov (United States)

Shao, Shuai

This dissertation covers the two major parts of my PhD research on statistical physics and complex networks: i) modeling a new type of attack -- localized attack, and investigating robustness of complex networks under this type of attack; ii) discovering the clustering structure in complex networks and its influence on the robustness of coupled networks. Complex networks appear in every aspect of our daily life and are widely studied in Physics, Mathematics, Biology, and Computer Science. One important property of complex networks is their robustness under attacks, which depends crucially on the nature of attacks and the structure of the networks themselves. Previous studies have focused on two types of attack: random attack and targeted attack, which, however, are insufficient to describe many real-world damages. Here we propose a new type of attack -- localized attack, and study the robustness of complex networks under this type of attack, both analytically and via simulation. On the other hand, we also study the clustering structure in the network, and its influence on the robustness of a complex network system. In the first part, we propose a theoretical framework to study the robustness of complex networks under localized attack based on percolation theory and generating function method. We investigate the percolation properties, including the critical threshold of the phase transition pc and the size of the giant component Pinfinity. We compare localized attack with random attack and find that while random regular (RR) networks are more robust against localized attack, Erdoḧs-Renyi (ER) networks are equally robust under both types of attacks. As for scale-free (SF) networks, their robustness depends crucially on the degree exponent lambda. The simulation results show perfect agreement with theoretical predictions. We also test our model on two real-world networks: a peer-to-peer computer network and an airline network, and find that the real-world networks

Complex structures in the Nash-Moser category

DEFF Research Database (Denmark)

Gravesen, Jens

1989-01-01

Working in the Nash-Moser category, it is shown that the harmonic and holomorphic differentials and the Weierstrass points on a closed Riemann surface depend smoothly on the complex structure. It is also shown that the space of complex structures on any compact surface forms a principal bundle over...

Complex photonic structures

International Nuclear Information System (INIS)

Wiersma, D.S.

2013-01-01

We discuss in detail the optical properties of complex photonic structures, in particular those with a dominating disorder component. We will focus on their general transport properties, as well as on their use as light sources (random lasers). The basis for the theory of multiple light scattering in random systems will be explained as a tutorial introduction to the topic, including the explicit calculation of the effect of coherent backscattering. We will discuss various structures that go beyond regular disordered ones, in particular Levy glasses, liquid crystals, and quasicrystals, and show examples of their optical properties both from a conceptual and practical point of view.

Structural design principles of complex bird songs: a network-based approach.

Directory of Open Access Journals (Sweden)

Kazutoshi Sasahara

Full Text Available Bird songs are acoustic communication signals primarily used in male-male aggression and in male-female attraction. These are often monotonous patterns composed of a few phrases, yet some birds have extremely complex songs with a large phrase repertoire, organized in non-random fashion with discernible patterns. Since structure is typically associated with function, the structures of complex bird songs provide important clues to the evolution of animal communication systems. Here we propose an efficient network-based approach to explore structural design principles of complex bird songs, in which the song networks--transition relationships among different phrases and the related structural measures--are employed. We demonstrate how this approach works with an example using California Thrasher songs, which are sequences of highly varied phrases delivered in succession over several minutes. These songs display two distinct features: a large phrase repertoire with a 'small-world' architecture, in which subsets of phrases are highly grouped and linked with a short average path length; and a balanced transition diversity amongst phrases, in which deterministic and non-deterministic transition patterns are moderately mixed. We explore the robustness of this approach with variations in sample size and the amount of noise. Our approach enables a more quantitative study of global and local structural properties of complex bird songs than has been possible to date.

A new entropy based method for computing software structural complexity

International Nuclear Information System (INIS)

Roca, Jose L.

2002-01-01

In this paper a new methodology for the evaluation of software structural complexity is described. It is based on the entropy evaluation of the random uniform response function associated with the so called software characteristic function SCF. The behavior of the SCF with the different software structures and their relationship with the number of inherent errors is investigated. It is also investigated how the entropy concept can be used to evaluate the complexity of a software structure considering the SCF as a canonical representation of the graph associated with the control flow diagram. The functions, parameters and algorithms that allow to carry out this evaluation are also introduced. After this analytic phase follows the experimental phase, verifying the consistency of the proposed metric and their boundary conditions. The conclusion is that the degree of software structural complexity can be measured as the entropy of the random uniform response function of the SCF. That entropy is in direct relationship with the number of inherent software errors and it implies a basic hazard failure rate for it, so that a minimum structure assures a certain stability and maturity of the program. This metric can be used, either to evaluate the product or the process of software development, as development tool or for monitoring the stability and the quality of the final product. (author)

A Simple Key for Identifying the Sibling Species of the Malaria Vector Anopheles gambiae (Giles Complex by Polytene Chromosome Cytogenetics

Directory of Open Access Journals (Sweden)

Music Temitope OBEMBE

2018-03-01

Full Text Available It has been established that Anopheles gambiae complex sibling species are the major Plasmodium malaria vectors in Africa; however, not all the sibling species transmit the infection. Easier molecular methods, PCR-based assays, have been developed to distinguish the several members of the A. gambiae complex. However, malaria vector research in less developed countries, particularly sub-Saharan Africa, is being hampered by the lack of PCR facilities in laboratories and the cost of carrying out the assay within lack of funding. Hence, the present study was designed to develop a simple identification key, based on an affordable method of polytene chromosome cytotaxonomy, for identifying the major P. falciparum vectors. The Identification Key was successfully used to identify two members of the A. gambiae complex, A. gambiae sensu stricto and A. arabiensis, which are the most potent malaria vectors in Africa; even so, it could not be used to establish the infective and the refractory strains.

Probing the structure of complex solids using a distributed computing approach-Applications in zeolite science

International Nuclear Information System (INIS)

French, Samuel A.; Coates, Rosie; Lewis, Dewi W.; Catlow, C. Richard A.

2011-01-01

We demonstrate the viability of distributed computing techniques employing idle desktop computers in investigating complex structural problems in solids. Through the use of a combined Monte Carlo and energy minimisation method, we show how a large parameter space can be effectively scanned. By controlling the generation and running of different configurations through a database engine, we are able to not only analyse the data 'on the fly' but also direct the running of jobs and the algorithms for generating further structures. As an exemplar case, we probe the distribution of Al and extra-framework cations in the structure of the zeolite Mordenite. We compare our computed unit cells with experiment and find that whilst there is excellent correlation between computed and experimentally derived unit cell volumes, cation positioning and short-range Al ordering (i.e. near neighbour environment), there remains some discrepancy in the distribution of Al throughout the framework. We also show that stability-structure correlations only become apparent once a sufficiently large sample is used. - Graphical Abstract: Aluminium distributions in zeolites are determined using e-science methods. Highlights: → Use of e-science methods to search configurationally space. → Automated control of space searching. → Identify key structural features conveying stability. → Improved correlation of computed structures with experimental data.

Crystal Structures of the Pro-Inflammatory Cytokine Interleukin-23 and Its Complex with a High-Affinity Neutralizing Antibody

Energy Technology Data Exchange (ETDEWEB)

Beyer, Brian M.; Ingram, Richard; Ramanathan, Lata; Reichert, Paul; Le, Hung V.; Madison, Vincent; Orth, Peter (SPRI)

2009-06-25

Interleukin (IL)-23 is a pro-inflammatory cytokine playing a key role in the pathogenesis of several autoimmune and inflammatory diseases. We have determined the crystal structures of the heterodimeric p19-p40 IL-23 and its complex with the Fab (antigen-binding fragment) of a neutralizing antibody at 2.9 and 1.9 {angstrom}, respectively. The IL-23 structure closely resembles that of IL-12. They share the common p40 subunit, and IL-23 p19 overlaps well with IL-12 p35. Along the hydrophilic heterodimeric interface, fewer charged residues are involved for IL-23 compared with IL-12. The binding site of the Fab is located exclusively on the p19 subunit, and comparison with published cytokine-receptor structures suggests that it overlaps with the IL-23 receptor binding site.

Modern structure of marketing communications complex

Directory of Open Access Journals (Sweden)

Hrebenyukova Elena

2015-08-01

Full Text Available The article presents the results of the desk research, in which the current structure of the marketing communications complex was analyzed. According to the results of the content analysis of scientific and educational literature in marketing it was proved that there is a certain structural asymmetry in today's complex of marketing communication: the rejection of impersonal tools and actualization of those which make possible personalized communication with the consumer.

A Multiscale Model of Morphological Complexity in Cities

DEFF Research Database (Denmark)

Heinrich, Mary Katherine; Ayres, Phil; Bar-Yam, Yaneer

2017-01-01

Approaches from complex systems science can support design decision-making by extracting important information about key dependencies from large, unstructured data sources. This paper presents an initial case study applying such approaches to city structure, by characterising low-level features a...

Structure and reactivity of a mononuclear gold(II) complex

Science.gov (United States)

Preiß, Sebastian; Förster, Christoph; Otto, Sven; Bauer, Matthias; Müller, Patrick; Hinderberger, Dariush; Hashemi Haeri, Haleh; Carella, Luca; Heinze, Katja

2017-12-01

Mononuclear gold(II) complexes are very rare labile species. Transient gold(II) species have been suggested in homogeneous catalysis and in medical applications, but their geometric and electronic structures have remained essentially unexplored: even fundamental data, such as the ionic radius of gold(II), are unknown. Now, an unprecedentedly stable neutral gold(II) complex of a porphyrin derivative has been isolated, and its structural and spectroscopic features determined. The gold atom adopts a 2+2 coordination mode in between those of gold(III) (four-coordinate square planar) and gold(I) (two-coordinate linear), owing to a second-order Jahn-Teller distortion enabled by the relativistically lowered 6s orbital of gold. The reactivity of this gold(II) complex towards dioxygen, nitrosobenzene and acids is discussed. This study provides insight on the ionic radius of gold(II), and allows it to be placed within the homologous series of nd9 Cu/Ag/Au divalent ions and the 5d8/9/10 Pt/Au/Hg 'relativistic' triad in the periodic table.

Complex of Key Instruments of Management of Operation Activity of a Small Business Trade Enterprise

Directory of Open Access Journals (Sweden)

Serdyuk Vira M.

2013-11-01

Full Text Available The article offers a complex of key instruments of management of operation activity of a small business trade enterprise, including: 1 budgeting of operation activity; 2 its accounting by norms and deviations from them; 3 monitoring of operational activity of an enterprise, which envisages analysis of revealed deviations. The article shows the most efficient way of realisation and practical use of the presented concept – application of the “standard-cost” scheme within the framework of which the following tasks are solved: 1 budgeting of income from operational activity; 2 establishment of standards of costs; 3 accumulation of data on factual income and expenditures; 4 analysis of deviations and reporting; and 5 introduction of necessary amendments. The article also offers an imitation model of analysis of dynamics of trade processes, which allows detection of key spheres of management of operation activity of a small trade enterprise and principles of carrying out an efficient and well thought over financial policy.

Structure of Complex Verb Forms in Meiteilon

Directory of Open Access Journals (Sweden)

Lourembam Surjit Singh

2016-12-01

Full Text Available 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 can be co-occurred together in a phrase as single functional word. Specifically, in the co-occurrences of two lexical items, the first component of lexical items has different semantic and syntactic functions in comparison to semantic and syntactic functions of the second component of lexical items. Such co-occurrences of two lexical items are the forms of complex verb that are covered with the term complex predicate in this work. The investigation in constructing complex predicate is thoroughly presenting in this work. Keywords: Structures, complex verb, conjunct verb, compound verb, complex predicate

Solution structure of the luzopeptin-DNA complex

International Nuclear Information System (INIS)

Zhang, Xiaolu; Patel, D.J.

1991-01-01

The luzopeptin-d(C-A-T-G) complex (1 drug/duplex) has been generated in aqueous solution and its structure characterized by a combined application of two-dimensional NMR experiments and molecular dynamics calculations. Once equivalent of luzopeptin binds to the self-complementary tetranucleotide duplex with the 2-fold symmetry of the antitumor agent and the DNA oligomer retained on complex formation. The authors have assigned the exchangeable and nonexchangeable proton resonances of luzopeptin and the d(C-A-T-G) duplex in the complex and identified the intermolecular proton-proton NOEs that define the alignment of the antitumor agent at its binding site in duplex DNA. The analysis was greatly aided by a large number of intermolecular NOEs involving exchangeable protons on both the luzopeptin and the DNA in the complex. The formation of cis peptide bonds for luzopeptin in the complex results in an increased separation of the long sides of the rectangular cyclic depsipeptide backbone and reorients in the glycine amide proton so that it can form an intermolecular hydrogen bond with the 2-carbonyl of T3 in the complex. This observation explains, in part, the requirement for Watson-Crick A·T pairs to be sandwiched between the quinolines at the bisintercalation site in the luzopeptin-DNA complex. The NMR studies on the luzopeptin-d(C-A-T-G) complex unequivocally establish that antitumor agents can undergo conformational transitions on complex formation with DNA, and it is the conformation of the drug in the complex that should serve as the starting point for drug design studies. The above structural details on the solution structure of the luzopeptin-DNA complex also explain the sequence selectivity of luzopeptin for bisintercalation at d(C-A)·d(T-G) steps in the d(C-A-T-G) duplex in solution

Synthesis and structure of cerium nitrosocarbonylcyanmethanid complex

International Nuclear Information System (INIS)

Gerasimenko, H.; Scopenko, V.V.; Kapshuk, A.A.

1998-01-01

Full text: The complex compound [CeL 4 Dy 2 ]Na*2Ac (where L- nitrosocarbonylcyanmethanid, Dy -- dipyridile, Ac - acetone) were synthesised by interaction of cerium chloride and sodium nitrosocarbonylcyanmethanid from acetone solution. After two hours of mixing the dipyridil solution in acetone was added for complex stabilization. After filtration solution was put to desiccator for crystallisation. The complex was studied using IR- and UV-spectroscopy. The structure of the complex was determined using X-ray structure analysis. It was found that the structure of the complex belongs to orthorhombic Pna2(1) syngony with the unit cell parameters 17.010, 16.280 and 16.340Angstroms, respectively. It was found that cerium in the compound was eight co-ordinated. Four nitroso ligands were co-ordinated by bidentate bridge method and two dipyridiles by bidentate-cycle method

Structural studies of cinnamoyl-CoA reductase and cinnamyl-alcohol dehydrogenase, key enzymes of monolignol biosynthesis.

Science.gov (United States)

Pan, Haiyun; Zhou, Rui; Louie, Gordon V; Mühlemann, Joëlle K; Bomati, Erin K; Bowman, Marianne E; Dudareva, Natalia; Dixon, Richard A; Noel, Joseph P; Wang, Xiaoqiang

2014-09-01

The enzymes cinnamoyl-CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) catalyze the two key reduction reactions in the conversion of cinnamic acid derivatives into monolignol building blocks for lignin polymers in plant cell walls. Here, we describe detailed functional and structural analyses of CCRs from Medicago truncatula and Petunia hybrida and of an atypical CAD (CAD2) from M. truncatula. These enzymes are closely related members of the short-chain dehydrogenase/reductase (SDR) superfamily. Our structural studies support a reaction mechanism involving a canonical SDR catalytic triad in both CCR and CAD2 and an important role for an auxiliary cysteine unique to CCR. Site-directed mutants of CAD2 (Phe226Ala and Tyr136Phe) that enlarge the phenolic binding site result in a 4- to 10-fold increase in activity with sinapaldehyde, which in comparison to the smaller coumaraldehyde and coniferaldehyde substrates is disfavored by wild-type CAD2. This finding demonstrates the potential exploitation of rationally engineered forms of CCR and CAD2 for the targeted modification of monolignol composition in transgenic plants. Thermal denaturation measurements and structural comparisons of various liganded and unliganded forms of CCR and CAD2 highlight substantial conformational flexibility of these SDR enzymes, which plays an important role in the establishment of catalytically productive complexes of the enzymes with their NADPH and phenolic substrates. © 2014 American Society of Plant Biologists. All rights reserved.

Social complexity parallels vocal complexity: a comparison of three nonhuman primate species

Directory of Open Access Journals (Sweden)

Hélène eBOUCHET

2013-07-01

Full Text Available Social factors play a key role in the structuring of vocal repertoires at the individual level, notably in nonhuman primates. Some authors suggested that, at the species level too, social life may have driven the evolution of communicative complexity, but this has rarely been empirically tested. Here, we use a comparative approach to address this issue. We investigated vocal variability, at both the call type and the repertoire levels, in three forest-dwelling species of Cercopithecinae presenting striking differences in their social systems, in terms of social organization as well as social structure. We collected female call recordings from twelve De Brazza’s monkeys (Cercopithecus neglectus, six Campbell’s monkeys (Cercopithecus campbelli and seven red-capped mangabeys (Cercocebus torquatus housed in similar conditions. First, we noted that the level of acoustic variability and individual distinctiveness found in several call types was related to their importance in social functioning. Contact calls, essential to intra-group cohesion, were the most individually distinctive regardless of the species, while threat calls were more structurally variable in mangabeys, the most ‘despotic’ of our three species. Second, we found a parallel between the degree of complexity of the species’ social structure and the size, diversity, and usage of its vocal repertoire. Mangabeys (most complex social structure called twice as often as guenons and displayed the largest and most complex repertoire. De Brazza’s monkeys (simplest social structure displayed the smallest and simplest repertoire. Campbell’s monkeys displayed an intermediate pattern. Providing evidence of higher levels of vocal variability in species presenting a more complex social system, our results are in line with the theory of a social-vocal coevolution of communicative abilities, opening new perspectives for comparative research on the evolution of communication systems in

Alpha complexes in protein structure prediction

DEFF Research Database (Denmark)

Winter, Pawel; Fonseca, Rasmus

2015-01-01

Reducing the computational effort and increasing the accuracy of potential energy functions is of utmost importance in modeling biological systems, for instance in protein structure prediction, docking or design. Evaluating interactions between nonbonded atoms is the bottleneck of such computations......-complexes from scratch for every configuration encountered during the search for the native structure would make this approach hopelessly slow. However, it is argued that kinetic a-complexes can be used to reduce the computational effort of determining the potential energy when "moving" from one configuration...... to a neighboring one. As a consequence, relatively expensive (initial) construction of an a-complex is expected to be compensated by subsequent fast kinetic updates during the search process. Computational results presented in this paper are limited. However, they suggest that the applicability of a...

Proximity of the Triangular Fibrocartilage Complex to Key Surrounding Structures and Safety Assessment of an Arthroscopic Repair Technique: A Cadaveric Study.

Science.gov (United States)

Kuremsky, Marshall A; Habet, Nahir; Peindl, Richard D; Gaston, R Glenn

2016-12-01

To quantify the distance of the dorsal ulnar sensory branch, floor of the extensor carpi ulnaris (ECU) subsheath, and ulnar neurovascular bundles from the triangular fibrocartilage complex (TFCC), and secondarily to assess the safety of an all-inside arthroscopic repair of the TFCC with a commonly used meniscal repair device with respect to the aforementioned structures. A custom K-wire with 1-mm gradation was used to determine the distance of at-risk structures from the periphery of the TFCC in 13 above-elbow human cadaver specimens. An all-inside repair of the TFCC at the location of a Palmer 1B tear was then performed using a commonly employed meniscal repair device. The distance from the deployed devices to the structure in closest proximity was then measured using digital calipers. The mean distance from the deployed device to the nearest structure of concern for iatrogenic injury was 9.4 mm (range, 5-15 mm). The closest structure to iatrogenic injury was usually, but not always, the dorsal ulnar sensory nerve in 9 of 13 wrists (69.2%) at 9.3 mm (range, 5-15 mm); on 3 occasions it was instead the ulnar nerve (23.1%) at 9.5 mm (range, 9-10 mm), and on 1 occasion 6 mm from the flexor digitorum profundus to the little finger (7.7%). Forearm rotation had no significant effect on measured distances (ulnar nerve: P = .98; dorsal sensory: P = .89; ECU: P = .90). The largest influence of forearm rotation was a 0.4-mm difference between pronation and supination with respect to the distance of the TFCC periphery on the ECU subsheath. An all-inside arthroscopic TFCC repair using a commonly used meniscal repair device appears safe with respect to nearby neurovascular structures and tendons under typical arthroscopic conditions. An all-inside arthroscopic TFCC repair using a commonly employed meniscal repair device appears safe in terms of proximity to important structures although further clinical investigation is warranted. Copyright © 2016 Arthroscopy

Knowledge structures and the acquisition of a complex skill.

Science.gov (United States)

Day, E A; Arthur, W; Gettman, D

2001-10-01

The purpose of this study was to examine the viability of knowledge structures as an operationalization of learning in the context of a task that required a high degree of skill. Over the course of 3 days, 86 men participated in 9 training sessions and learned a complex video game. At the end of acquisition, participants' knowledge structures were assessed. After a 4-day nonpractice interval, trainees completed tests of skill retention and skill transfer. Findings indicated that the similarity of trainees' knowledge structures to an expert structure was correlated with skill acquisition and was predictive of skill retention and skill transfer. However, the magnitude of these effects was dependent on the method used to derive the expert referent structure. Moreover, knowledge structures mediated the relationship between general cognitive ability and skill-based performance.

Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

Directory of Open Access Journals (Sweden)

Maike Bublitz

2015-07-01

Full Text Available Membrane proteins are key players in biological systems, mediating signalling events and the specific transport of e.g. ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.

Structural studies of P-type ATPase–ligand complexes using an X-ray free-electron laser

Energy Technology Data Exchange (ETDEWEB)

Bublitz, Maike; Nass, Karol; Drachmann, Nikolaj D.; Markvardsen, Anders J.; Gutmann, Matthias J.; Barends, Thomas R. M.; Mattle, Daniel; Shoeman, Robert L.; Doak, R. Bruce; Boutet, Sébastien; Messerschmidt, Marc; Seibert, Marvin M.; Williams, Garth J.; Foucar, Lutz; Reinhard, Linda; Sitsel, Oleg; Gregersen, Jonas L.; Clausen, Johannes D.; Boesen, Thomas; Gotfryd, Kamil; Wang, Kai-Tuo; Olesen, Claus; Møller, Jesper V.; Nissen, Poul; Schlichting, Ilme

2015-06-11

Membrane proteins are key players in biological systems, mediating signalling events and the specific transport ofe.g.ions and metabolites. Consequently, membrane proteins are targeted by a large number of currently approved drugs. Understanding their functions and molecular mechanisms is greatly dependent on structural information, not least on complexes with functionally or medically important ligands. Structure determination, however, is hampered by the difficulty of obtaining well diffracting, macroscopic crystals. Here, the feasibility of X-ray free-electron-laser-based serial femtosecond crystallography (SFX) for the structure determination of membrane protein–ligand complexes using microcrystals of various native-source and recombinant P-type ATPase complexes is demonstrated. The data reveal the binding sites of a variety of ligands, including lipids and inhibitors such as the hallmark P-type ATPase inhibitor orthovanadate. By analyzing the resolution dependence of ligand densities and overall model qualities, SFX data quality metrics as well as suitable refinement procedures are discussed. Even at relatively low resolution and multiplicity, the identification of ligands can be demonstrated. This makes SFX a useful tool for ligand screening and thus for unravelling the molecular mechanisms of biologically active proteins.

Choosing the Best Enzyme Complex Structure Made Easy.

Science.gov (United States)

Das, Sayoni; Orengo, Christine

2018-04-03

In this issue of Structure, Tyzack et al. (2018) present a study of enzyme-ligand complexes in the PDB and show that the molecular similarity of bound and cognate ligands can be used to choose the most biologically appropriate complex structure for analysis when multiple structures are available. Copyright © 2018 Elsevier Ltd. All rights reserved.

Learning Latent Structure in Complex Networks

DEFF Research Database (Denmark)

Mørup, Morten; Hansen, Lars Kai

such as the Modularity, it has recently been shown that latent structure in complex networks is learnable by Bayesian generative link distribution models (Airoldi et al., 2008, Hofman and Wiggins, 2008). In this paper we propose a new generative model that allows representation of latent community structure......Latent structure in complex networks, e.g., in the form of community structure, can help understand network dynamics, identify heterogeneities in network properties, and predict ‘missing’ links. While most community detection algorithms are based on optimizing heuristic clustering objectives...... as in the previous Bayesian approaches and in addition allows learning of node specific link properties similar to that in the modularity objective. We employ a new relaxation method for efficient inference in these generative models that allows us to learn the behavior of very large networks. We compare the link...

Supramolecular structure of glibenclamide and β-cyclodextrins complexes.

Science.gov (United States)

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.

The complex band structure for armchair graphene nanoribbons

International Nuclear Information System (INIS)

Zhang Liu-Jun; Xia Tong-Sheng

2010-01-01

Using a tight binding transfer matrix method, we calculate the complex band structure of armchair graphene nanoribbons. The real part of the complex band structure calculated by the transfer matrix method fits well with the bulk band structure calculated by a Hermitian matrix. The complex band structure gives extra information on carrier's decay behaviour. The imaginary loop connects the conduction and valence band, and can profoundly affect the characteristics of nanoscale electronic device made with graphene nanoribbons. In this work, the complex band structure calculation includes not only the first nearest neighbour interaction, but also the effects of edge bond relaxation and the third nearest neighbour interaction. The band gap is classified into three classes. Due to the edge bond relaxation and the third nearest neighbour interaction term, it opens a band gap for N = 3M − 1. The band gap is almost unchanged for N = 3M + 1, but decreased for N = 3M. The maximum imaginary wave vector length provides additional information about the electrical characteristics of graphene nanoribbons, and is also classified into three classes

Surface Structures Formed by a Copper(II Complex of Alkyl-Derivatized Indigo

Directory of Open Access Journals (Sweden)

Akinori Honda

2016-10-01

Full Text Available Assembled structures of dyes have great influence on their coloring function. For example, metal ions added in the dyeing process are known to prevent fading of color. Thus, we have investigated the influence of an addition of copper(II ion on the surface structure of alkyl-derivatized indigo. Scanning tunneling microscope (STM analysis revealed that the copper(II complexes of indigo formed orderly lamellar structures on a HOPG substrate. These lamellar structures of the complexes are found to be more stable than those of alkyl-derivatized indigos alone. Furthermore, 2D chirality was observed.

Classification of smooth structures on a homotopy complex ...

Indian Academy of Sciences (India)

Abstract. We classify, up to diffeomorphism, all closed smooth manifolds homeo- morphic to the complex projective n-space CPn, where n = 3 and 4. Let M2n be a closed smooth 2n-manifold homotopy equivalent to CPn. We show that, up to diffeo- morphism, M6 has a unique differentiable structure and M8 has at most two ...

Classification of smooth structures on a homotopy complex ...

Indian Academy of Sciences (India)

We classify, up to diffeomorphism, all closed smooth manifolds homeomorphic to the complex projective n -space C P n , where n = 3 and 4. Let M 2 n be a closed smooth 2 n -manifold homotopy equivalent to C P n . We show that, up to diffeomorphism, M 6 has a unique differentiable structure and M 8 has at most two ...

Post-structuralism, Complexity and Poetics.

OpenAIRE

Dillon, Michael

2000-01-01

Post-structuralism and complexity are plural and diverse modes of thought that share a common subscription to the �anteriority of radical relationality�. They nonetheless subscribe to a different ethic of life because they address the anteriority of radical relationality in different ways. Complexity remains strategic in its bid to become a power-knowledge of the laws of becoming. It derives that strategic ethic from its scientific interest in the implicate order of non-linearity that is ...

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.

Science.gov (United States)

Robinson, Philip J; Trnka, Michael J; Bushnell, David A; Davis, Ralph E; Mattei, Pierre-Jean; Burlingame, Alma L; Kornberg, Roger D

2016-09-08

A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure reveals two components of functional significance, absent from previous structures, a protein kinase complex and the Mediator-activator interaction region. It thereby shows how the kinase and its target, the C-terminal domain of the polymerase, control Med-PIC interaction and transcription. Copyright © 2016 Elsevier Inc. All rights reserved.

Structural and Topology Optimization of Complex Civil Engineering Structures

DEFF Research Database (Denmark)

Hald, Frederik; Kirkegaard, Poul Henning; Andersen, Lars Vabbersgaard

2013-01-01

This paper shows the use of topology optimization for finding an optimized form for civil engineering structures. Today topology optimization and shape optimization have been integrated in several commercial finite element codes. Here, the topology of two complex civil engineering structures...

Insight into the structures and stabilities of Tc and Re DMSA complexes: A computational study

International Nuclear Information System (INIS)

Blanco González, Alejandro; Hernández Valdés, Daniel; García Fleitas, Ariel; Rodríguez Riera, Zalua; Jáuregui Haza, Ulises

2016-01-01

Meso-2,3-dimercaptosuccinic acid (DMSA) is used in nuclear medicine as ligand for preparation of radiopharmaceuticals for diagnostic and therapy. DMSA has been the subject of numerous investigations during the past three decades and new and significant information of the chemistry and pharmacology of DMSA complexes have emerged. In comparison to other ligands, the structure of some DMSA complexes is unclear up today. The structures and applications of DMSA complexes are strictly dependent on the chemical conditions of their preparation, especially pH and the ratio of components. A computational study of M-DMSA (M = Tc, Re) complexes has been performed using density functional theory. Different isomers for M(V) and M(III) complexes were study. The pH influence over ligand structures was taken into account and the solvent effect was evaluated using an implicit solvation model. The fully optimized complex syn-endo Re(V)-DMSA shows a geometry similar to the X-ray data and was used to validate the methodology. Moreover, new alternative structures for the renal agent 99mTc(III)-DMSA were proposed and computationally studied. For two complex structures, a larger stability respect to that proposed in the literature was obtained. Furthermore, Tc(V)-DMSA complexes are more stable than the Tc(III)-DMSA proposed structures. In general, Re complexes are more stables than the corresponding Tc ones. (author)

Social complexity parallels vocal complexity: a comparison of three non-human primate species.

Science.gov (United States)

Bouchet, Hélène; Blois-Heulin, Catherine; Lemasson, Alban

2013-01-01

Social factors play a key role in the structuring of vocal repertoires at the individual level, notably in non-human primates. Some authors suggested that, at the species level too, social life may have driven the evolution of communicative complexity, but this has rarely been empirically tested. Here, we use a comparative approach to address this issue. We investigated vocal variability, at both the call type and the repertoire levels, in three forest-dwelling species of Cercopithecinae presenting striking differences in their social systems, in terms of social organization as well as social structure. We collected female call recordings from twelve De Brazza's monkeys (Cercopithecus neglectus), six Campbell's monkeys (Cercopithecus campbelli) and seven red-capped mangabeys (Cercocebus torquatus) housed in similar conditions. First, we noted that the level of acoustic variability and individual distinctiveness found in several call types was related to their importance in social functioning. Contact calls, essential to intra-group cohesion, were the most individually distinctive regardless of the species, while threat calls were more structurally variable in mangabeys, the most "despotic" of our three species. Second, we found a parallel between the degree of complexity of the species' social structure and the size, diversity, and usage of its vocal repertoire. Mangabeys (most complex social structure) called twice as often as guenons and displayed the largest and most complex repertoire. De Brazza's monkeys (simplest social structure) displayed the smallest and simplest repertoire. Campbell's monkeys displayed an intermediate pattern. Providing evidence of higher levels of vocal variability in species presenting a more complex social system, our results are in line with the theory of a social-vocal coevolution of communicative abilities, opening new perspectives for comparative research on the evolution of communication systems in different animal taxa.

Group actions, non-Kähler complex manifolds and SKT structures

Directory of Open Access Journals (Sweden)

Poddar Mainak

2018-02-01

Full Text Available We give a construction of integrable complex structures on the total space of a smooth principal bundle over a complex manifold, with an even dimensional compact Lie group as structure group, under certain conditions. This generalizes the constructions of complex structure on compact Lie groups by Samelson and Wang, and on principal torus bundles by Calabi-Eckmann and others. It also yields large classes of new examples of non-Kähler compact complex manifolds. Moreover, under suitable restrictions on the base manifold, the structure group, and characteristic classes, the total space of the principal bundle admits SKT metrics. This generalizes recent results of Grantcharov et al. We study the Picard group and the algebraic dimension of the total space in some cases. We also use a slightly generalized version of the construction to obtain (non-Kähler complex structures on tangential frame bundles of complex orbifolds.

Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans.

Science.gov (United States)

Fraune, Johanna; Alsheimer, Manfred; Volff, Jean-Nicolas; Busch, Karoline; Fraune, Sebastian; Bosch, Thomas C G; Benavente, Ricardo

2012-10-09

The synaptonemal complex (SC) is a key structure of meiosis, mediating the stable pairing (synapsis) of homologous chromosomes during prophase I. Its remarkable tripartite structure is evolutionarily well conserved and can be found in almost all sexually reproducing organisms. However, comparison of the different SC protein components in the common meiosis model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus revealed no sequence homology. This discrepancy challenged the hypothesis that the SC arose only once in evolution. To pursue this matter we focused on the evolution of SYCP1 and SYCP3, the two major structural SC proteins of mammals. Remarkably, our comparative bioinformatic and expression studies revealed that SYCP1 and SYCP3 are also components of the SC in the basal metazoan Hydra. In contrast to previous assumptions, we therefore conclude that SYCP1 and SYCP3 form monophyletic groups of orthologous proteins across metazoans.

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

Energy Technology Data Exchange (ETDEWEB)

Mulepati, Sabin [Johns Hopkins Univ., Baltimore, MD (United States); Heroux, Annie; Bailey, Scott [Johns Hopkins Univ., Baltimore, MD (United States)

2014-09-19

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 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.

Compact complex surfaces with geometric structures related to split quaternions

International Nuclear Information System (INIS)

Davidov, Johann; Grantcharov, Gueo; Mushkarov, Oleg; Yotov, Miroslav

2012-01-01

We study the problem of existence of geometric structures on compact complex surfaces that are related to split quaternions. These structures, called para-hypercomplex, para-hyperhermitian and para-hyperkähler, are analogs of the hypercomplex, hyperhermitian and hyperkähler structures in the definite case. We show that a compact 4-manifold carries a para-hyperkähler structure iff it has a metric of split signature together with two parallel, null, orthogonal, pointwise linearly independent vector fields. Every compact complex surface admitting a para-hyperhermitian structure has vanishing first Chern class and we show that, unlike the definite case, many of these surfaces carry infinite-dimensional families of such structures. We provide also compact examples of complex surfaces with para-hyperhermitian structures which are not locally conformally para-hyperkähler. Finally, we discuss the problem of non-existence of para-hyperhermitian structures on Inoue surfaces of type S 0 and provide a list of compact complex surfaces which could carry para-hypercomplex structures.

Stochastic transport through complex comb structures

International Nuclear Information System (INIS)

Zaburdaev, V. Yu.; Popov, P. V.; Romanov, A. S.; Chukbar, K. V.

2008-01-01

A unified rigorous approach is used to derive fractional differential equations describing subdiffusive transport through comb structures of various geometrical complexity. A general nontrivial effect of the initial particle distribution on the subsequent evolution is exposed. Solutions having qualitative features of practical importance are given for joined structures with widely different fractional exponents

Using Florida Keys Reference Sites As a Standard for Restoration of Forest Structure in Everglades Tree Islands

International Nuclear Information System (INIS)

Ross, M.S.; Sah, J.P.; Ruiz, P.L.; Ross, M.S.; Ogurcak, D.E.

2010-01-01

In south Florida, tropical hardwood forests (hammocks) occur in Everglades tree islands and as more extensive forests in coastal settings in the nearby Florida Keys. Keys hammocks have been less disturbed by humans, and many qualify as old-growth, while Everglades hammocks have received much heavier use. With improvement of tree island condition an important element in Everglades restoration efforts, we examined stand structure in 23 Keys hammocks and 69 Everglades tree islands. Based on Stand Density Index and tree diameter distributions, many Everglades hammocks were characterized by low stocking and under-representation in the smaller size classes. In contrast, most Keys forests had the dense canopies and open under stories usually associated with old-growth hardwood hammocks. Subject to the same caveats that apply to off-site references elsewhere, structural information from mature Keys hammocks can be helpful in planning and implementing forest restoration in Everglades tree islands. In many of these islands, such restoration might involve supplementing tree stocking by planting native trees to produce more complete site utilization and a more open under story.

Isotope-edited proton NMR study on the structure of a pepsin/inhibitor complex

International Nuclear Information System (INIS)

Fesik, S.W.; Luly, J.R.; Erickson, J.W.; Abad-Zapatero, C.

1988-01-01

A general approach is illustrated for providing detailed structural information on large enzyme/inhibitor complexes using NMR spectroscopy. The method involves the use of isotopically labeled ligands to simplify two-dimensional NOE spectra of large molecular complexes by isotope-editing techniques. With this approach, the backbone and side-chain conformations (at the P 2 and P 3 sites) of a tightly bound inhibitor of porcine pepsin have bene determined. In addition, structural information on the active site of pepsin has been obtained. Due to the sequence homology between porcine pepsin and human renin, this structural information may prove useful for modeling renin/inhibitor complexes with the ultimate goal of designing more effective renin inhibitors. Moreover, this general approach can be applied to study other biological systems of interest such as other enzyme/inhibitor complexes, ligands bound to soluble receptors, and enzyme/substrate interactions

Conformational flexibility of BECN1: Essential to its key role in autophagy and beyond: BECN1 Structure and Mechanism

Energy Technology Data Exchange (ETDEWEB)

Mei, Yang [Department of Chemistry and Biochemistry, North Dakota State University, Fargo North Dakota 58108-6050; Glover, Karen [Department of Chemistry and Biochemistry, North Dakota State University, Fargo North Dakota 58108-6050; Su, Minfei [Department of Chemistry and Biochemistry, North Dakota State University, Fargo North Dakota 58108-6050; Sinha, Sangita C. [Department of Chemistry and Biochemistry, North Dakota State University, Fargo North Dakota 58108-6050

2016-08-13

BECN1 (Beclin 1), a highly conserved eukaryotic protein, is a key regulator of autophagy, a cellular homeostasis pathway, and also participates in vacuolar protein sorting, endocytic trafficking, and apoptosis. BECN1 is important for embryonic development, the innate immune response, tumor suppression, and protection against neurodegenerative disorders, diabetes, and heart disease. BECN1 mediates autophagy as a core component of the class III phosphatidylinositol 3-kinase complexes. However, the exact mechanism by which it regulates the activity of these complexes, or mediates its other diverse functions is unclear. BECN1 interacts with several diverse protein partners, perhaps serving as a scaffold or interaction hub for autophagy. Based on extensive structural, biophysical and bioinformatics analyses, BECN1 consists of an intrinsically disordered region (IDR), which includes a BH3 homology domain (BH3D); a flexible helical domain (FHD); a coiled-coil domain (CCD); and a β-α-repeated autophagy-specific domain (BARAD). Each of these BECN1 domains mediates multiple diverse interactions that involve concomitant conformational changes. Thus, BECN1 conformational flexibility likely plays a key role in facilitating diverse protein interactions. Further, BECN1 conformation and interactions are also modulated by numerous post-translational modifications. A better structure-based understanding of the interplay between different BECN1 conformational and binding states, and the impact of post-translational modifications will be essential to elucidating the mechanism of its multiple biological roles.

Reinforcing Visual Grouping Cues to Communicate Complex Informational Structure.

Science.gov (United States)

Bae, Juhee; Watson, Benjamin

2014-12-01

In his book Multimedia Learning [7], Richard Mayer asserts that viewers learn best from imagery that provides them with cues to help them organize new information into the correct knowledge structures. Designers have long been exploiting the Gestalt laws of visual grouping to deliver viewers those cues using visual hierarchy, often communicating structures much more complex than the simple organizations studied in psychological research. Unfortunately, designers are largely practical in their work, and have not paused to build a complex theory of structural communication. If we are to build a tool to help novices create effective and well structured visuals, we need a better understanding of how to create them. Our work takes a first step toward addressing this lack, studying how five of the many grouping cues (proximity, color similarity, common region, connectivity, and alignment) can be effectively combined to communicate structured text and imagery from real world examples. To measure the effectiveness of this structural communication, we applied a digital version of card sorting, a method widely used in anthropology and cognitive science to extract cognitive structures. We then used tree edit distance to measure the difference between perceived and communicated structures. Our most significant findings are: 1) with careful design, complex structure can be communicated clearly; 2) communicating complex structure is best done with multiple reinforcing grouping cues; 3) common region (use of containers such as boxes) is particularly effective at communicating structure; and 4) alignment is a weak structural communicator.

Structural Studies of Cinnamoyl-CoA Reductase and Cinnamyl-Alcohol Dehydrogenase, Key Enzymes of Monolignol Biosynthesis[C][W

Science.gov (United States)

Pan, Haiyun; Zhou, Rui; Louie, Gordon V.; Mühlemann, Joëlle K.; Bomati, Erin K.; Bowman, Marianne E.; Dudareva, Natalia; Dixon, Richard A.; Noel, Joseph P.; Wang, Xiaoqiang

2014-01-01

The enzymes cinnamoyl-CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) catalyze the two key reduction reactions in the conversion of cinnamic acid derivatives into monolignol building blocks for lignin polymers in plant cell walls. Here, we describe detailed functional and structural analyses of CCRs from Medicago truncatula and Petunia hybrida and of an atypical CAD (CAD2) from M. truncatula. These enzymes are closely related members of the short-chain dehydrogenase/reductase (SDR) superfamily. Our structural studies support a reaction mechanism involving a canonical SDR catalytic triad in both CCR and CAD2 and an important role for an auxiliary cysteine unique to CCR. Site-directed mutants of CAD2 (Phe226Ala and Tyr136Phe) that enlarge the phenolic binding site result in a 4- to 10-fold increase in activity with sinapaldehyde, which in comparison to the smaller coumaraldehyde and coniferaldehyde substrates is disfavored by wild-type CAD2. This finding demonstrates the potential exploitation of rationally engineered forms of CCR and CAD2 for the targeted modification of monolignol composition in transgenic plants. Thermal denaturation measurements and structural comparisons of various liganded and unliganded forms of CCR and CAD2 highlight substantial conformational flexibility of these SDR enzymes, which plays an important role in the establishment of catalytically productive complexes of the enzymes with their NADPH and phenolic substrates. PMID:25217505

Structural Analysis of Complex Networks

CERN Document Server

Dehmer, Matthias

2011-01-01

Filling a gap in literature, this self-contained book presents theoretical and application-oriented results that allow for a structural exploration of complex networks. The work focuses not only on classical graph-theoretic methods, but also demonstrates the usefulness of structural graph theory as a tool for solving interdisciplinary problems. Applications to biology, chemistry, linguistics, and data analysis are emphasized. The book is suitable for a broad, interdisciplinary readership of researchers, practitioners, and graduate students in discrete mathematics, statistics, computer science,

Synthesis, characterization and crystal structure of a ...

African Journals Online (AJOL)

The Mo atom in the complex is in octahedral coordination. Thermal stability of the complex has also been studied. KEY WORDS: Molybdenum complex, Hydrazone ligand, Crystal structure, X-ray diffraction, Thermal property. Bull. Chem. Soc. Ethiop. 2014, 28(3), 409-414. DOI: http://dx.doi.org/10.4314/bcse.v28i3.10 ...

A formalism for scattering of complex composite structures. I. Applications to branched structures of asymmetric sub-units

DEFF Research Database (Denmark)

Svaneborg, Carsten; Pedersen, Jan Skov

2012-01-01

to structural connectivity is completely decoupled from internal structure of the sub-units. This allows sub-units to be replaced by more complex structures. We illustrate the physical interpretation of the formalism diagrammatically. By applying a self-consistency requirement, we derive the pair distributions...

Structure of a preternary complex involving a prokaryotic NHEJ DNA polymerase.

Science.gov (United States)

Brissett, Nigel C; Martin, Maria J; Pitcher, Robert S; Bianchi, Julie; Juarez, Raquel; Green, Andrew J; Fox, Gavin C; Blanco, Luis; Doherty, Aidan J

2011-01-21

In many prokaryotes, a specific DNA primase/polymerase (PolDom) is required for nonhomologous end joining (NHEJ) repair of DNA double-strand breaks (DSBs). Here, we report the crystal structure of a catalytically active conformation of Mycobacterium tuberculosis PolDom, consisting of a polymerase bound to a DNA end with a 3' overhang, two metal ions, and an incoming nucleotide but, significantly, lacking a primer strand. This structure represents a polymerase:DNA complex in a preternary intermediate state. This polymerase complex occurs in solution, stabilizing the enzyme on DNA ends and promoting nucleotide extension of short incoming termini. We also demonstrate that the invariant Arg(220), contained in a conserved loop (loop 2), plays an essential role in catalysis by regulating binding of a second metal ion in the active site. We propose that this NHEJ intermediate facilitates extension reactions involving critically short or noncomplementary DNA ends, thus promoting break repair and minimizing sequence loss during DSB repair. Copyright © 2011 Elsevier Inc. All rights reserved.

Structures of NodZ α1,6-fucosyltransferase in complex with GDP and GDP-fucose

Energy Technology Data Exchange (ETDEWEB)

Brzezinski, Krzysztof [Argonne National Laboratory, Argonne, IL 60439 (United States); Polish Academy of Sciences, 61-704 Poznan (Poland); Dauter, Zbigniew [Argonne National Laboratory, Argonne, IL 60439 (United States); Jaskolski, Mariusz, E-mail: mariuszj@amu.edu.pl [Polish Academy of Sciences, 61-704 Poznan (Poland); A. Mickiewicz University, 60-780 Poznan (Poland); Argonne National Laboratory, Argonne, IL 60439 (United States)

2012-02-01

Crystal structures of the bacterial α1,6-fucosyltransferase NodZ in complex with GDP and GDP-fucose are presented. Rhizobial NodZ α1,6-fucosyltransferase (α1,6-FucT) catalyzes the transfer of the fucose (Fuc) moiety from guanosine 5′-diphosphate-β-l-fucose to the reducing end of the chitin oligosaccharide core during Nod-factor (NF) biosynthesis. NF is a key signalling molecule required for successful symbiosis with a legume host for atmospheric nitrogen fixation. To date, only two α1,6-FucT structures have been determined, both without any donor or acceptor molecule that could highlight the structural background of the catalytic mechanism. Here, the first crystal structures of α1,6-FucT in complex with its substrate GDP-Fuc and with GDP, which is a byproduct of the enzymatic reaction, are presented. The crystal of the complex with GDP-Fuc was obtained through soaking of native NodZ crystals with the ligand and its structure has been determined at 2.35 Å resolution. The fucose residue is exposed to solvent and is disordered. The enzyme–product complex crystal was obtained by cocrystallization with GDP and an acceptor molecule, penta-N-acetyl-l-glucosamine (penta-NAG). The structure has been determined at 1.98 Å resolution, showing that only the GDP molecule is present in the complex. In both structures the ligands are located in a cleft formed between the two domains of NodZ and extend towards the C-terminal domain, but their conformations differ significantly. The structures revealed that residues in three regions of the C-terminal domain, which are conserved among α1,2-, α1,6- and protein O-fucosyltransferases, are involved in interactions with the sugar-donor molecule. There is also an interaction with the side chain of Tyr45 in the N-terminal domain, which is very unusual for a GT-B-type glycosyltransferase. Only minor conformational changes of the protein backbone are observed upon ligand binding. The only exception is a movement of the loop

A structural model of the E. coli PhoB Dimer in the transcription initiation complex

Directory of Open Access Journals (Sweden)

Tung Chang-Shung

2012-03-01

Full Text Available Abstract Background There exist > 78,000 proteins and/or nucleic acids structures that were determined experimentally. Only a small portion of these structures corresponds to those of protein complexes. While homology modeling is able to exploit knowledge-based potentials of side-chain rotomers and backbone motifs to infer structures for new proteins, no such general method exists to extend our understanding of protein interaction motifs to novel protein complexes. Results We use a Motif Binding Geometries (MBG approach, to infer the structure of a protein complex from the database of complexes of homologous proteins taken from other contexts (such as the helix-turn-helix motif binding double stranded DNA, and demonstrate its utility on one of the more important regulatory complexes in biology, that of the RNA polymerase initiating transcription under conditions of phosphate starvation. The modeled PhoB/RNAP/σ-factor/DNA complex is stereo-chemically reasonable, has sufficient interfacial Solvent Excluded Surface Areas (SESAs to provide adequate binding strength, is physically meaningful for transcription regulation, and is consistent with a variety of known experimental constraints. Conclusions Based on a straightforward and easy to comprehend concept, "proteins and protein domains that fold similarly could interact similarly", a structural model of the PhoB dimer in the transcription initiation complex has been developed. This approach could be extended to enable structural modeling and prediction of other bio-molecular complexes. Just as models of individual proteins provide insight into molecular recognition, catalytic mechanism, and substrate specificity, models of protein complexes will provide understanding into the combinatorial rules of cellular regulation and signaling.

Modelling the structure of complex networks

DEFF Research Database (Denmark)

Herlau, Tue

networks has been independently studied as mathematical objects in their own right. As such, there has been both an increased demand for statistical methods for complex networks as well as a quickly growing mathematical literature on the subject. In this dissertation we explore aspects of modelling complex....... The next chapters will treat some of the various symmetries, representer theorems and probabilistic structures often deployed in the modelling complex networks, the construction of sampling methods and various network models. The introductory chapters will serve to provide context for the included written...

Modeling the Structure and Complexity of Engineering Routine Design Problems

NARCIS (Netherlands)

Jauregui Becker, Juan Manuel; Wits, Wessel Willems; van Houten, Frederikus J.A.M.

2011-01-01

This paper proposes a model to structure routine design problems as well as a model of its design complexity. The idea is that having a proper model of the structure of such problems enables understanding its complexity, and likewise, a proper understanding of its complexity enables the development

Structural design of SBWR reactor building complex using microcomputers

International Nuclear Information System (INIS)

Mandagi, K.; Rajagopal, R.S.; Sawhney, P.S.; Gou, P.F.

1993-01-01

The design concept of Simplified Boiling Water Reactor (SBWR) plant is based on simplicity and passive features to enhance safety and reliability, improve performance, and increase economic viability. The SBWR utilizes passive systems such as Gravity Driven Core-Cooling System (GDCS) and Passive Containment Cooling System (PCCS). To suit these design features the Reactor Building (RB) complex of the SBWR is configured as an integrated structure consisting of a cylindrical Reinforced Concrete Containment Vessel (RCCV) surrounded by square reinforced concrete safety envelope and outer box structures, all sharing a common reinforced concrete basemat. This paper describes the structural analysis and design aspects of the RB complex. A 3D STARDYNE finite element model has been developed for the structural analysis of the complex using a PC Compaq 486/33L microcomputer. The structural analysis is performed for service and factored load conditions for the applicable loading combinations. The dynamic responses of containment structures due to pool hydrodynamic loads have been calculated by an axisymmetric shell model using COSMOS/M program. The RCCV is designed in accordance with ASME Section 3, Division 2 Code. The rest of the RB which is classified as Seismic Category 1 structure is designed in accordance with the ACI 349 Code. This paper shows that microcomputers can be efficiently used for the analysis and design of large and complex structures such as RCCV and Reactor Building complex. The use of microcomputers can result in significant savings in the computational cost compared with that of mainframe computers

Phase behavior and structure of stable complexes between a long polyanion and a branched polycation

Science.gov (United States)

Mengarelli, Valentina; Zeghal, Mehdi; Auvray, Loïc; Clemens, Daniel

2011-08-01

The association between oppositely charged branched polyethylenimine (BPEI) and polymethacrylic acid (PMA) in the dilute regime is investigated using turbidimetric titration and electrophoretic mobility measurements. The complexation is controlled by tuning continuously the pH-sensitive charge of the polyacid in acidic solution. The formation of soluble and stable positively charged complexes is a cooperative process characterized by the existence of two regimes of weak and strong complexation. In the regime of weak complexation, a long PMA chain overcharged by several BPEI molecules forms a binary complex. As the charge of the polyacid increases, these binary complexes condense at a well defined charge ratio of the mixture to form large positively charged aggregates. The overcharging and the existence of two regimes of complexation are analyzed in the light of recent theories. The structure of the polyelectrolytes is investigated at higher polymer concentration by small angle neutron scattering. Binary complexes of finite size present an open structure where the polyacid chains connecting a small number of BPEI molecules have shrunk slightly. In the condensed complexes, BPEI molecules, wrapped by polyacid chains, form networks of stretched necklaces.

Crystal structure of the Msx-1 homeodomain/DNA complex.

Science.gov (United States)

Hovde, S; Abate-Shen, C; Geiger, J H

2001-10-09

The Msx-1 homeodomain protein plays a crucial role in craniofacial, limb, and nervous system development. Homeodomain DNA-binding domains are comprised of 60 amino acids that show a high degree of evolutionary conservation. We have determined the structure of the Msx-1 homeodomain complexed to DNA at 2.2 A resolution. The structure has an unusually well-ordered N-terminal arm with a unique trajectory across the minor groove of the DNA. DNA specificity conferred by bases flanking the core TAAT sequence is explained by well ordered water-mediated interactions at Q50. Most interactions seen at the TAAT sequence are typical of the interactions seen in other homeodomain structures. Comparison of the Msx-1-HD structure to all other high resolution HD-DNA complex structures indicate a remarkably well-conserved sphere of hydration between the DNA and protein in these complexes.

Synthesis, Crystal Structure of a Novel Mn Complex with Nicotinoyl-Glycine

Directory of Open Access Journals (Sweden)

Xin Wang

2016-12-01

Full Text Available A novel manganese complex, C16H26MnN4O12, was synthesized by the reaction of nicotinoyl-glycine and NaOH in an ethanol/water solution and structurally characterized by elemental analysis, UV-vis spectrum, IR spectrum and single-crystal X-ray diffraction analysis. The crystal of the complex belongs to the triclinic space group P1 with a = 7.8192(16 Å, b = 8.8800(18 Å, c = 9.0142(18 Å, α = 83.14(3°, β = 65.27(3°, γ = 81.67(3°, V = 516.3(2 Å3, Z = 1, Dx = 1.542 mg·m−3, μ = 0.66 mm−1, F(000 = 271, and final R1 = 0.0381, ωR2 = 0.0964. The nicotinoyl-glycine ligand acts as a bridging ligand to connect the manganese ions by the hydrogen interactions; thus, the complex expands into a 3D supramolecular net structure.

Three-dimensional structure of the γ-secretase complex

International Nuclear Information System (INIS)

Ogura, Toshihiko; Mio, Kazuhiro; Hayashi, Ikuo; Miyashita, Hiroyuki; Fukuda, Rie; Kopan, Raphael; Kodama, Tatsuhiko; Hamakubo, Takao; Iwastubo, Takeshi; Tomita, Taisuke; Sato, Chikara

2006-01-01

γ-Secretase belongs to an atypical class of aspartic proteases that hydrolyzes peptide bonds within the transmembrane domain of substrates, including amyloid-β precursor protein and Notch. γ-Secretase is comprised of presenilin, nicastrin, APH-1, and PEN-2 which form a large multimeric membrane protein complex, the three-dimensional structure of which is unknown. To gain insight into the structure of this complex enzyme, we purified functional γ-secretase complex reconstituted in Sf9 cells and analyzed it using negative stain electron microscopy and 3D reconstruction techniques. Analysis of 2341 negatively stained particle images resulted in the three-dimensional representation of γ-secretase at a resolution of 48 A. The structure occupies a volume of 560 x 320 x 240 A and resembles a flat heart comprised of two oppositely faced, dimpled domains. A low density space containing multiple pores resides between the domains. Some of the dimples in the putative transmembrane region may house the catalytic site. The large dimensions are consistent with the observation that γ-secretase activity resides within a high molecular weight complex

Atomic Resolution Imaging of Nanoscale Structural Ordering in a Complex Metal Oxide Catalyst

KAUST Repository

Zhu, Yihan; Wang, Qingxiao; Zhao, Lan; Teng, Baiyang; Lu, Weimin; Han, Yu

2012-01-01

The determination of the atomic structure of a functional material is crucial to understanding its "structure-to-property" relationship (e.g., the active sites in a catalyst), which is however challenging if the structure possesses complex

Discrete symmetries and the complex structure of Calabi-Yau manifolds

International Nuclear Information System (INIS)

Ross, G.G.

1988-01-01

We show how the discrete symmetries, which may be present after Calabi-Yau compactification for specific choices of the complex structure, extend to the h 2,1 moduli - the scalar fields whose vacuum expectation values determine the complex structure. This allows us to determine much about the coupling of the moduli and hence the energetically favoured complex structure. The discrete symmetry transformation properties of the moduli are worked out in detail for a three-generation Calabi-Yau model and it is shown how minimization of the effective potential involving these fields selects the complex structure which leaves unbroken a set of discrete symmetries. The phenomenological implications of the symmetries are briefly discussed. (orig.)

When complex is easy on the mind: internal repetition of visual information in complex objects is a source of perceptual fluency

NARCIS (Netherlands)

Linda Steg; Roos Pals; Ayça Berfu Ünal; Yannick Joye

2015-01-01

Across 3 studies, we investigated whether visual complexity deriving from internally repeating visual information over many scale levels is a source of perceptual fluency. Such continuous repetition of visual information is formalized in fractal geometry and is a key-property of natural structures.

Jealousy Graphs: Structure and Complexity of Decentralized Stable Matching

Science.gov (United States)

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

Structures of Mycobacterium Tuberculosis Folylpolyglutamate Synthase Complexed With ADP And AMPPCD

Energy Technology Data Exchange (ETDEWEB)

Young, P.G.; Smith, C.A.; Metcalf, P.; Baker, E.N.

2009-05-28

Folate derivatives are essential vitamins for cell growth and replication, primarily because of their central role in reactions of one-carbon metabolism. Folates require polyglutamation to be efficiently retained within the cell and folate-dependent enzymes have a higher affinity for the polyglutamylated forms of this cofactor. Polyglutamylation is dependent on the enzyme folylpolyglutamate synthetase (FPGS), which catalyzes the sequential addition of several glutamates to folate. FPGS is essential for the growth and survival of important bacterial species, including Mycobacterium tuberculosis, and is a potential drug target. Here, the crystal structures of M. tuberculosis FPGS in complex with ADP and AMPPCP are reported at 2.0 and 2.3 angstroms resolution, respectively. The structures reveal a deeply buried nucleotide-binding site, as in the Escherichia coli and Lactobacillus casei FPGS structures, and a long extended groove for the binding of folate substrates. Differences from the E. coli and L. casei FPGS structures are seen in the binding of a key divalent cation, the carbamylation state of an essential lysine side chain and the adoption of an 'open' position by the active-site beta5-alpha6 loop. These changes point to coordinated events that are associated with dihydropteroate/folate binding and the catalysis of the new amide bond with an incoming glutamate residue.

Large, dynamic, multi-protein complexes: a challenge for structural biology

Czech Academy of Sciences Publication Activity Database

Rozycki, B.; Bouřa, Evžen

2014-01-01

Roč. 26, č. 46 (2014), 463103/1-463103/11 ISSN 0953-8984 R&D Projects: GA MŠk LO1302 EU Projects: European Commission(XE) 333916 - STARPI4K Institutional support: RVO:61388963 Keywords : protein structure * multi-protein complexes * hybrid methods of structural biology Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.346, year: 2014

Evaluation of aseismic integrity in the HTTR core-bottom structure. V. On the static and dynamic behavior of graphite HTTR key-keyway structures

International Nuclear Information System (INIS)

Futakawa, M.; Iyoku, T.

1996-01-01

For pt.IV see ibid., vol.154, p.83-95, 1995. The graphite components in high temperature gas-cooled reactors are connected to each other through a key-keyway structure that has gaps between the key and the keyway to accommodate thermal expansion. Because a dynamic load concentrates on the key-keyway structure during earthquakes, it is considered to be a crucial element for assessing the integrity of the graphite components. A combination of experiments and analyses was employed to investigate the dynamic behavior of the key-keyway structure, i.e. the equivalent stiffness associated with vibrational characteristics of the graphite components and the stress distribution under dynamic loading. The experiments were performed using a graphite scale model and a dynamic photo-elastic method. The analysis was carried out using the finite element method (FEM) code ABAQUS, taking account of the contact behavior between the key and the keyway. The following conclusions were derived. (1) The equivalent stiffness of the key-keyway structure shows nonlinearity, owing to the contact deformation. (2) The equivalent stiffness evaluated by the FEM analysis, taking account of the non-linear contact deformation, is applicable for predicting the vibrational characteristics of the key-keyway structure. (3) The stress concentration under dynamic loading is lower than or nearly equal to that under static loading. The maximum stress concentration of the seismic load can be sufficiently evaluated under static loading conditions. (orig.)

The RecQ helicase-topoisomerase III-Rmi1 complex: a DNA structure-specific 'dissolvasome'?

DEFF Research Database (Denmark)

Mankouri, Hocine W; Hickson, Ian D

2007-01-01

structures, and we propose here that it functions in a coordinated fashion as a DNA structure-specific 'dissolvasome'. Little is known about how the RTR complex might be regulated or targeted to various DNA structures in vivo. Recent findings indicate that the components of the RTR complex might activate...... the cell cycle checkpoint machinery as well as be a target of checkpoint kinases, suggesting that these events are crucial to ensure faithful DNA replication and chromosome segregation....

Crystallization and preliminary X-ray structural studies of a Melan-A pMHC–TCR complex

International Nuclear Information System (INIS)

Yuan, Fang; Georgiou, Theonie; Hillon, Theresa; Gostick, Emma; Price, David A.; Sewell, Andrew K.; Moysey, Ruth; Gavarret, Jessie; Vuidepot, Annelise; Sami, Malkit; Bell, John I.; Gao, George F.; Rizkallah, Pierre J.; Jakobsen, Bent K.

2007-01-01

A preliminary X-ray crystal structural study of a soluble cognate T-cell receptor (TCR) in complex with a pMHC presenting the Melan-A peptide (ELAGIGILTV) is reported. The TCR and pMHC were refolded, purified and mixed together to form complexes, which were crystallized using the sitting-drop vapour-diffusion method. Single TCR–pMHC complex crystals were cryocooled and used for data collection. Melanocytes are specialized pigmented cells that are found in all healthy skin tissue. In certain individuals, diseased melanocytes can form malignant tumours, melanomas, which cause the majority of skin-cancer-related deaths. The melanoma-associated antigenic peptides are presented on cell surfaces via the class I major histocompatibility complex (MHC). Among the melanoma-associated antigens, the melanoma self-antigen A/melanoma antigen recognized by T cells (Melan-A/MART-1) has attracted attention because of its wide expression in primary and metastatic melanomas. Here, a preliminary X-ray crystal structural study of a soluble cognate T-cell receptor (TCR) in complex with a pMHC presenting the Melan-A peptide (ELAGIGILTV) is reported. The TCR and pMHC were refolded, purified and mixed together to form complexes, which were crystallized using the sitting-drop vapour-diffusion method. Single TCR–pMHC complex crystals were cryocooled and used for data collection. Diffraction data showed that these crystals belonged to space group P4 1 /P4 3 , with unit-cell parameters a = b = 120.4, c = 81.6 Å. A complete data set was collected to 3.1 Å and the structure is currently being analysed

Identification of a key structural element for protein folding within beta-hairpin turns.

Science.gov (United States)

Kim, Jaewon; Brych, Stephen R; Lee, Jihun; Logan, Timothy M; Blaber, Michael

2003-05-09

Specific residues in a polypeptide may be key contributors to the stability and foldability of the unique native structure. Identification and prediction of such residues is, therefore, an important area of investigation in solving the protein folding problem. Atypical main-chain conformations can help identify strains within a folded protein, and by inference, positions where unique amino acids may have a naturally high frequency of occurrence due to favorable contributions to stability and folding. Non-Gly residues located near the left-handed alpha-helical region (L-alpha) of the Ramachandran plot are a potential indicator of structural strain. Although many investigators have studied mutations at such positions, no consistent energetic or kinetic contributions to stability or folding have been elucidated. Here we report a study of the effects of Gly, Ala and Asn substitutions found within the L-alpha region at a characteristic position in defined beta-hairpin turns within human acidic fibroblast growth factor, and demonstrate consistent effects upon stability and folding kinetics. The thermodynamic and kinetic data are compared to available data for similar mutations in other proteins, with excellent agreement. The results have identified that Gly at the i+3 position within a subset of beta-hairpin turns is a key contributor towards increasing the rate of folding to the native state of the polypeptide while leaving the rate of unfolding largely unchanged.

Structural dynamics of the MecA-ClpC complex: a type II AAA+ protein unfolding machine.

Science.gov (United States)

Liu, Jing; Mei, Ziqing; Li, Ningning; Qi, Yutao; Xu, Yanji; Shi, Yigong; Wang, Feng; Lei, Jianlin; Gao, Ning

2013-06-14

The MecA-ClpC complex is a bacterial type II AAA(+) molecular machine responsible for regulated unfolding of substrates, such as transcription factors ComK and ComS, and targeting them to ClpP for degradation. The six subunits of the MecA-ClpC complex form a closed barrel-like structure, featured with three stacked rings and a hollow passage, where substrates are threaded and translocated through successive pores. Although the general concepts of how polypeptides are unfolded and translocated by internal pore loops of AAA(+) proteins have long been conceived, the detailed mechanistic model remains elusive. With cryoelectron microscopy, we captured four different structures of the MecA-ClpC complexes. These complexes differ in the nucleotide binding states of the two AAA(+) rings and therefore might presumably reflect distinctive, representative snapshots from a dynamic unfolding cycle of this hexameric complex. Structural analysis reveals that nucleotide binding and hydrolysis modulate the hexameric complex in a number of ways, including the opening of the N-terminal ring, the axial and radial positions of pore loops, the compactness of the C-terminal ring, as well as the relative rotation between the two nucleotide-binding domain rings. More importantly, our structural and biochemical data indicate there is an active allosteric communication between the two AAA(+) rings and suggest that concerted actions of the two AAA(+) rings are required for the efficiency of the substrate unfolding and translocation. These findings provide important mechanistic insights into the dynamic cycle of the MecA-ClpC unfoldase and especially lay a foundation toward the complete understanding of the structural dynamics of the general type II AAA(+) hexamers.

Structure of rhenium (5) complexes with petroleum organic sulfur compounds

International Nuclear Information System (INIS)

Akhmadieva, R.G.; Yusupova, N.A.; Numanov, N.U.; Basitova, S.M.

1985-01-01

Structure of Re(5) complexes with petroleum sulfides (L) of ReOCl 3 (L) 2 composition is studied by the UV- and IR-spectroscopy method in a short-wave and long-wave ranges. It is shown that Re(5) complex with L are of the form of flattened octahedron,where three Cl atoms and one L molecule are arranged in the plane around Re atom. The structure is analogous to structure of Re complexes with synthetic cyclic sulfides

Structural Behavior of a Long-Span Partially Earth-Anchored Cable-Stayed Bridge during Installation of a Key Segment by Thermal Prestressing

Directory of Open Access Journals (Sweden)

Sang-Hyo Kim

2016-08-01

Full Text Available This study investigated structural behavior of long-span partially earth-anchored cable-stayed bridges with a main span length of 810 m that use a new key segment closing method based on a thermal prestressing technique. A detailed construction sequence analysis matched with the free cantilever method (FCM was performed using a three-dimensional finite element (FE model of a partially earth-anchored cable-stayed bridge. The new method offers an effective way of connecting key segments by avoiding large movements resulting from the removal of the longitudinal restraint owing to the asymmetry of axial forces in the girders near the pylons. The new method develops new member forces through the process of heating the cantilever system before installing the key segment and cooling the system continuously after installing key segments. The resulting forces developed by the thermal process enhance the structural behavior of partially earth-anchored cable-stayed bridges owing to decreased axial forces in the girders.

Prescribed burning consumes key forest structural components: implications for landscape heterogeneity.

Science.gov (United States)

Holland, Greg J; Clarke, Michael F; Bennett, Andrew F

2017-04-01

Prescribed burning to achieve management objectives is a common practice in fire-prone regions worldwide. Structural components of habitat that are combustible and slow to develop are particularly susceptible to change associated with prescribed burning. We used an experimental, "whole-landscape" approach to investigate the effect of differing patterns of prescribed burning on key habitat components (logs, stumps, dead trees, litter cover, litter depth, and understorey vegetation). Twenty-two landscapes (each ~100 ha) were selected in a dry forest ecosystem in southeast Australia. Experimental burns were conducted in 16 landscapes (stratified by burn extent) while six served as untreated controls. We measured habitat components prior to and after burning. Landscape burn extent ranged from 22% to 89% across the 16 burn treatments. With the exception of dead standing trees (no change), all measures of habitat components declined as a consequence of burning. The degree of loss increased as the extent to which a landscape was burned also increased. Prescribed burning had complex effects on the spatial heterogeneity (beta diversity) of structural components within landscapes. Landscapes that were more heterogeneous pre-fire were homogenized by burning, while those that were more homogenous pre-fire tended to display greater differentiation post-burning. Thus, the notion that patch mosaic burning enhances heterogeneity at the landscape-scale depends on prior conditions. These findings have important management implications. Where prescribed burns must be undertaken, effects on important resources can be moderated via control of burn characteristics (e.g., burn extent). Longer-term impacts of prescribed burning will be strongly influenced by the return interval, given the slow rate at which some structural components accumulate (decades to centuries). Management of habitat structural components is important given the critical role they play in (1) provision of habitat

Characterization of measurement errors using structure-from-motion and photogrammetry to measure marine habitat structural complexity.

Science.gov (United States)

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.

Anisotropic behavior and complex colinear magnetic structures of cerium and actinide intermetallics

International Nuclear Information System (INIS)

Cooper, B.R.

1977-01-01

A review is given of the experimental situation and degree of theoretical understanding for the occurrence of complex colinear magnetic structures in cerium and actinide intermetallics of NaCl structure. In doing this, emphasis is on the qualitative nature of the anisotropic effects necessary to understand the behavior. With this in mind we focus on the I to IA magnetic structure transition, and indeed more simply, on the occurrence of the IA magnetic structure which appears for CeBi, UAs, and some of the mixed uranium monopnictide-monochalcogenides. We show how the experimental observations involving properties related to the IA magnetic structure indicate important qualitative features of the physical mechanism involved. Through discussion of the possible analogue to the situation in UO 2 , the idea is introduced that magnetoelastic effects involving internal rearrangement modes may play a key role in the occurrence of the IA structure. Internal rearrangement modes are modes where one ionic species remains at its site in the undistorted crystal structure, and the other species is displaced from its position in the undistorted structure. We show that in a very natural way one can anticipate the possible occurrence of an internal rearrangement mode having a four-layer, periodic displacement sequence for planes for one species in the NaCl structure crystals, while the other species remains undisplaced. The presence of such a static lattice mode is susceptible to direct experimental observation. (author)

Using embedded design structures to unravel a complex decision in a product development system

DEFF Research Database (Denmark)

McKay, Alison; Sammonds, George; Ahmed-Kristensen, Saeema

2017-01-01

because of ambiguity in available design definitions. This paper reports research that investigated the role of complex decision making in a quality incident that occurred in the development of a complex product system. A case study approach with document analysis and semi-structured interviews was used....... Data were analysed using lenses from both social sciences and engineering design. In this paper, we report the use of embedded design structures to gain insights into the downstream consequences of design decisions. Results indicate that embedded product, process and supply network structures have......Early design decisions have an impact on downstream product development processes. Poor decisions can reduce efficiency and effectiveness, and have a detrimental effect on product quality, delivery time, and cost. However, the range of tools suitable for use in early design is limited, in part...

Atomic Resolution Imaging of Nanoscale Structural Ordering in a Complex Metal Oxide Catalyst

KAUST Repository

Zhu, Yihan

2012-08-28

The determination of the atomic structure of a functional material is crucial to understanding its "structure-to-property" relationship (e.g., the active sites in a catalyst), which is however challenging if the structure possesses complex inhomogeneities. Here, we report an atomic structure study of an important MoVTeO complex metal oxide catalyst that is potentially useful for the industrially relevant propane-based BP/SOHIO process. We combined aberration-corrected scanning transmission electron microscopy with synchrotron powder X-ray crystallography to explore the structure at both nanoscopic and macroscopic scales. At the nanoscopic scale, this material exhibits structural and compositional order within nanosized "domains", while the domains show disordered distribution at the macroscopic scale. We proposed that the intradomain compositional ordering and the interdomain electric dipolar interaction synergistically induce the displacement of Te atoms in the Mo-V-O channels, which determines the geometry of the multifunctional metal oxo-active sites.

Uranium complexes with macrosyclic polyethers. Synthesis and structural chemical analysis

International Nuclear Information System (INIS)

Elbasyouny, A.

1983-01-01

This dissertation reports about studies on the chemical coordination behaviour of uranium of oxidation stages IV and VI with regard to twelve different macrocyclic ligands. For the preparation of the complexes, for every system a different method has been developed. The elementary analysis of the various complexes including the uranium had been done by X-ray fluorescence analysis, and the structural characterization proceeded via vibrational, uv-vis and emission spectroscopy as well as 1 H-NMR and 13 C-spin-lattice relaxation time studies. Conformational analysis of the polyethers used allowed the structural changes in the complexes to be observed. The structural analysis of the hydrous uranium VI crown ether complexes yielded information of characteristic features of these types of complexes. The first coordination sphere of the uranyl ion with covalently bonded anion remains unchanged. As to the water content, there is a certain range. Depending upon the solvent used, the complexes have two or four H 2 O molecules per formula unit. (orig./EF) [de

Complex leadership as a way forward for transformational missional leadership in a denominational structure

Directory of Open Access Journals (Sweden)

C.J.P. (Nelus Niemandt

2015-08-01

Full Text Available The research investigates the role of leadership in the transformation of denominational structures towards a missional ecclesiology, and focusses on the Highveld Synod of the Dutch Reformed Church. It describes the missional journey of the denomination, and interprets the transformation. The theory of ‘complex leadership’ in complex systems is applied to the investigation of the impact of leadership on a denominational structure. The theory identifies three mechanisms used by leaders as enablers in emergent, self-organisation systems: (1 Leaders disrupt existing patterns, (2 they encourage novelty, and (3 they act as sensemakers. These insights are applied as a tool to interpret the missional transformation of a denomination.

Structural insights into transcription complexes

NARCIS (Netherlands)

Berger, I.; Blanco, A.G.; Boelens, R.; Cavarelli, J.; Coll, M.; Folkers, G.E.; Nie, Y.; Pogenberg, V.; Schultz, P.; Wilmanns, M.; Moras, D.; Poterszman, A.

2011-01-01

Control of transcription allows the regulation of cell activity in response to external stimuli and research in the field has greatly benefited from efforts in structural biology. In this review, based on specific examples from the European SPINE2-COMPLEXES initiative, we illustrate the impact of

Information visualization for the Structural Complexity Management Approach

OpenAIRE

Maurer, Maik;Braun, Thomas;Lindemann, Udo

2017-01-01

The handling of complexity poses an important challenge and a success factor for product design. A considerable percentage of complexity results from dependencies between system elements – as adaptations to single system elements can cause far-reaching consequences. The Structural Complexity Management (SCM) approach provides a five-step procedure that supports users in the identification, acquisition, analysis and optimization of system dependencies. The approach covers the handling of multi...

Determining Complex Structures using Docking Method with Single Particle Scattering Data

Directory of Open Access Journals (Sweden)

Haiguang Liu

2017-04-01

Full Text Available Protein complexes are critical for many molecular functions. Due to intrinsic flexibility and dynamics of complexes, their structures are more difficult to determine using conventional experimental methods, in contrast to individual subunits. One of the major challenges is the crystallization of protein complexes. Using X-ray free electron lasers (XFELs, it is possible to collect scattering signals from non-crystalline protein complexes, but data interpretation is more difficult because of unknown orientations. Here, we propose a hybrid approach to determine protein complex structures by combining XFEL single particle scattering data with computational docking methods. Using simulations data, we demonstrate that a small set of single particle scattering data collected at random orientations can be used to distinguish the native complex structure from the decoys generated using docking algorithms. The results also indicate that a small set of single particle scattering data is superior to spherically averaged intensity profile in distinguishing complex structures. Given the fact that XFEL experimental data are difficult to acquire and at low abundance, this hybrid approach should find wide applications in data interpretations.

A density-based clustering model for community detection in complex networks

Science.gov (United States)

Zhao, Xiang; Li, Yantao; Qu, Zehui

2018-04-01

Network clustering (or graph partitioning) is an important technique for uncovering the underlying community structures in complex networks, which has been widely applied in various fields including astronomy, bioinformatics, sociology, and bibliometric. In this paper, we propose a density-based clustering model for community detection in complex networks (DCCN). The key idea is to find group centers with a higher density than their neighbors and a relatively large integrated-distance from nodes with higher density. The experimental results indicate that our approach is efficient and effective for community detection of complex networks.

Structures of NodZ α1,6-fucosyltransferase in complex with GDP and GDP-fucose.

Science.gov (United States)

Brzezinski, Krzysztof; Dauter, Zbigniew; Jaskolski, Mariusz

2012-02-01

Rhizobial NodZ α1,6-fucosyltransferase (α1,6-FucT) catalyzes the transfer of the fucose (Fuc) moiety from guanosine 5'-diphosphate-β-L-fucose to the reducing end of the chitin oligosaccharide core during Nod-factor (NF) biosynthesis. NF is a key signalling molecule required for successful symbiosis with a legume host for atmospheric nitrogen fixation. To date, only two α1,6-FucT structures have been determined, both without any donor or acceptor molecule that could highlight the structural background of the catalytic mechanism. Here, the first crystal structures of α1,6-FucT in complex with its substrate GDP-Fuc and with GDP, which is a byproduct of the enzymatic reaction, are presented. The crystal of the complex with GDP-Fuc was obtained through soaking of native NodZ crystals with the ligand and its structure has been determined at 2.35 Å resolution. The fucose residue is exposed to solvent and is disordered. The enzyme-product complex crystal was obtained by cocrystallization with GDP and an acceptor molecule, penta-N-acetyl-L-glucosamine (penta-NAG). The structure has been determined at 1.98 Å resolution, showing that only the GDP molecule is present in the complex. In both structures the ligands are located in a cleft formed between the two domains of NodZ and extend towards the C-terminal domain, but their conformations differ significantly. The structures revealed that residues in three regions of the C-terminal domain, which are conserved among α1,2-, α1,6- and protein O-fucosyltransferases, are involved in interactions with the sugar-donor molecule. There is also an interaction with the side chain of Tyr45 in the N-terminal domain, which is very unusual for a GT-B-type glycosyltransferase. Only minor conformational changes of the protein backbone are observed upon ligand binding. The only exception is a movement of the loop located between strand βC2 and helix αC3. In addition, there is a shift of the αC3 helix itself upon GDP

Mesoscopic Self-Assembly: A Shift to Complexity

Directory of Open Access Journals (Sweden)

Massimo eMastrangeli

2015-06-01

Full Text Available By focusing on the construction of thermodynamically stable structures, the self-assembly of mesoscopic systems has proven capable of formidable achievements in the bottom-up engineering of micro- and nanosystems. Yet, inspired by an analogous evolution in supramolecular chemistry, synthetic mesoscopic self-assembly may have a lot more ahead, within reach of a shift toward fully three-dimensional architectures, collective interactions of building blocks and kinetic control. All over these challenging fronts, complexity holds the key.

Structure of octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens in a complex with phosphate

Energy Technology Data Exchange (ETDEWEB)

Trofimov, A. A.; Polyakov, K. M., E-mail: kostya@eimb.relarn.ru [Russian Academy of Sciences, Engelhardt Institute of Molecular Biology (Russian Federation); Boiko, K. M.; Filimonenkov, A. A. [Russian Academy of Sciences, Bach Institute of Biochemistry (Russian Federation); Dorovatovskii, P. V. [Kurchatov Center for Synchrotron Radiation and Nanotechnology (Russian Federation); Tikhonova, T. V.; Popov, V. O. [Russian Academy of Sciences, Bach Institute of Biochemistry (Russian Federation); Koval' chuk, M. V. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

2010-01-15

Octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens (TvNiR) catalyzes the reduction of nitrite and hydroxylamine to ammonia. The structures of the free enzyme and of the enzyme in complexes with the substrate (nitrite ion) and the inhibitor (azide ion) have been solved previously. In this study we report the structures of the oxidized complex of TvNiR with phosphate and of this complex reduced by europium(II) chloride (1.8- and 2.0-A resolution, the R factors are 15.9 and 16.7%, respectively) and the structure of the enzyme in the complex with cyanide (1.76-A resolution, the R factor is 16.5%), which was prepared by soaking a crystal of the oxidized phosphate complex of TvNiR. In the active site of the enzyme, the phosphate ion binds to the iron ion of the catalytic heme and to the side chains of the catalytic residues Arg131, Tyr303, and His361. The cyanide ion is coordinated to the heme-iron ion and is hydrogen bonded to the residue His361. In the structure of reduced TvNiR, the phosphate ion is bound in the same manner as in the structure of oxidized TvNiR, and the nine{sub c}oordinated europium ion is located on the surface of one of the crystallographically independent monomers of the enzyme.

Structure of octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens in a complex with phosphate

International Nuclear Information System (INIS)

Trofimov, A. A.; Polyakov, K. M.; Boiko, K. M.; Filimonenkov, A. A.; Dorovatovskii, P. V.; Tikhonova, T. V.; Popov, V. O.; Koval'chuk, M. V.

2010-01-01

Octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens (TvNiR) catalyzes the reduction of nitrite and hydroxylamine to ammonia. The structures of the free enzyme and of the enzyme in complexes with the substrate (nitrite ion) and the inhibitor (azide ion) have been solved previously. In this study we report the structures of the oxidized complex of TvNiR with phosphate and of this complex reduced by europium(II) chloride (1.8- and 2.0-A resolution, the R factors are 15.9 and 16.7%, respectively) and the structure of the enzyme in the complex with cyanide (1.76-A resolution, the R factor is 16.5%), which was prepared by soaking a crystal of the oxidized phosphate complex of TvNiR. In the active site of the enzyme, the phosphate ion binds to the iron ion of the catalytic heme and to the side chains of the catalytic residues Arg131, Tyr303, and His361. The cyanide ion is coordinated to the heme-iron ion and is hydrogen bonded to the residue His361. In the structure of reduced TvNiR, the phosphate ion is bound in the same manner as in the structure of oxidized TvNiR, and the nine c oordinated europium ion is located on the surface of one of the crystallographically independent monomers of the enzyme.

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

Science.gov (United States)

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.

Metallacyclopentadienes: structural features and coordination in transition metal complexes

International Nuclear Information System (INIS)

Dolgushin, Fedor M; Yanovsky, Aleksandr I; Antipin, Mikhail Yu

2004-01-01

Results of structural studies of polynuclear transition metal complexes containing the metallacyclopentadiene fragment are overviewed. The structural features of the complexes in relation to the nature of the substituents in the organic moiety of the metallacycles, the nature of the transition metals and their ligand environment are analysed. The main structural characteristics corresponding to different modes of coordination of metallacyclopentadienes to one or two additional metal centres are revealed.

Identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor–ligand complex

Energy Technology Data Exchange (ETDEWEB)

Andersen, Jacob Lauwring, E-mail: jla@mb.au.dk [Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C (Denmark); Schrøder, Tenna Juul; Christensen, Søren [H. Lundbeck A/S, Ottiliavej 9, 2500 Valby (Denmark); Strandbygård, Dorthe [Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C (Denmark); Pallesen, Lone Tjener [Aarhus University, Ole Worms Allé 3, 8000 Aarhus C (Denmark); García-Alai, Maria Marta [Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C (Denmark); Lindberg, Samsa; Langgård, Morten; Eskildsen, Jørgen Calí; David, Laurent; Tagmose, Lena; Simonsen, Klaus Baek; Maltas, Philip James; Rønn, Lars Christian Biilmann; Jong, Inge E. M. de; Malik, Ibrahim John; Egebjerg, Jan; Karlsson, Jens-Jacob [H. Lundbeck A/S, Ottiliavej 9, 2500 Valby (Denmark); Uppalanchi, Srinivas; Sakumudi, Durga Rao; Eradi, Pradheep [GVK BioScience, Plot No. 28 A, IDA Nacharam, Hyderabad 500 076 (India); Watson, Steven P., E-mail: jla@mb.au.dk [H. Lundbeck A/S, Ottiliavej 9, 2500 Valby (Denmark); Thirup, Søren, E-mail: jla@mb.au.dk [Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C (Denmark)

2014-02-01

The identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor–ligand complex are reported. Sortilin is a type I membrane glycoprotein belonging to the vacuolar protein sorting 10 protein (Vps10p) family of sorting receptors and is most abundantly expressed in the central nervous system. Sortilin has emerged as a key player in the regulation of neuronal viability and has been implicated as a possible therapeutic target in a range of disorders. Here, the identification of AF40431, the first reported small-molecule ligand of sortilin, is reported. Crystals of the sortilin–AF40431 complex were obtained by co-crystallization and the structure of the complex was solved to 2.7 Å resolution. AF40431 is bound in the neurotensin-binding site of sortilin, with the leucine moiety of AF40431 mimicking the binding mode of the C-terminal leucine of neurotensin and the 4-methylumbelliferone moiety of AF40431 forming π-stacking with a phenylalanine.

Identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor–ligand complex

International Nuclear Information System (INIS)

Andersen, Jacob Lauwring; Schrøder, Tenna Juul; Christensen, Søren; Strandbygård, Dorthe; Pallesen, Lone Tjener; García-Alai, Maria Marta; Lindberg, Samsa; Langgård, Morten; Eskildsen, Jørgen Calí; David, Laurent; Tagmose, Lena; Simonsen, Klaus Baek; Maltas, Philip James; Rønn, Lars Christian Biilmann; Jong, Inge E. M. de; Malik, Ibrahim John; Egebjerg, Jan; Karlsson, Jens-Jacob; Uppalanchi, Srinivas; Sakumudi, Durga Rao; Eradi, Pradheep; Watson, Steven P.; Thirup, Søren

2014-01-01

The identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor–ligand complex are reported. Sortilin is a type I membrane glycoprotein belonging to the vacuolar protein sorting 10 protein (Vps10p) family of sorting receptors and is most abundantly expressed in the central nervous system. Sortilin has emerged as a key player in the regulation of neuronal viability and has been implicated as a possible therapeutic target in a range of disorders. Here, the identification of AF40431, the first reported small-molecule ligand of sortilin, is reported. Crystals of the sortilin–AF40431 complex were obtained by co-crystallization and the structure of the complex was solved to 2.7 Å resolution. AF40431 is bound in the neurotensin-binding site of sortilin, with the leucine moiety of AF40431 mimicking the binding mode of the C-terminal leucine of neurotensin and the 4-methylumbelliferone moiety of AF40431 forming π-stacking with a phenylalanine

Structural insights into the interaction of the conserved mammalian proteins GAPR-1 and Beclin 1, a key autophagy protein

Energy Technology Data Exchange (ETDEWEB)

Li, Yue; Zhao, Yuting; Su, Minfei; Glover, Karen; Chakravarthy, Srinivas; Colbert, Christopher L.; Levine, Beth; Sinha, Sangita C.

2017-08-29

Mammalian Golgi-associated plant pathogenesis-related protein 1 (GAPR-1) is a negative autophagy regulator that binds Beclin 1, a key component of the autophagosome nucleation complex. Beclin 1 residues 267–284 are required for binding GAPR-1. Here, sequence analyses, structural modeling, mutagenesis combined with pull-down assays, X-ray crystal structure determination and small-angle X-ray scattering were used to investigate the Beclin 1–GAPR-1 interaction. Five conserved residues line an equatorial GAPR-1 surface groove that is large enough to bind a peptide. A model of a peptide comprising Beclin 1 residues 267–284 docked onto GAPR-1, built using theCABS-dockserver, indicates that this peptide binds to this GAPR-1 groove. Mutation of the five conserved residues lining this groove, H54A/E86A/G102K/H103A/N138G, abrogates Beclin 1 binding. The 1.27 Å resolution X-ray crystal structure of this pentad mutant GAPR-1 was determined. Comparison with the wild-type (WT) GAPR-1 structure shows that the equatorial groove of the pentad mutant is shallower and more positively charged, and therefore may not efficiently bind Beclin 1 residues 267–284, which include many hydrophobic residues. Both WT and pentad mutant GAPR-1 crystallize as dimers, and in each case the equatorial groove of one subunit is partially occluded by the other subunit, indicating that dimeric GAPR-1 is unlikely to bind Beclin 1. SAXS analysis of WT and pentad mutant GAPR-1 indicates that in solution the WT forms monomers, while the pentad mutant is primarily dimeric. Thus, changes in the structure of the equatorial groove combined with the improved dimerization of pentad mutant GAPR-1 are likely to abrogate binding to Beclin 1.

Synthesis, structure and luminescence properties of lanthanide complex with a new tetrapodal ligand featuring salicylamide arms

International Nuclear Information System (INIS)

Song Xueqin; Wen Xiaoguang; Liu Weisheng; Wang Daqi

2010-01-01

A new tetrapodal ligand 1,1,1-tetrakis{[(2'-(2-furfurylaminoformyl))phenoxyl]methyl}methane (L) has been prepared and their coordination chemistry with Ln III ions has been investigated. The structure of {[Ln 4 L 3 (NO 3 ) 12 ].H 2 O} ∞ (Ln=Nd, Eu)] shows the binodal 4,3-connected three-dimensional interpenetration coordination polymers with topology of a (8 6 ) 3 (8 3 ) 4 notation. [DyL(NO 3 ) 3 (H 2 O) 2 ].0.5CH 3 OH and [ErL(NO 3 ) 3 (H 2 O) (CH 3 OH)].CH 3 COCH 3 is a 1:1 mononuclear complex with interesting supramolecular features. The structure of [NdL(H 2 O) 6 ].3ClO 4 .3H 2 O is a 2:1 mononuclear complex which further self-assembled through hydrogen bond to form a three-dimensional supramolecular structures. The result presented here indicates that both subtle variation of the terminal group and counter anions can be applied in the modulation of the overall molecular structures of lanthanide complex of salicylamide derivatives due to the structure specialties of this type of ligand. The luminescence properties of the Eu III complex are also studied in detail. - Grapical Abstract: We present here a series of zero- to three-dimensional lanthanide coordination structures and luminescence properties of Eu(III) complex of a new tetrapodal ligand.

Structure and function of complex carbohydrates active in regulating plant-microbe interactions

Energy Technology Data Exchange (ETDEWEB)

Albersheim, P; Darvill, A G; McNeil, M

1981-01-01

A key regulatory role of complex carbohydrates in the interactions between plants and microbes has been established. The complex carbohydrates act as regulatory molecules or hormones in that the carbohydrates induce de novo protein synthesis in receptive cells. The first complex carbohydrate recognized to possess such regulatory properties is a polysaccharide (PS) present in the walls of fungi. Hormonal concentrations of this PS elicit plant cells to accumulate phytoalexins (antibiotics). More recently we have recognized that a PS in the walls of growing plant cells also elicits phytoalexin accumulation; microbes and viruses may cause the release of active fragments of this endogenous elicitor. Another PS in plant cell walls is the Proteinase Inhibitor Inducing Factor (PIIF). This hormone appears to protect plants by inducing synthesis in plants of proteins which specifically inhibit digestive enzymes of insects and bacteria. Glycoproteins secreted by incompatible races (races that do not infect the plant) of a fungal pathogen of soybeans protect seedlings from attack by compatible races. Glycoproteins from compatible races do not protect the seedlings. The acidic PS secreted by the nitrogen-fixing rhizobia appear to function in the infection of legumes by the rhizobia. W.D. Bauer and his co-workers have evidence that these PS are required for the development of root hairs capable of being infected by symbiont rhizobia. Current knowledge of the structures of these biologically active complex carbohydrates will be presented.

Structure of an antibody in complex with its mucin domain linear epitope that is protective against Ebola virus.

Science.gov (United States)

Olal, Daniel; Kuehne, Ana I; Bale, Shridhar; Halfmann, Peter; Hashiguchi, Takao; Fusco, Marnie L; Lee, Jeffrey E; King, Liam B; Kawaoka, Yoshihiro; Dye, John M; Saphire, Erica Ollmann

2012-03-01

Antibody 14G7 is protective against lethal Ebola virus challenge and recognizes a distinct linear epitope in the prominent mucin-like domain of the Ebola virus glycoprotein GP. The structure of 14G7 in complex with its linear peptide epitope has now been determined to 2.8 Å. The structure shows that this GP sequence forms a tandem β-hairpin structure that binds deeply into a cleft in the antibody-combining site. A key threonine at the apex of one turn is critical for antibody interaction and is conserved among all Ebola viruses. This work provides further insight into the mechanism of protection by antibodies that target the protruding, highly accessible mucin-like domain of Ebola virus and the structural framework for understanding and characterizing candidate immunotherapeutics.

The evolution of cerebellum structure correlates with nest complexity.

Science.gov (United States)

Hall, Zachary J; Street, Sally E; Healy, Susan D

2013-01-01

Across the brains of different bird species, the cerebellum varies greatly in the amount of surface folding (foliation). The degree of cerebellar foliation is thought to correlate positively with the processing capacity of the cerebellum, supporting complex motor abilities, particularly manipulative skills. Here, we tested this hypothesis by investigating the relationship between cerebellar foliation and species-typical nest structure in birds. Increasing complexity of nest structure is a measure of a bird's ability to manipulate nesting material into the required shape. Consistent with our hypothesis, avian cerebellar foliation increases as the complexity of the nest built increases, setting the scene for the exploration of nest building at the neural level.

Chemistry and structure of technetium complexes

International Nuclear Information System (INIS)

Baldas, J.; Boas, J.F.; Bonnyman, J.; Williams, G.A.

1983-01-01

The structures of tris(2-aminobenzenethiolato) technetium(VI) and dichlorobis(diethyldithiocarbamato) thionitrosyltechnetium(V) have been determined by single crystal x-ray diffraction analysis. The preparation and chemistry of thiocyanato complexes of technetium have been investigated

Complexity in plasma. A grand view of self-organization

International Nuclear Information System (INIS)

Sato, Tetsuya.

1994-11-01

The central theme of the Complexity is the inquest of the creation of ordered structure in nature. Extensive computer simulations on plasmas have revealed that self-organization is governed by the three key processes, i.e. energy pumping, entropy expulsion and nonlinearity. A system exhibits characteristically different self-organization, depending on whether the energy pumping is instantaneous or continuous, or whether the produced entropy is expulsed or reserved. The nonlinearity acts to bring a nonequilibrium state into a bifurcation, thus resulting in a new structure along with an anomalous entropy production. (author)

Isolation and structure-function characterization of a signaling-active rhodopsin-G protein complex.

Science.gov (United States)

Gao, Yang; Westfield, Gerwin; Erickson, Jon W; Cerione, Richard A; Skiniotis, Georgios; Ramachandran, Sekar

2017-08-25

The visual photo-transduction cascade is a prototypical G protein-coupled receptor (GPCR) signaling system, in which light-activated rhodopsin (Rho*) is the GPCR catalyzing the exchange of GDP for GTP on the heterotrimeric G protein transducin (G T ). This results in the dissociation of G T into its component α T -GTP and β 1 γ 1 subunit complex. Structural information for the Rho*-G T complex will be essential for understanding the molecular mechanism of visual photo-transduction. Moreover, it will shed light on how GPCRs selectively couple to and activate their G protein signaling partners. Here, we report on the preparation of a stable detergent-solubilized complex between Rho* and a heterotrimer (G T *) comprising a Gα T /Gα i1 chimera (α T *) and β 1 γ 1 The complex was formed on native rod outer segment membranes upon light activation, solubilized in lauryl maltose neopentyl glycol, and purified with a combination of affinity and size-exclusion chromatography. We found that the complex is fully functional and that the stoichiometry of Rho* to Gα T * is 1:1. The molecular weight of the complex was calculated from small-angle X-ray scattering data and was in good agreement with a model consisting of one Rho* and one G T *. The complex was visualized by negative-stain electron microscopy, which revealed an architecture similar to that of the β 2 -adrenergic receptor-G S complex, including a flexible α T * helical domain. The stability and high yield of the purified complex should allow for further efforts toward obtaining a high-resolution structure of this important signaling complex. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural characterization and antimicrobial activities of transition metal complexes of a hydrazone ligand

Science.gov (United States)

Bakale, Raghavendra P.; Naik, Ganesh N.; Machakanur, Shrinath S.; Mangannavar, Chandrashekhar V.; Muchchandi, Iranna S.; Gudasi, Kalagouda B.

2018-02-01

A hydrazone ligand has been synthesized by the condensation of 2-nitrobenzaldehyde and hydralazine, and its Co(II), Ni(II), Cu(II) and Zn(II) complexes have been reported. Structural characterization of the ligand and its metal complexes has been performed by various spectroscopic [IR, NMR, UV-Vis, Mass], thermal and other physicochemical methods. The structure of the ligand and its Ni(II) complex has been characterized by single crystal X-ray diffraction studies. All the synthesized compounds have been screened for in vitro antimicrobial activity. The antibacterial activity is tested against Gram-positive strains Enterococcus faecalis, Streptococcus mutans and Staphylococcus aureus and Gram-negative strains Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae using ciprofloxacin as the reference standard. Antifungal activity is tested against Candida albicans, Aspergillus fumigatus and Aspergillus niger using ketoconazole as the reference standard. The minimum inhibitory concentration (MIC) was determined for test compounds as well as for reference standard. Ligand, Cu(II) and Zn(II) complexes have shown excellent activity against Candida albicans.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

Directory of Open Access Journals (Sweden)

Chen Chun

2008-03-01

Full Text Available Abstract Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1 present a robust and effective way for RNA structural data compression; (2 design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool

Crystal structures of T. b. rhodesiense adenosine kinase complexed with inhibitor and activator: implications for catalysis and hyperactivation.

Directory of Open Access Journals (Sweden)

Sabine Kuettel

2011-05-01

Full Text Available BACKGROUND: The essential purine salvage pathway of Trypanosoma brucei bears interesting catalytic enzymes for chemotherapeutic intervention of Human African Trypanosomiasis. Unlike mammalian cells, trypanosomes lack de novo purine synthesis and completely rely on salvage from their hosts. One of the key enzymes is adenosine kinase which catalyzes the phosphorylation of ingested adenosine to form adenosine monophosphate (AMP utilizing adenosine triphosphate (ATP as the preferred phosphoryl donor. METHODS AND FINDINGS: Here, we present the first structures of Trypanosoma brucei rhodesiense adenosine kinase (TbrAK: the structure of TbrAK in complex with the bisubstrate inhibitor P(1,P(5-di(adenosine-5'-pentaphosphate (AP5A at 1.55 Å, and TbrAK complexed with the recently discovered activator 4-[5-(4-phenoxyphenyl-2H-pyrazol-3-yl]morpholine (compound 1 at 2.8 Å resolution. CONCLUSIONS: The structural details and their comparison give new insights into substrate and activator binding to TbrAK at the molecular level. Further structure-activity relationship analyses of a series of derivatives of compound 1 support the observed binding mode of the activator and provide a possible mechanism of action with respect to their activating effect towards TbrAK.

A Method to Predict the Structure and Stability of RNA/RNA Complexes.

Science.gov (United States)

Xu, Xiaojun; Chen, Shi-Jie

2016-01-01

RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.

Complex-Dynamic Cosmology and Emergent World Structure

OpenAIRE

Kirilyuk, Andrei P.

2004-01-01

Universe structure emerges in the unreduced, complex-dynamic interaction process with the simplest initial configuration (two attracting homogeneous fields, quant-ph/9902015). The unreduced interaction analysis gives intrinsically creative cosmology, describing the real, explicitly emerging world structure with dynamic randomness on each scale. Without imposing any postulates or entities, we obtain physically real space, time, elementary particles with their detailed structure and intrinsic p...

A Multiscale Model of Morphological Complexity in Cities - Characterising Emergent Homogeneity and Heterogeneity

DEFF Research Database (Denmark)

Heinrich, Mary Katherine; Ayres, Phil; Bar-Yam, Yaneer

2017-01-01

Approaches from complex systems science can support design decision-making by extracting important information about key dependencies from large, unstructured data sources. This paper presents an initial case study applying such approaches to city structure, by characterising low-level features a...

Scintillometry in urban and complex environments: a review

International Nuclear Information System (INIS)

Ward, Helen C

2017-01-01

Knowledge of turbulent exchange in complex environments is relevant to a wide range of hydro-meteorological applications. Observations are required to improve understanding and inform model parameterisations but the very nature of complex environments presents challenges for measurements. Scintillometry offers several advantages as a technique for providing spatially-integrated turbulence data (structure parameters and fluxes), particularly in areas that would be impracticable to monitor using eddy covariance, such as across a valley, above a city or over heterogeneous landscapes. Despite much of scintillometry theory assuming flat, homogeneous surfaces and ideal conditions, over the last 20 years scintillometers have been deployed in increasingly complex locations, including urban and mountainous areas. This review draws together fundamental and applied research in complex environments, to assess what has been learnt, summarise the state-of-the-art and identify key areas for future research. Particular attention is given to evidence, or relative lack thereof, of the impact of complex environments on scintillometer data. Practical and theoretical considerations to account for the effects of complexity are discussed, with the aim of developing measurement capability towards more reliable and accurate observations in future. The usefulness of structure parameter measurements (in addition to fluxes, which must be derived using similarity theory) should not be overlooked, particularly when comparing or combining scintillometry with other measurement techniques and model simulations. (paper)

Structural insights into SUN-KASH complexes across the nuclear envelope

Institute of Scientific and Technical Information of China (English)

Wenjia Wang; Zhaocai Zhou; Zhubing Shi; Shi Jiao; Cuicui Chen; Huizhen Wang; Guoguang Liu; Qiang Wang; Yun Zhao; Mark I Greene

2012-01-01

Linker of the nucleoskeleton and the cytoskeleton (LINC) complexes are composed of SUN and KASH domaincontaining proteins and bridge the inner and outer membranes of the nuclear envelope.LINC complexes play critical roles in nuclear positioning,cell polarization and cellular stiffness.Previously,we reported the homotrimeric structure of human SUN2.We have now determined the crystal structure of the human SUN2-KASH complex.In the complex structure,the SUN domain homotrimer binds to three independent "hook"-like KASH peptides.The overall conformation of the SUN domain in the complex closely resembles the SUN domain in its apo state.A major conformational change involves the AA'-loop of KASH-bound SUN domain,which rearranges to form a mini β-sheet that interacts with the KASH peptide.The PPPT motif of the KASH domain fits tightly into a hydrophobic pocket on the homotrimeric interface of the SUN domain,which we termed the BI-pocket.Moreover,two adjacent protomers of the SUN domain homotrimer sandwich the KASH domain by hydrophobic interaction and hydrogen bonding.Mutations of these binding sites disrupt or reduce the association between the SUN and KASH domains in vitro.In addition,transfection of wild-type,but not mutant,SUN2 promotes cell migration in Ovcar-3 cells.These results provide a structural model of the LINC complex,which is essential for additional study of the physical and functional coupling between the cytoplasm and the nucleoplasm.

Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases

Science.gov (United States)

Xu, Qifang; Malecka, Kimberly L.; Fink, Lauren; Jordan, E. Joseph; Duffy, Erin; Kolander, Samuel; Peterson, Jeffrey; Dunbrack, Roland L.

2016-01-01

Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Crystal structures of several homomeric protein kinase complexes have a serine, threonine, or tyrosine autophosphorylation site of one kinase monomer located in the active site of another monomer, a structural complex that we call an “autophosphorylation complex.” We developed and applied a structural bioinformatics method to identify all such autophosphorylation kinase complexes in X-ray crystallographic structures in the Protein Data Bank (PDB). We identified 15 autophosphorylation complexes in the PDB, of which 5 complexes had not previously been described in the publications describing the crystal structures. These 5 consist of tyrosine residues in the N-terminal juxtamembrane regions of colony stimulating factor 1 receptor (CSF1R, Tyr561) and EPH receptor A2 (EPHA2, Tyr594), tyrosine residues in the activation loops of the SRC kinase family member LCK (Tyr394) and insulin-like growth factor 1 receptor (IGF1R, Tyr1166), and a serine in a nuclear localization signal region of CDC-like kinase 2 (CLK2, Ser142). Mutations in the complex interface may alter autophosphorylation activity and contribute to disease; therefore we mutated residues in the autophosphorylation complex interface of LCK and found that two mutations impaired autophosphorylation (T445V and N446A) and mutation of Pro447 to Ala, Gly, or Leu increased autophosphorylation. The identified autophosphorylation sites are conserved in many kinases, suggesting that, by homology, these complexes may provide insight into autophosphorylation complex interfaces of kinases that are relevant drug targets. PMID:26628682

Structures of an Apo and a Binary Complex of an Evolved Archeal B Family DNA Polymerase Capable of Synthesising Highly Cy-Dye Labelled DNA

Science.gov (United States)

Wynne, Samantha A.; Pinheiro, Vitor B.; Holliger, Philipp; Leslie, Andrew G. W.

2013-01-01

Thermophilic DNA polymerases of the polB family are of great importance in biotechnological applications including high-fidelity PCR. Of particular interest is the relative promiscuity of engineered versions of the exo- form of polymerases from the Thermo- and Pyrococcales families towards non-canonical substrates, which enables key advances in Next-generation sequencing. Despite this there is a paucity of structural information to guide further engineering of this group of polymerases. Here we report two structures, of the apo form and of a binary complex of a previously described variant (E10) of Pyrococcus furiosus (Pfu) polymerase with an ability to fully replace dCTP with Cyanine dye-labeled dCTP (Cy3-dCTP or Cy5-dCTP) in PCR and synthesise highly fluorescent “CyDNA” densely decorated with cyanine dye heterocycles. The apo form of Pfu-E10 closely matches reported apo form structures of wild-type Pfu. In contrast, the binary complex (in the replicative state with a duplex DNA oligonucleotide) reveals a closing movement of the thumb domain, increasing the contact surface with the nascent DNA duplex strand. Modelling based on the binary complex suggests how bulky fluorophores may be accommodated during processive synthesis and has aided the identification of residues important for the synthesis of unnatural nucleic acid polymers. PMID:23940661

Structure-function relationship in complex brain networks expressed by hierarchical synchronization

International Nuclear Information System (INIS)

Zhou Changsong; Zemanova, Lucia; Zamora-Lopez, Gorka; Hilgetag, Claus C; Kurths, Juergen

2007-01-01

The brain is one of the most complex systems in nature, with a structured complex connectivity. Recently, large-scale corticocortical connectivities, both structural and functional, have received a great deal of research attention, especially using the approach of complex network analysis. Understanding the relationship between structural and functional connectivity is of crucial importance in neuroscience. Here we try to illuminate this relationship by studying synchronization dynamics in a realistic anatomical network of cat cortical connectivity. We model the nodes (cortical areas) by a neural mass model (population model) or by a subnetwork of interacting excitable neurons (multilevel model). We show that if the dynamics is characterized by well-defined oscillations (neural mass model and subnetworks with strong couplings), the synchronization patterns are mainly determined by the node intensity (total input strengths of a node) and the detailed network topology is rather irrelevant. On the other hand, the multilevel model with weak couplings displays more irregular, biologically plausible dynamics, and the synchronization patterns reveal a hierarchical cluster organization in the network structure. The relationship between structural and functional connectivity at different levels of synchronization is explored. Thus, the study of synchronization in a multilevel complex network model of cortex can provide insights into the relationship between network topology and functional organization of complex brain networks

Structure-function relationship in complex brain networks expressed by hierarchical synchronization

Energy Technology Data Exchange (ETDEWEB)

Zhou Changsong [Institute of Physics, University of Potsdam, PF 601553, 14415 Potsdam (Germany); Zemanova, Lucia [Institute of Physics, University of Potsdam, PF 601553, 14415 Potsdam (Germany); Zamora-Lopez, Gorka [Institute of Physics, University of Potsdam, PF 601553, 14415 Potsdam (Germany); Hilgetag, Claus C [Jacobs University Bremen, Campus Ring 6, Rm 116, D-28759 Bremen (Germany); Kurths, Juergen [Institute of Physics, University of Potsdam, PF 601553, 14415 Potsdam (Germany)

2007-06-15

The brain is one of the most complex systems in nature, with a structured complex connectivity. Recently, large-scale corticocortical connectivities, both structural and functional, have received a great deal of research attention, especially using the approach of complex network analysis. Understanding the relationship between structural and functional connectivity is of crucial importance in neuroscience. Here we try to illuminate this relationship by studying synchronization dynamics in a realistic anatomical network of cat cortical connectivity. We model the nodes (cortical areas) by a neural mass model (population model) or by a subnetwork of interacting excitable neurons (multilevel model). We show that if the dynamics is characterized by well-defined oscillations (neural mass model and subnetworks with strong couplings), the synchronization patterns are mainly determined by the node intensity (total input strengths of a node) and the detailed network topology is rather irrelevant. On the other hand, the multilevel model with weak couplings displays more irregular, biologically plausible dynamics, and the synchronization patterns reveal a hierarchical cluster organization in the network structure. The relationship between structural and functional connectivity at different levels of synchronization is explored. Thus, the study of synchronization in a multilevel complex network model of cortex can provide insights into the relationship between network topology and functional organization of complex brain networks.

Linking Wave Forcing to Coral Cover and Structural Complexity Across Coral Reef Flats

Science.gov (United States)

Harris, D. L.; Rovere, A.; Parravicini, V.; Casella, E.

2015-12-01

The hydrodynamic regime is a significant component in the geomorphic and ecological development of coral reefs. The energy gradients and flow conditions generated by the breaking and transformation of waves across coral reef crests and flats drive changes in geomorphic structure, and coral growth form and distribution. One of the key aspects in regulating the wave energy propagating across reef flats is the rugosity or roughness of the benthic substrate. Rugosity and structural complexity of coral reefs is also a key indicator of species diversity, ecological functioning, and reef health. However, the links between reef rugosity, coral species distribution and abundance, and hydrodynamic forcing are poorly understood. In this study we examine this relationship by using high resolution measurement of waves in the surf zone and coral reef benthic structure.Pressure transducers (logging at 4 Hz) were deployed in cross reef transects at two sites (Tiahura and Ha'apiti reef systems) in Moorea, French Polynesia with wave characteristics determined on a wave by wave basis. A one dimensional hydrodynamic model (XBeach) was calibrated from this data to determine wave processes on the reef flats under average conditions. Transects of the reef benthic structure were conducted using photographic analysis and the three dimensional reef surface was constructed using structure from motion procedures. From this analysis reef rugosity, changes in coral genus and growth form, and across reef shifts in benthic community were determined. The results show clear changes in benthic assemblages along wave energy gradients with some indication of threshold values of wave induced bed shear stress above which live coral cover was reduced. Reef rugosity was shown to be significantly along the cross-reef transect which has important implications for accurate assessment of wave dissipation across coral reef flats. Links between reef rugosity and coral genus were also observed and may indicate

Multi-frequency complex network from time series for uncovering oil-water flow structure.

Science.gov (United States)

Gao, Zhong-Ke; Yang, Yu-Xuan; Fang, Peng-Cheng; Jin, Ning-De; Xia, Cheng-Yi; Hu, Li-Dan

2015-02-04

Uncovering complex oil-water flow structure represents a challenge in diverse scientific disciplines. This challenge stimulates us to develop a new distributed conductance sensor for measuring local flow signals at different positions and then propose a novel approach based on multi-frequency complex network to uncover the flow structures from experimental multivariate measurements. In particular, based on the Fast Fourier transform, we demonstrate how to derive multi-frequency complex network from multivariate time series. We construct complex networks at different frequencies and then detect community structures. Our results indicate that the community structures faithfully represent the structural features of oil-water flow patterns. Furthermore, we investigate the network statistic at different frequencies for each derived network and find that the frequency clustering coefficient enables to uncover the evolution of flow patterns and yield deep insights into the formation of flow structures. Current results present a first step towards a network visualization of complex flow patterns from a community structure perspective.

Electronic structure of transition metal-isocorrole complexes: A first quantum chemical study

NARCIS (Netherlands)

van Oort, B; Tangen, E; Ghosh, A.

2004-01-01

DFT calculations indicate that the broad electronic-structural features of metalloisocorroles are rather similar to those of analogous metallocorroles. Thus, like their corrole analogues, many metalloisocorroles feature substantially non-innocent ligands. Another key point is that both corroles and

Syntheses and a Solid State Structure of a Dinuclear Molybdenum(V Complex with Pyridine

Directory of Open Access Journals (Sweden)

Jon Zubieta

2010-01-01

Full Text Available A mononuclear complex [MoOCl4(H2O]− readily forms a metal−metal bonded {Mo2O4}2+ core. A high content of pyridine in the reaction mixture prevents further aggregation of dinuclear cores into larger clusters and a neutral, dinuclear complex with the [Mo2O4Cl2(Py4] composition is isolated as a product. Solid state structures of two compounds containing this complex, [Mo2O4Cl2(Py4]·2.25Py (1 and [Mo2O4Cl2(Py4]·1.5PyHCl (2, were investigated by X-ray crystallography.

Structural imbalances as a key factor of unemployment in the Russian labor market

Directory of Open Access Journals (Sweden)

I V Trotsuk

2015-12-01

Full Text Available In recent years, the problems of the Russian labor market, especially the scale and characteristics of youth unemployment, get very emotional and negative coverage in the scientific and journalistic discourses. The authors seek to show without any emotional evaluations what are the objective macroeconomic causes of the current situation with unemployment, especially youth unemployment. First, the authors identify the main challenges the labor market faces today in terms of the interaction of its key actors (workers, owners of the means of production, educational institutions and various intermediaries, including the state regulating the features of labor recruitment. Second, the article shows the main trends of the last decade that change the structure of employment of the economically active population. Third, the authors name the basic structural imbalances in the Russian labor market, primarily structural and professional imbalance between the demand for labor, the demand for vocational training and offer of educational services, which is quite evident, albeit in different ways, in all spheres of the economy. Fourth, the article describes the specific features of the youth labor market as both affected and contributing to the structural imbalances. Finally, the authors propose a methodology of macroeconomic forecasting that may reduce the problems the Russian society faces in the field of employment.

Nanofluidic structures with complex three-dimensional surfaces

International Nuclear Information System (INIS)

Stavis, Samuel M; Gaitan, Michael; Strychalski, Elizabeth A

2009-01-01

Nanofluidic devices have typically explored a design space of patterns limited by a single nanoscale structure depth. A method is presented here for fabricating nanofluidic structures with complex three-dimensional (3D) surfaces, utilizing a single layer of grayscale photolithography and standard integrated circuit manufacturing tools. This method is applied to construct nanofluidic devices with numerous (30) structure depths controlled from ∼10 to ∼620 nm with an average standard deviation of 1 cm. A prototype 3D nanofluidic device is demonstrated that implements size exclusion of rigid nanoparticles and variable nanoscale confinement and deformation of biomolecules.

Spectral investigation of a complex space charge structure in plasma

International Nuclear Information System (INIS)

Gurlui, S.; Dimitriu, D. G.; Ionita, C.; Schrittwieser, R. W.

2009-01-01

Complex space charge structures bordered by electrical double layers were spectrally investigated in argon plasma in the domain 400-1000 nm, identifying the lines corresponding to the transitions from different excited states of argon. The electron excitation temperature in the argon atoms was estimated from the spectral lines intensity ratio. (authors)

Elucidating the 3D structures of Al(iii)-Aβ complexes: a template free strategy based on the pre-organization hypothesis.

Science.gov (United States)

Mujika, Jon I; Rodríguez-Guerra Pedregal, Jaime; Lopez, Xabier; Ugalde, Jesus M; Rodríguez-Santiago, Luis; Sodupe, Mariona; Maréchal, Jean-Didier

2017-07-01

Senile plaques are extracellular deposits found in patients with Alzheimer's Disease (AD) and are mainly formed by insoluble fibrils of β-amyloid (Aβ) peptides. The mechanistic details about how AD develops are not fully understood yet, but metals such as Cu, Zn, or Fe are proposed to have a non-innocent role. Many studies have also linked the non biological metal aluminum with AD, a species whose concentration in the environment and food has been constantly increasing since the industrial revolution. Gaining a molecular picture of how Al(iii) interacts with an Aβ peptide is of fundamental interest to improve understanding of the many variables in the evolution of AD. So far, no consensus has been reached on how this metal interacts with Aβ, partially due to the experimental complexity of detecting and quantifying the resulting Al(iii)-Aβ complexes. Computational chemistry arises as a powerful alternative to investigate how Al(iii) can interact with Aβ peptides, as suitable strategies could shed light on the metal-peptide description at the molecular level. However, the absence of any reliable template that could be used for the modeling of the metallopeptide structure makes computational insight extremely difficult. Here, we present a novel strategy to generate accurate 3D models of the Al(iii)-Aβ complexes, which still circumvents first principles simulations of metal binding to peptides of Aβ. The key to this approach lies in the identification of experimental structures of the isolated peptide that are favourably pre-organized for the binding of a given metal in configurations of the first coordination sphere that were previously identified as the most stable with amino acid models. This approach solves the problem of the absence of clear structural templates for novel metallopeptide constructs. The posterior refinement of the structures via QM/MM and MD calculations allows us to provide, for the first time, physically sound models for Al

A large scale analysis of information-theoretic network complexity measures using chemical structures.

Directory of Open Access Journals (Sweden)

Matthias Dehmer

Full Text Available This paper aims to investigate information-theoretic network complexity measures which have already been intensely used in mathematical- and medicinal chemistry including drug design. Numerous such measures have been developed so far but many of them lack a meaningful interpretation, e.g., we want to examine which kind of structural information they detect. Therefore, our main contribution is to shed light on the relatedness between some selected information measures for graphs by performing a large scale analysis using chemical networks. Starting from several sets containing real and synthetic chemical structures represented by graphs, we study the relatedness between a classical (partition-based complexity measure called the topological information content of a graph and some others inferred by a different paradigm leading to partition-independent measures. Moreover, we evaluate the uniqueness of network complexity measures numerically. Generally, a high uniqueness is an important and desirable property when designing novel topological descriptors having the potential to be applied to large chemical databases.

Survey of large protein complexes D. vulgaris reveals great structural diversity

Energy Technology Data Exchange (ETDEWEB)

Han, B.-G.; Dong, M.; Liu, H.; Camp, L.; Geller, J.; Singer, M.; Hazen, T. C.; Choi, M.; Witkowska, H. E.; Ball, D. A.; Typke, D.; Downing, K. H.; Shatsky, M.; Brenner, S. E.; Chandonia, J.-M.; Biggin, M. D.; Glaeser, R. M.

2009-08-15

An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr {approx} 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate {approx}10 times greater than that of previous 'proteomic' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.

Coherent structures in a supersonic complex nozzle

Science.gov (United States)

Magstadt, Andrew; Berry, Matthew; Glauser, Mark

2016-11-01

The jet flow from a complex supersonic nozzle is studied through experimental measurements. The nozzle's geometry is motivated by future engine designs for high-performance civilian and military aircraft. This rectangular jet has a single plane of symmetry, an additional shear layer (referred to as a wall jet), and an aft deck representative of airframe integration. The core flow operates at a Mach number of Mj , c = 1 . 6 , and the wall jet is choked (Mj , w = 1 . 0). This high Reynolds number jet flow is comprised of intense turbulence levels, an intricate shock structure, shear and boundary layers, and powerful corner vortices. In the present study, stereo PIV measurements are simultaneously sampled with high-speed pressure measurements, which are embedded in the aft deck, and far-field acoustics in the anechoic chamber at Syracuse University. Time-resolved schlieren measurements have indicated the existence of strong flow events at high frequencies, at a Strouhal number of St = 3 . 4 . These appear to result from von Kàrmàn vortex shedding within the nozzle and pervade the entire flow and acoustic domain. Proper orthogonal decomposition is applied on the current data to identify coherent structures in the jet and study the influence of this vortex street. AFOSR Turbulence and Transition Program (Grant No. FA9550-15-1-0435) with program managers Dr. I. Leyva and Dr. R. Ponnappan.

Synthesis of the reported structure of piperazirum using a nitro-Mannich reaction as the key stereochemical determining step

Directory of Open Access Journals (Sweden)

James C. Anderson

2013-08-01

Full Text Available Piperazirum, isolated from Arum palaestinum Boiss, was originally assigned as r-3,c-5-diisobutyl-c-6-isopropylpiperazin-2-one. The reported structure was synthesised diastereoselectively using a key nitro-Mannich reaction to set up the C5/C6 relative stereochemistry. The structure was unambiguously assigned by single crystal X-ray diffraction but the spectroscopic data did not match those reported for the natural product. The structure of the natural product must therefore be revised.

Multifaceted Modularity: A Key for Stepwise Building of Hierarchical Complexity in Actinide Metal–Organic Frameworks

Energy Technology Data Exchange (ETDEWEB)

Dolgopolova, Ekaterina A. [Department; Ejegbavwo, Otega A. [Department; Martin, Corey R. [Department; Smith, Mark D. [Department; Setyawan, Wahyu [Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Karakalos, Stavros G. [College; Henager, Charles H. [Pacific Northwest National Laboratory, Richland, Washington 99352, United States; zur Loye, Hans-Conrad [Department; Shustova, Natalia B. [Department

2017-11-07

Growing necessity for efficient nuclear waste management is a driving force for development of alternative architectures towards fundamental understanding of mechanisms involved in actinide integration inside extended structures. In this manuscript, metal-organic frameworks (MOFs) were investigated as a model system for engineering radionuclide containing materials through utilization of unprecedented MOF modularity, which cannot be replicated in any other type of materials. Through the implementation of recent synthetic advances in the MOF field, hierarchical complexity of An-materials were built stepwise, which was only feasible due to preparation of the first examples of actinide-based frameworks with “unsaturated” metal nodes. The first successful attempts of solid-state metathesis and metal node extension in An-MOFs are reported, and the results of the former approach revealed drastic differences in chemical behavior of extended structures versus molecular species. Successful utilization of MOF modularity also allowed us to structurally characterize the first example of bimetallic An-An nodes. To the best of our knowledge, through combination of solid-state metathesis, guest incorporation, and capping linker installation, we were able to achieve the highest Th wt% in mono- and bi-actinide frameworks with minimal structural density. Overall, combination of a multistep synthetic approach with homogeneous actinide distribution and moderate solvothermal conditions could make MOFs an exceptionally powerful tool to address fundamental questions responsible for chemical behavior of An-based extended structures, and therefore, shed light on possible optimization of nuclear waste administration.

The ligament of Parks as a key anatomical structure for safer hemorrhoidectomy: Anatomic study and a simple surgical note

Directory of Open Access Journals (Sweden)

Menelaos Zoulamoglou

2017-12-01

Full Text Available Hemorrhoids are a common anal disorder which affects both men and women of all ages. One out of ten patients with hemorrhoidal disease, requires surgical treatment. Unfortunately though, hemorrhoidectomy is closely related to complications that can be present early or late postoperatively. In the present manuscript, the safe surgical technique which emphasizes to the identification of the key anatomical structure of the ligament of Parks (Trietz's muscle is adequately described. A total of 200 patients with grades III and IV hemorrhoids, underwent Milligan-Morgan or Ferguson's hemorrhoidectomy. The mucosal ligament of Parks was identified to all patients and was used as a key anatomical structure through the excision of the hemorrhoids. Its identification guides surgeons during the operation and reduces the major problem of postoperative complications. Finally, since the mucosal ligament of Parks represents a constantly identifiable landmark, it allows simple and reliable identification of the internal sphincter muscle and minimizes the probability of postoperative complications.

Self-assembly of a double-helical complex of sodium.

Science.gov (United States)

Bell, T W; Jousselin, H

1994-02-03

Spontaneous self-organization of helical and multiple-helical molecular structures occurs on several levels in living organisms. Key examples are alpha-helical polypeptides, double-helical nucleic acids and helical protein structures, including F-actin, microtubules and the protein sheath of the tobacco mosaic virus. Although the self-assembly of double-helical transition-metal complexes bears some resemblance to the molecular organization of double-stranded DNA, selection between monohelical, double-helical and triple-helical structures is determined largely by the size and geometrical preference of the tightly bound metal. Here we present an example of double-helical assembly induced by the weaker and non-directional interactions of an alkali-metal ion with an organic ligand that is pre-organized into a coil. We have characterized the resulting complex by two-dimensional NMR and fast-atom-bombardment mass spectrometry. These results provide a step toward the creation of molecular tubes or ion channels consisting of intertwined coils.

A Corner-Point-Grid-Based Voxelization Method for Complex Geological Structure Model with Folds

Science.gov (United States)

Chen, Qiyu; Mariethoz, Gregoire; Liu, Gang

2017-04-01

3D voxelization is the foundation of geological property modeling, and is also an effective approach to realize the 3D visualization of the heterogeneous attributes in geological structures. The corner-point grid is a representative data model among all voxel models, and is a structured grid type that is widely applied at present. When carrying out subdivision for complex geological structure model with folds, we should fully consider its structural morphology and bedding features to make the generated voxels keep its original morphology. And on the basis of which, they can depict the detailed bedding features and the spatial heterogeneity of the internal attributes. In order to solve the shortage of the existing technologies, this work puts forward a corner-point-grid-based voxelization method for complex geological structure model with folds. We have realized the fast conversion from the 3D geological structure model to the fine voxel model according to the rule of isocline in Ramsay's fold classification. In addition, the voxel model conforms to the spatial features of folds, pinch-out and other complex geological structures, and the voxels of the laminas inside a fold accords with the result of geological sedimentation and tectonic movement. This will provide a carrier and model foundation for the subsequent attribute assignment as well as the quantitative analysis and evaluation based on the spatial voxels. Ultimately, we use examples and the contrastive analysis between the examples and the Ramsay's description of isoclines to discuss the effectiveness and advantages of the method proposed in this work when dealing with the voxelization of 3D geologic structural model with folds based on corner-point grids.

Structure of HLA-A*1101 in complex with a hepatitis B peptide homologue

DEFF Research Database (Denmark)

Blicher, Thomas; Kastrup, Jette Sandholm; Pedersen, Lars Østergaard

2006-01-01

A high-resolution structure of the human MHC-I molecule HLA-A*1101 is presented in which it forms a complex with a sequence homologue of a peptide that occurs naturally in hepatitis B virus DNA polymerase. The sequence of the bound peptide is AIMPARFYPK, while that of the corresponding natural...

On dependence of stability of lanthanum complexes with aminopolycarboxylic acids on the complex structure

International Nuclear Information System (INIS)

Poluehktov, N.S.; Meshkova, S.B.; Danilkovich, M.M.; Topilova, Z.M.

1985-01-01

Regularities in changes of stability constants of lanthanum complexes with aminopolycarboxylic acids (APA) versus their structure are studied, The stability of lathanum-APA complexes depends mainly on the number of carboxyl groups in a ligand molecule. At that, the highest stability constant is characteristic of a complex with a ligand, containing 3 nitrogen atoms and 5 carboxyl groups, in the presenoe of which the lanthanum ion coordination sphere gets satupated. The oxyethy group introduction into a ligand molecule also improves the lanthanum complex stability but to a lesser degree than during the introduction of a carboxyl group. The number of nitrogen atoms in a ligand polecule affects insignificantly the complex stability constant value, and the elongation of a chain of CH 2 groups, separating nitrogen atoms, reduces the constant to a -0.6 power

Key Technologies of the Hydraulic Structures of the Three Gorges Project

Directory of Open Access Journals (Sweden)

Xinqiang Niu

2016-09-01

Full Text Available To date, the Three Gorges Project is the largest hydro junction in the world. It is the key project for the integrated water resource management and development of the Changjiang River. The technology of the project, with its huge scale and comprehensive benefits, is extremely complicated, and the design difficulty is greater than that of any other hydro project in the world. A series of new design theories and methods have been proposed and applied in the design and research process. Many key technological problems regarding hydraulic structures have been overcome, such as a gravity dam with multi-layer large discharge orifices, a hydropower station of giant generating units, and a giant continual multi-step ship lock with a high water head.

Application of the Moessbauer effect to the study of the structure of transition metal complexes; Applications de l'effet Mossbauer a l'etude de la structure des complexes des metaux de transition

Energy Technology Data Exchange (ETDEWEB)

Tsymbal, C [Commissariat a l' Energie Atomique, Grenoble (France). Centre d' Etudes Nucleaires

1968-07-01

In this survey, the structural investigations of transition metal complexes by the hyperfine interactions in the Moessbauer effect are described. The isomer shift provides a unique tool for estimating s electrons covalency in high spin complexes and one of the best pieces of evidence for the importance of bacle donation in low spin complexes. The electric field gradient deriving from quadrupole coupling measurements is correlated with the energy levels distribution of d orbitals in high spin complexes, whereas in low spin complexes it originates from the unbalanced d electrons. (authors) [French] Dans cette etude, nous decrivons les applications des interactions hyperfines dans l' effet Mossbauer a l'etude de la structure des complexes des metaux de transition. Le deplacement isomerique donne des informations tres utiles sur la covalence des electrons s dans les complexes a spin eleve et met en evidence d'une maniere nette l'importance du phenomene de 'bacle donation' dans les complexes a spin faible. Le gradient de champ electrique qui provient des mesures d'interaction quadripolaire est lie a la distribution des niveaux d'energie des orbitales d dans les complexes a spin eleve alors que dans les complexes a spin faible, il est provoque par des electrons d non apparies. (auteurs)

Spinors in euclidean field theory, complex structures and discrete symmetries

International Nuclear Information System (INIS)

Wetterich, C.

2011-01-01

We discuss fermions for arbitrary dimensions and signature of the metric, with special emphasis on euclidean space. Generalized Majorana spinors are defined for d=2,3,4,8,9mod8, independently of the signature. These objects permit a consistent analytic continuation of Majorana spinors in Minkowski space to euclidean signature. Compatibility of charge conjugation with complex conjugation requires for euclidean signature a new complex structure which involves a reflection in euclidean time. The possible complex structures for Minkowski and euclidean signature can be understood in terms of a modulo two periodicity in the signature. The concepts of a real action and hermitean observables depend on the choice of the complex structure. For a real action the expectation values of all hermitean multi-fermion observables are real. This holds for arbitrary signature, including euclidean space. In particular, a chemical potential is compatible with a real action for the euclidean theory. We also discuss the discrete symmetries of parity, time reversal and charge conjugation for arbitrary dimension and signature.

Reaction-diffusion controlled growth of complex structures

Science.gov (United States)

Noorduin, Willem; Mahadevan, L.; Aizenberg, Joanna

2013-03-01

Understanding how the emergence of complex forms and shapes in biominerals came about is both of fundamental and practical interest. Although biomineralization processes and organization strategies to give higher order architectures have been studied extensively, synthetic approaches to mimic these self-assembled structures are highly complex and have been difficult to emulate, let alone replicate. The emergence of solution patterns has been found in reaction-diffusion systems such as Turing patterns and the BZ reaction. Intrigued by this spontaneous formation of complexity we explored if similar processes can lead to patterns in the solid state. We here identify a reaction-diffusion system in which the shape of the solidified products is a direct readout of the environmental conditions. Based on insights in the underlying mechanism, we developed a toolbox of engineering strategies to deterministically sculpt patterns and shapes, and combine different morphologies to create a landscape of hierarchical multi scale-complex tectonic architectures with unprecedented levels of complexity. These findings may hold profound implications for understanding, mimicking and ultimately expanding upon nature's morphogenesis strategies, allowing the synthesis of advanced highly complex microscale materials and devices. WLN acknowledges the Netherlands Organization for Scientific Research for financial support

Ligand complex structures of l-amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 and its conformational change.

Science.gov (United States)

Im, Dohyun; Matsui, Daisuke; Arakawa, Takatoshi; Isobe, Kimiyasu; Asano, Yasuhisa; Fushinobu, Shinya

2018-03-01

l-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 (l-AAO/MOG) catalyzes both the oxidative deamination and oxidative decarboxylation of the α-group of l-Lys to produce a keto acid and amide, respectively. l-AAO/MOG exhibits limited specificity for l-amino acid substrates with a basic side chain. We previously determined its ligand-free crystal structure and identified a key residue for maintaining the dual activities. Here, we determined the structures of l-AAO/MOG complexed with l-Lys, l-ornithine, and l-Arg and revealed its substrate recognition. Asp238 is located at the ceiling of a long hydrophobic pocket and forms a strong interaction with the terminal, positively charged group of the substrates. A mutational analysis on the D238A mutant indicated that the interaction is critical for substrate binding but not for catalytic control between the oxidase/monooxygenase activities. The catalytic activities of the D238E mutant unexpectedly increased, while the D238F mutant exhibited altered substrate specificity to long hydrophobic substrates. In the ligand-free structure, there are two channels connecting the active site and solvent, and a short region located at the dimer interface is disordered. In the l-Lys complex structure, a loop region is displaced to plug the channels. Moreover, the disordered region in the ligand-free structure forms a short helix in the substrate complex structures and creates the second binding site for the substrate. It is assumed that the amino acid substrate enters the active site of l-AAO/MOG through this route. The atomic coordinates and structure factors (codes 5YB6, 5YB7, and 5YB8) have been deposited in the Protein Data Bank (http://wwpdb.org/). 1.4.3.2 (l-amino acid oxidase), 1.13.12.2 (lysine 2-monooxygenase).

Synthesis, structure, and properties of supramolecular charge-transfer complexes between bis(18-crown-6)stilbene and ammonioalkyl derivatives of 4,4'-bipyridine and 2,7-diazapyrene.

Science.gov (United States)

Vedernikov, Artem I; Ushakov, Evgeny N; Efremova, Asya A; Kuz'mina, Lyudmila G; Moiseeva, Anna A; Lobova, Natalia A; Churakov, Andrei V; Strelenko, Yuri A; Alfimov, Michael V; Howard, Judith A K; Gromov, Sergey P

2011-08-19

4,4'-Bipyridine and 2,7-diazapyrene derivatives (A) having two ammonioalkyl N-substituents were synthesized. The complex formation of these compounds with bis(18-crown-6)stilbene (D) was studied by spectrophotometry, cyclic voltammetry, (1)H NMR spectroscopy, and X-ray diffraction analysis. In MeCN, π-donor D and π-acceptors A form supramolecular 1:1 (D·A) and 2:1 (D·A·D) charge-transfer complexes. The D·A complexes have a pseudocyclic structure as a result of ditopic binding of the ammonium groups to the crown-ether fragments. The better the geometric matching between the components, the higher the stability of the D·A complexes (log K up to 9.39). A key driving force of the D·A·D complex formation is the excessive steric strain in the precursor D·A complexes. The pseudocyclic D·A complexes involving the ammoniopropyl derivative of 4,4'-bipyridine were obtained as single crystals. Crystallization of the related ammonioethyl derivative was accompanied by transition of the D·A complexes to a structure of the (D·A)(m) coordination polymer type.

A single frequency component-based re-estimated MUSIC algorithm for impact localization on complex composite structures

International Nuclear Information System (INIS)

Yuan, Shenfang; Bao, Qiao; Qiu, Lei; Zhong, Yongteng

2015-01-01

The growing use of composite materials on aircraft structures has attracted much attention for impact monitoring as a kind of structural health monitoring (SHM) method. Multiple signal classification (MUSIC)-based monitoring technology is a promising method because of its directional scanning ability and easy arrangement of the sensor array. However, for applications on real complex structures, some challenges still exist. The impact-induced elastic waves usually exhibit a wide-band performance, giving rise to the difficulty in obtaining the phase velocity directly. In addition, composite structures usually have obvious anisotropy, and the complex structural style of real aircrafts further enhances this performance, which greatly reduces the localization precision of the MUSIC-based method. To improve the MUSIC-based impact monitoring method, this paper first analyzes and demonstrates the influence of measurement precision of the phase velocity on the localization results of the MUSIC impact localization method. In order to improve the accuracy of the phase velocity measurement, a single frequency component extraction method is presented. Additionally, a single frequency component-based re-estimated MUSIC (SFCBR-MUSIC) algorithm is proposed to reduce the localization error caused by the anisotropy of the complex composite structure. The proposed method is verified on a real composite aircraft wing box, which has T-stiffeners and screw holes. Three typical categories of 41 impacts are monitored. Experimental results show that the SFCBR-MUSIC algorithm can localize impact on complex composite structures with an obviously improved accuracy. (paper)

Solving complex and disordered surface structures with electron diffraction

International Nuclear Information System (INIS)

Van Hove, M.A.

1987-10-01

The past of surface structure determination with low-energy electron diffraction (LEED) will be briefly reviewed, setting the stage for a discussion of recent and future developments. The aim of these developments is to solve complex and disordered surface structures. Some efficient solutions to the theoretical and experimental problems will be presented. Since the theoretical problems dominate, the emphasis will be on theoretical approaches to the calculation of the multiple scattering of electrons through complex and disordered surfaces. 49 refs., 13 figs., 1 tab

DYNECHARM++: a toolkit to simulate coherent interactions of high-energy charged particles in complex structures

Science.gov (United States)

Bagli, Enrico; Guidi, Vincenzo

2013-08-01

A toolkit for the simulation of coherent interactions between high-energy charged particles and complex crystal structures, called DYNECHARM++ has been developed. The code has been written in C++ language taking advantage of this object-oriented programing method. The code is capable to evaluating the electrical characteristics of complex atomic structures and to simulate and track the particle trajectory within them. Calculation method of electrical characteristics based on their expansion in Fourier series has been adopted. Two different approaches to simulate the interaction have been adopted, relying on the full integration of particle trajectories under the continuum potential approximation and on the definition of cross-sections of coherent processes. Finally, the code has proved to reproduce experimental results and to simulate interaction of charged particles with complex structures.

A series of 2D metal-quinolone complexes: Syntheses, structures, and physical properties

Energy Technology Data Exchange (ETDEWEB)

He, Jiang-Hong [College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Xiao, Dong-Rong, E-mail: xiaodr98@yahoo.com.cn [College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Chen, Hai-Yan; Sun, Dian-Zhen; Yan, Shi-Wei; Wang, Xin; Ye, Zhong-Li [College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Luo, Qun-Li, E-mail: qlluo@swu.edu.cn [College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Wang, En-Bo, E-mail: wangeb889@nenu.edu.cn [Key Laboratory of Polyoxometalate Science of Ministry of Education, Department of Chemistry, Northeast Normal University, Changchun 130024 (China)

2013-02-15

Six novel 2D metal-quinolone complexes, namely [Cd(cfH)(bpdc)]{center_dot}H{sub 2}O (1), [M(norfH)(bpdc)]{center_dot}H{sub 2}O (M=Cd (2) and Mn (3)), [Mn{sub 2}(cfH)(odpa)(H{sub 2}O){sub 3}]{center_dot}0.5H{sub 2}O (4), [Co{sub 2}(norfH)(bpta)({mu}{sub 2}-H{sub 2}O)(H{sub 2}O){sub 2}]{center_dot}H{sub 2}O (5) and [Co{sub 3}(saraH){sub 2}(Hbpta){sub 2}(H{sub 2}O){sub 4}]{center_dot}9H{sub 2}O (6) (cfH=ciprofloxacin, norfH=norfloxacin, saraH=sarafloxacin, bpdc=4,4 Prime -biphenyldicarboxylate, odpa=4,4 Prime -oxydiphthalate, bpta=3,3 Prime ,4,4 Prime -biphenyltetracarboxylate) have been synthesized and characterized. Compounds 1-3 consist of 2D arm-shaped layers based on the 1D {l_brace}M(COO){r_brace}{sub n}{sup n+} chains. Compounds 4 and 5 display 2D structures based on tetranuclear manganese or cobalt clusters with (3,6)-connected kgd topology. Compound 6 exhibits a 2D bilayer structure, which represents the first example of metal-quinolone complexes with 2D bilayer structure. By inspection of the structures of 1-6, it is believed that the long aromatic polycarboxylate ligands are important for the formation of 2D metal-quinolone complexes. The magnetic properties of compounds 3-6 was studied, indicating the existence of antiferromagnetic interactions. Furthermore, the luminescent properties of compounds 1-2 are discussed. - Graphical abstract: Six novel 2D metal-quinolone complexes have been prepared by self-assemblies of the quinolones and metal salts in the presence of long aromatic polycarboxylates. Highlights: Black-Right-Pointing-Pointer Compounds 1-3 consist of novel 2D arm-shaped layers based on the 1D {l_brace}M(COO){r_brace}{sub n}{sup n+} chains. Black-Right-Pointing-Pointer Compounds 4 and 5 are two novel 2D layers based on tetranuclear Mn or Co clusters with kgd topology. Black-Right-Pointing-Pointer Compound 6 is the first example of metal-quinolone complexes with 2D bilayer structure. Black-Right-Pointing-Pointer Compounds 1-6 represent six unusual

Hydrothermal synthesis, crystal structure, luminescent and magnetic properties of a new mononuclear GdIII coordination complex

Science.gov (United States)

Coban, Mustafa Burak

2018-06-01

A new GdIII coordination complex, {[Gd(2-stp)2(H2O)6].2(4,4'-bipy).4(H2O)}, complex 1, (2-stp = 2-sulfoterephthalate anion and 4,4'-bipy = 4,4'-bipyridine), has been synthesized by hydrothermal method and characterized by elemental analysis, solid state UV-Vis and FT-IR spectroscopy, single-crystal X-ray diffraction, solid state photoluminescence and variable-temperature magnetic measurements. The crystal structure determination shows that GdIII ions are eight coordinated and adopt a distorted square-antiprismatic geometry. Molecules interacting through intra- and intermolecular (O-H⋯O, O-H⋯N) hydrogen bonds in complex 1, give rise to 3D hydrogen bonded structure and the discrete lattice 4,4'-bipy molecules occupy the channel of the 3D structure. π-π stacking interactions also exist 4,4'-bipy-4,4'-bipy and 4,4'-bipy-2-stp molecule rings in 3D structures. Additionally, solid state photoluminescence properties of complex 1 at room temperature have been investigated. Under the excitation of UV light (at 349 nm), the complex 1 exhibited green emissions (at 505 nm) of GdIII ion in the visible region. Furthermore, Variable-temperature magnetic susceptibility and isothermal magnetization as function of external magnetic field studies reveal that complex 1 displays possible antiferromagnetic interaction.

The Similar Structures and Control Problems of Complex Systems

Institute of Scientific and Technical Information of China (English)

无

2002-01-01

In this paper, the naturally evolving complex systems, such as biotic and social ones, are considered. Focusing on their structures, a feature is noteworthy, i.e., the similarity in structures. The relations between the functions and behaviors of these systems and their similar structures will be studied. Owing to the management of social systems and the course of evolution of biotic systems may be regarded as control processes, the researches will be within the scope of control problems. Moreover, since it is difficult to model for biotic and social systems, it will start with the control problems of complex systems, possessing similar structures, in engineering.The obtained results show that for either linear or nonlinear systems and for a lot of control problemssimilar structures lead to a series of simplifications. In general, the original system may be decomposed into reduced amount of subsystems with lower dimensions and simpler structures. By virtue of such subsystems, the control problems of original system can be solved more simply.At last, it turns round to observe the biotic and social systems and some analyses are given.

A mononuclear zinc(II) complex with piroxicam: Crystal structure, DNA- and BSA-binding studies; in vitro cell cytotoxicity and molecular modeling of oxicam complexes

Science.gov (United States)

Jannesari, Zahra; Hadadzadeh, Hassan; Amirghofran, Zahra; Simpson, Jim; Khayamian, Taghi; Maleki, Batool

2015-02-01

A new mononuclear Zn(II) complex, trans-[Zn(Pir)2(DMSO)2], where Pir- is 4-hydroxy-2-methyl-N-2-pyridyl-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (piroxicam), has been synthesized and characterized. The crystal structure of the complex was obtained by the single crystal X-ray diffraction technique. The interaction of the complex with DNA and BSA was investigated. The complex interacts with FS-DNA by two binding modes, viz., electrostatic and groove binding (major and minor). The microenvironment and the secondary structure of BSA are changed in the presence of the complex. The anticancer effects of the seven complexes of oxicam family were also determined on the human K562 cell lines and the results showed reasonable cytotoxicities. The interactions of the oxicam complexes with BSA and DNA were modeled by molecular docking and molecular dynamic simulation methods.

Predicting protein complexes using a supervised learning method combined with local structural information.

Science.gov (United States)

Dong, Yadong; Sun, Yongqi; Qin, Chao

2018-01-01

The existing protein complex detection methods can be broadly divided into two categories: unsupervised and supervised learning methods. Most of the unsupervised learning methods assume that protein complexes are in dense regions of protein-protein interaction (PPI) networks even though many true complexes are not dense subgraphs. Supervised learning methods utilize the informative properties of known complexes; they often extract features from existing complexes and then use the features to train a classification model. The trained model is used to guide the search process for new complexes. However, insufficient extracted features, noise in the PPI data and the incompleteness of complex data make the classification model imprecise. Consequently, the classification model is not sufficient for guiding the detection of complexes. Therefore, we propose a new robust score function that combines the classification model with local structural information. Based on the score function, we provide a search method that works both forwards and backwards. The results from experiments on six benchmark PPI datasets and three protein complex datasets show that our approach can achieve better performance compared with the state-of-the-art supervised, semi-supervised and unsupervised methods for protein complex detection, occasionally significantly outperforming such methods.

Solving complex band structure problems with the FEAST eigenvalue algorithm

Science.gov (United States)

Laux, S. E.

2012-08-01

With straightforward extension, the FEAST eigenvalue algorithm [Polizzi, Phys. Rev. B 79, 115112 (2009)] is capable of solving the generalized eigenvalue problems representing traveling-wave problems—as exemplified by the complex band-structure problem—even though the matrices involved are complex, non-Hermitian, and singular, and hence outside the originally stated range of applicability of the algorithm. The obtained eigenvalues/eigenvectors, however, contain spurious solutions which must be detected and removed. The efficiency and parallel structure of the original algorithm are unaltered. The complex band structures of Si layers of varying thicknesses and InAs nanowires of varying radii are computed as test problems.

Phase behaviour and structure of stable complexes of oppositely charged polyelectrolytes

Science.gov (United States)

Mengarelli, V.; Auvray, L.; Zeghal, M.

2009-03-01

We study the formation and structure of stable electrostatic complexes between oppositely charged polyelectrolytes, a long polymethacrylic acid and a shorter polyethylenimine, at low pH, where the polyacid is weakly charged. We explore the phase diagram as a function of the charge and concentration ratio of the constituents. In agreement with theory, turbidity and ζ potential measurements show two distinct regimes of weak and strong complexation, which appear successively as the pH is increased and are separated by a well-defined limit. Weak complexes observed by neutron scattering and contrast matching have an open, non-compact structure, while strong complexes are condensed.

Structural properties and complexity of a new network class: Collatz step graphs.

Directory of Open Access Journals (Sweden)

Frank Emmert-Streib

Full Text Available In this paper, we introduce a biologically inspired model to generate complex networks. In contrast to many other construction procedures for growing networks introduced so far, our method generates networks from one-dimensional symbol sequences that are related to the so called Collatz problem from number theory. The major purpose of the present paper is, first, to derive a symbol sequence from the Collatz problem, we call the step sequence, and investigate its structural properties. Second, we introduce a construction procedure for growing networks that is based on these step sequences. Third, we investigate the structural properties of this new network class including their finite scaling and asymptotic behavior of their complexity, average shortest path lengths and clustering coefficients. Interestingly, in contrast to many other network models including the small-world network from Watts & Strogatz, we find that CS graphs become 'smaller' with an increasing size.

Structure of a WW domain-containing fragment of dystrophin complexed with {beta}-dystroglycan.

Energy Technology Data Exchange (ETDEWEB)

Huang, X.; Poy, F.; Zhang, R.; Joachimiak, A.; Sudol, M.; Eck, M. J.; Biosciences Division; Dana Farber Cancer Inst.; Harvard Medical School; Mount Sinai School of Medicine

2000-08-01

Dystrophin and {beta}-dystroglycan are components of the dystrophin--glycoprotein complex (DGC), a multimolecular assembly that spans the cell membrane and links the actin cytoskeleton to the extracellular basal lamina. Defects in the dystrophin gene are the cause of Duchenne and Becker muscular dystrophies. The C-terminal region of dystrophin binds the cytoplasmic tail of {beta}-dystroglycan, in part through the interaction of its WW domain with a proline-rich motif in the tail of {beta}-dystroglycan. Here we report the crystal structure of this portion of dystrophin in complex with the proline-rich binding site in {beta}-dystroglycan. The structure shows that the dystrophin WW domain is embedded in an adjacent helical region that contains two EF-hand-like domains. The {beta}-dystroglycan peptide binds a composite surface formed by the WW domain and one of these EF-hands. Additionally, the structure reveals striking similarities in the mechanisms of proline recognition employed by WW domains and SH3 domains.

Photonic crystals, light manipulation, and imaging in complex nematic structures

Science.gov (United States)

Ravnik, Miha; Å timulak, Mitja; Mur, Urban; Čančula, Miha; Čopar, Simon; Žumer, Slobodan

2016-03-01

Three selected approaches for manipulation of light by complex nematic colloidal and non-colloidal structures are presented using different own custom developed theoretical and modelling approaches. Photonic crystals bands of distorted cholesteric liquid crystal helix and of nematic colloidal opals are presented, also revealing distinct photonic modes and density of states. Light propagation along half-integer nematic disclinations is shown with changes in the light polarization of various winding numbers. As third, simulated light transmission polarization micrographs of nematic torons are shown, offering a new insight into the complex structure characterization. Finally, this work is a contribution towards using complex soft matter in optics and photonics for advanced light manipulation.

DNA complexes with Ni nanoparticles: structural and functional properties

Energy Technology Data Exchange (ETDEWEB)

Tatarinova, Olga N.; Smirnov, Igor P. [Research Institute for Physico-Chemical Medicine of the Federal Medical-Biological Agency of the Russian Federation (Russian Federation); Safenkova, Irina V. [A.N. Bach Institute of Biochemistry (Russian Federation); Varizhuk, Anna M.; Pozmogova, Galina E., E-mail: pozmge@gmail.com [Research Institute for Physico-Chemical Medicine of the Federal Medical-Biological Agency of the Russian Federation (Russian Federation)

2012-10-15

Supramolecular complexes of biopolymers based on magnetic nanoparticles play an important role in creation of biosensors, implementation of theragnostic and gene therapeutic methods and biosafety evaluation. We investigated the impact of DNA interactions with nanoparticles of nickel (nNi) on the integrity and functionality of DNA. Data obtained by mass spectrometry, electrophoresis, TEM and AFM microscopy techniques, bacterial transformation, and real-time PCR provide evidence that ssDNA and plasmid DNA (pDNA) efficiently form complexes with nNi. AFM data suggest that the complexes are necklace-type structures, in which nanoparticles are randomly distributed along the DNA chains, rather than highly entangled clot-type structures. After desorption, observed DNA characteristics in bioanalytical and biological systems remain unchanged. Only supercoiled pDNA was nicked, but remained, as well as a plasmid-nNi complex, active in expression vector assays. These results are very important for creation of new methods of DNA immobilization and controlled manipulation.

DNA complexes with Ni nanoparticles: structural and functional properties

International Nuclear Information System (INIS)

Tatarinova, Olga N.; Smirnov, Igor P.; Safenkova, Irina V.; Varizhuk, Anna M.; Pozmogova, Galina E.

2012-01-01

Supramolecular complexes of biopolymers based on magnetic nanoparticles play an important role in creation of biosensors, implementation of theragnostic and gene therapeutic methods and biosafety evaluation. We investigated the impact of DNA interactions with nanoparticles of nickel (nNi) on the integrity and functionality of DNA. Data obtained by mass spectrometry, electrophoresis, TEM and AFM microscopy techniques, bacterial transformation, and real-time PCR provide evidence that ssDNA and plasmid DNA (pDNA) efficiently form complexes with nNi. AFM data suggest that the complexes are necklace-type structures, in which nanoparticles are randomly distributed along the DNA chains, rather than highly entangled clot-type structures. After desorption, observed DNA characteristics in bioanalytical and biological systems remain unchanged. Only supercoiled pDNA was nicked, but remained, as well as a plasmid–nNi complex, active in expression vector assays. These results are very important for creation of new methods of DNA immobilization and controlled manipulation.

Searching for new thermoelectrics in chemically and structurally complex bismuth chalcogenides

Energy Technology Data Exchange (ETDEWEB)

Chung, D Y; Hogan, T; Schindler, J; Iordanidis, L; Brazis, P; Kannewurf, C R; Chen, B; Uher, C; Kanatzidis, M G

1997-07-01

A solid state chemistry synthetic approach towards identifying new materials with potentially superior thermoelectric properties is presented. Materials with complex compositions and structures also have complex electronic structures which may give rise to high thermoelectric powers and at the same time possess low thermal conductivities. The structures and thermoelectric properties of several new promising compounds with K-Bi-Se, K-Bi-S, Ba-Bi-Te, Cs-Bi-Te, and Rb-bi-Te are reported.

Synthesis, structures and properties of a series of manganese coordination complexes constructed from dicarboxylic fluorene derivatives

Energy Technology Data Exchange (ETDEWEB)

Li Xing, E-mail: lixing@nbu.edu.cn [State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211 (China); Zhao Xiuhua; Bing Yue; Zha Meiqin; Xie Hongzhen; Guo Zhiyong [State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211 (China)

2013-01-15

Assembly reactions of 9,9-diethylfluorene-2,7-dicarboxylic acid (H{sub 2}DFDC) and Mn(CH{sub 3}COO){sub 2}{center_dot}4H{sub 2}O or MnCl{sub 2}{center_dot}4H{sub 2}O by tuning of various secondary ligands such as 2,2 Prime -bipyridine (2,2 Prime -bpy), 4,4 Prime -bipyridine (4,4 Prime -bpy) or 1,3-bis(4-pyridyl)propane) (bpp), gave rise to four complexes {l_brace} [Mn{sub 2}(DFDC){sub 2}(DMF){sub 2}]{center_dot}H{sub 2}O{r_brace} {sub n} (1), [Mn(DFDC)(2,2 Prime -bpy)]{sub n} (2), {l_brace} [Mn{sub 2}(DFDC){sub 2}(4,4 Prime -bpy){sub 2}]{center_dot}2CH{sub 3}OH{r_brace} {sub n} (3), and {l_brace} [Mn{sub 4}(DFDC){sub 4}(bpp){sub 2}(CH{sub 3}OH){sub 3} (H{sub 2}O){sub 3}]{center_dot}3(CH{sub 3}OH){center_dot}3(H{sub 2}O){r_brace} {sub n} (4). Single crystal X-ray diffraction analysis reveal that complex 1 is three dimensional structure with rhombic channels filled by guest water molecules; 2 presents a close-packed structure with high thermal stability; 3 exhibits a three dimensional framework with micro-porous channels filled by guest methanol molecules and 4 is a two-dimensional structure. The photoluminescent properties of 1-4 have been studied, respectively, showing that the Mn(II) ions, accessorial organic ligands or crystal structures exert important influences on the photoluminescence emissions of H{sub 2}DFDC ligands. Thermogravimetric analysis show that the complexes have remarkably high thermal stability. Magnetic susceptibility measurements have been finished and discussed for the complexes. - Graphical abstract: Assembly of 9,9-diethylfluorene-2,7-dicarboxylic acid and Mn(II) salts by tuning of various accessorial ligands resulted in four manganese complexes with different topological frameworks. Highlights: Black-Right-Pointing-Pointer Four manganese complexes based on 9,9-diethylfluorene-2,7-dicarboxylic acid were obtained. Black-Right-Pointing-Pointer The complexes were structurally characterized by single-crystal X-ray diffraction. Black

Applying Statistical and Complex Network Methods to Explore the Key Signaling Molecules of Acupuncture Regulating Neuroendocrine-Immune Network

Directory of Open Access Journals (Sweden)

Kuo Zhang

2018-01-01

Full Text Available The mechanisms of acupuncture are still unclear. In order to reveal the regulatory effect of manual acupuncture (MA on the neuroendocrine-immune (NEI network and identify the key signaling molecules during MA modulating NEI network, we used a rat complete Freund’s adjuvant (CFA model to observe the analgesic and anti-inflammatory effect of MA, and, what is more, we used statistical and complex network methods to analyze the data about the expression of 55 common signaling molecules of NEI network in ST36 (Zusanli acupoint, and serum and hind foot pad tissue. The results indicate that MA had significant analgesic, anti-inflammatory effects on CFA rats; the key signaling molecules may play a key role during MA regulating NEI network, but further research is needed.

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

Science.gov (United States)

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-function relations in oxaloacetate decarboxylase complex. Fluorescence and infrared approaches to monitor oxomalonate and Na(+ binding effect.

Directory of Open Access Journals (Sweden)

Thierry Granjon

Full Text Available BACKGROUND: Oxaloacetate decarboxylase (OAD is a member of the Na(+ transport decarboxylase enzyme family found exclusively in anaerobic bacteria. OAD of Vibrio cholerae catalyses a key step in citrate fermentation, converting the chemical energy of the decarboxylation reaction into an electrochemical gradient of Na(+ ions across the membrane, which drives endergonic membrane reactions such as ATP synthesis, transport and motility. OAD is a membrane-bound enzyme composed of alpha, beta and gamma subunits. The alpha subunit contains the carboxyltransferase catalytic site. METHODOLOGY/PRINCIPAL FINDINGS: In this report, spectroscopic techniques were used to probe oxomalonate (a competitive inhibitor of OAD with respect to oxaloacetate and Na(+ effects on the enzyme tryptophan environment and on the secondary structure of the OAD complex, as well as the importance of each subunit in the catalytic mechanism. An intrinsic fluorescence approach, Red Edge Excitation Shift (REES, indicated that solvent molecule mobility in the vicinity of OAD tryptophans was more restricted in the presence of oxomalonate. It also demonstrated that, although the structure of OAD is sensitive to the presence of NaCl, oxomalonate was able to bind to the enzyme even in the absence of Na(+. REES changes due to oxomalonate binding were also observed with the alphagamma and alpha subunits. Infrared spectra showed that OAD, alphagamma and alpha subunits have a main component band centered between 1655 and 1650 cm(-1 characteristic of a high content of alpha helix structures. Addition of oxomalonate induced a shift of the amide-I band of OAD toward higher wavenumbers, interpreted as a slight decrease of beta sheet structures and a concomitant increase of alpha helix structures. Oxomalonate binding to alphagamma and alpha subunits also provoked secondary structure variations, but these effects were negligible compared to OAD complex. CONCLUSION: Oxomalonate binding affects the

CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.

Science.gov (United States)

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.

Optimal map of the modular structure of complex networks

International Nuclear Information System (INIS)

Arenas, A; Borge-Holthoefer, J; Gomez, S; Zamora-Lopez, G

2010-01-01

The modular structure is pervasive in many complex networks of interactions observed in natural, social and technological sciences. Its study sheds light on the relation between the structure and the function of complex systems. Generally speaking, modules are islands of highly connected nodes separated by a relatively small number of links. Every module can have the contributions of links from any node in the network. The challenge is to disentangle these contributions to understand how the modular structure is built. The main problem is that the analysis of a certain partition into modules involves, in principle, as much data as the number of modules times the number of nodes. To confront this challenge, here we first define the contribution matrix, the mathematical object containing all the information about the partition of interest, and then we use truncated singular value decomposition to extract the best representation of this matrix in a plane. The analysis of this projection allows us to scrutinize the skeleton of the modular structure, revealing the structure of individual modules and their interrelations.

Model-based flaw localization from perturbations in the dynamic response of complex mechanical structures

Energy Technology Data Exchange (ETDEWEB)

Chambers, D H

2009-02-24

A new method of locating structural damage using measured differences in vibrational response and a numerical model of the undamaged structure has been presented. This method is particularly suited for complex structures with little or no symmetry. In a prior study the method successively located simulated damage from measurements of the vibrational response on two simple structures. Here we demonstrate that it can locate simulated damage in a complex structure. A numerical model of a complex structure was used to calculate the structural response before and after the introduction of a void. The method can now be considered for application to structures of programmatic interest. It could be used to monitor the structural integrity of complex mechanical structures and assemblies over their lifetimes. This would allow early detection of damage, when repair is relatively easy and inexpensive. It would also allow one to schedule maintenance based on actual damage instead of a time schedule.

Three-Dimentional Structures of Autophosphorylation Complexes in Crystals of Protein Kinases

KAUST Repository

Dumbrack, Roland

2016-01-26

Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Several autophosphorylation complexes have been identified in crystals of protein kinases, with a known serine, threonine, or tyrosine autophosphorylation site of one kinase monomer sitting in the active site of another monomer of the same protein in the crystal. We utilized a structural bioinformatics method to identify all such autophosphorylation complexes in X-ray crystallographic structures in the Protein Data Bank (PDB) by generating all unique kinase/kinase interfaces within and between asymmetric units of each crystal and measuring the distance between the hydroxyl oxygen of potential autophosphorylation sites and the oxygen atoms of the active site aspartic acid residue side chain. We have identified 15 unique autophosphorylation complexes in the PDB, of which 5 complexes have not previously been described in the relevant publications on the crystal structures (N-terminal juxtamembrane regions of CSF1R and EPHA2, activation loop tyrosines of LCK and IGF1R, and a serine in a nuclear localization signal region of CLK2. Mutation of residues in the autophosphorylation complex interface of LCK either severely impaired autophosphorylation or increased it. Taking the autophosphorylation complexes as a whole and comparing them with peptide-substrate/kinase complexes, we observe a number of important features among them. The novel and previously observed autophosphorylation sites are conserved in many kinases, indicating that by homology we can extend the relevance of these complexes to many other clinically relevant drug targets.

Vibrational spectroscopy and structural analysis of complex uranium compounds (review)

International Nuclear Information System (INIS)

Umreiko, D.S.; Nikanovich, M.V.

1985-01-01

The paper reports on the combined application of experimental and theoretical methods of vibrational spectroscopy together with low-temperature luminescence data to determine the characteristic features of the formation and structure of complex systems, not only containing ligands directly coordinated to the CA uranium, but also associated with the extraspherical polyatomic electrically charged particles: organic cations. These include uranyl complexes and heterocyclical amines. Studied here were compounds of tetra-halouranylates with pyridine and its derivates, as well as dipyridyl, quinoline and phenanthroline. Structural schemes are also proposed for other uranyl complexes with protonated heterocyclical amines with a more complicated composition, which correctly reflect their spectroscopic properties

Structural dynamics of a noncovalent charge transfer complex from femtosecond stimulated Raman spectroscopy.

Science.gov (United States)

Fujisawa, Tomotsumi; Creelman, Mark; Mathies, Richard A

2012-09-06

Femtosecond stimulated Raman spectroscopy is used to examine the structural dynamics of photoinduced charge transfer within a noncovalent electron acceptor/donor complex of pyromellitic dianhydride (PMDA, electron acceptor) and hexamethylbenzene (HMB, electron donor) in ethylacetate and acetonitrile. The evolution of the vibrational spectrum reveals the ultrafast structural changes that occur during the charge separation (Franck-Condon excited state complex → contact ion pair) and the subsequent charge recombination (contact ion pair → ground state complex). The Franck-Condon excited state is shown to have significant charge-separated character because its vibrational spectrum is similar to that of the ion pair. The charge separation rate (2.5 ps in ethylacetate and ∼0.5 ps in acetonitrile) is comparable to solvation dynamics and is unaffected by the perdeuteration of HMB, supporting the dominant role of solvent rearrangement in charge separation. On the other hand, the charge recombination slows by a factor of ∼1.4 when using perdeuterated HMB, indicating that methyl hydrogen motions of HMB mediate the charge recombination process. Resonance Raman enhancement of the HMB vibrations in the complex reveals that the ring stretches of HMB, and especially the C-CH(3) deformations are the primary acceptor modes promoting charge recombination.

Structural basis for energy transduction by respiratory alternative complex III.

Science.gov (United States)

Sousa, Joana S; Calisto, Filipa; Langer, Julian D; Mills, Deryck J; Refojo, Patrícia N; Teixeira, Miguel; Kühlbrandt, Werner; Vonck, Janet; Pereira, Manuela M

2018-04-30

Electron transfer in respiratory chains generates the electrochemical potential that serves as energy source for the cell. Prokaryotes can use a wide range of electron donors and acceptors and may have alternative complexes performing the same catalytic reactions as the mitochondrial complexes. This is the case for the alternative complex III (ACIII), a quinol:cytochrome c/HiPIP oxidoreductase. In order to understand the catalytic mechanism of this respiratory enzyme, we determined the structure of ACIII from Rhodothermus marinus at 3.9 Å resolution by single-particle cryo-electron microscopy. ACIII presents a so-far unique structure, for which we establish the arrangement of the cofactors (four iron-sulfur clusters and six c-type hemes) and propose the location of the quinol-binding site and the presence of two putative proton pathways in the membrane. Altogether, this structure provides insights into a mechanism for energy transduction and introduces ACIII as a redox-driven proton pump.

Remedial Strategies in Structural Proteomics: Expression, Purification, And Crystallization of the Vav1/Rac1 Complex

Energy Technology Data Exchange (ETDEWEB)

Brooun, A.; Foster, S.A.; Chrencik, H.E.; Chien, E.Y.T.; Kolatkar, A.R.; Streiff, M.; Ramage, P.; Widmer, H.; Weckbecker, G.; Kuhn, P.

2007-07-03

The signal transduction pathway involving the Vav1 guanine nucleotide exchange factor (GEF) and the Rac1 GTPase plays several key roles in the immune response mediated by the T cell receptor. Vav1 is also a unique member of the GEF family in that it contains a cysteine-rich domain (CRD) that is critical for Rac1 binding and maximal guanine nucleotide exchange activity, and thus may provide a unique protein-protein interface compared to other GEF/GTPase pairs. Here, we have applied a number of remedial structural proteomics strategies, such as construct and expression optimization, surface mutagenesis, limited proteolysis, and protein formulation to successfully express, purify, and crystallize the Vav1-DH-PH-CRD/Rac1 complex in an active conformation. We have also systematically characterized various Vav1 domains in a GEF assay and Rac1 in vitro binding experiments. In the context of Vav1-DH-PH-CRD, the zinc finger motif of the CRD is required for the expression of stable Vav1, as well as for activity in both a GEF assay and in vitro formation of a Vav1/Rac1 complex suitable for biophysical and structural characterization. Our data also indicate that the isolated CRD maintains a low level of specific binding to Rac1, appears to be folded based on 1D NMR analysis and coordinates two zinc ions based on ICP-MS analysis. The protein reagents generated here are essential tools for the determination of a three dimensional Vav1/Rac1 complex crystal structure and possibly for the identification of inhibitors of the Vav1/Rac1 protein-protein interaction with potential to inhibit lymphocyte activation.

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

Energy Technology Data Exchange (ETDEWEB)

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.; Campbell, Elizabeth A.

2017-07-13

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.

A Key Event Path Analysis Approach for Integrated Systems

Directory of Open Access Journals (Sweden)

Jingjing Liao

2012-01-01

Full Text Available By studying the key event paths of probabilistic event structure graphs (PESGs, a key event path analysis approach for integrated system models is proposed. According to translation rules concluded from integrated system architecture descriptions, the corresponding PESGs are constructed from the colored Petri Net (CPN models. Then the definitions of cycle event paths, sequence event paths, and key event paths are given. Whereafter based on the statistic results after the simulation of CPN models, key event paths are found out by the sensitive analysis approach. This approach focuses on the logic structures of CPN models, which is reliable and could be the basis of structured analysis for discrete event systems. An example of radar model is given to characterize the application of this approach, and the results are worthy of trust.

Crystal Structure of Botulinum Neurotoxin A2 in Complex with the Human Protein Receptor SV2C Reveals Plasticity in Receptor Binding

Directory of Open Access Journals (Sweden)

Robert Gustafsson

2018-04-01

Full Text Available Botulinum neurotoxins (BoNTs are a family of highly dangerous bacterial toxins, with seven major serotypes (BoNT/A-G. Members of BoNTs, BoNT/A1 and BoNT/B1, have been utilized to treat an increasing number of medical conditions. The clinical trials are ongoing for BoNT/A2, another subtype of BoNT/A, which showed promising therapeutic properties. Both BoNT/A1 and BoNT/A2 utilize three isoforms of synaptic vesicle protein SV2 (SV2A, B, and C as their protein receptors. We here present a high resolution (2.0 Å co-crystal structure of the BoNT/A2 receptor-binding domain in complex with the human SV2C luminal domain. The structure is similar to previously reported BoNT/A-SV2C complexes, but a shift of the receptor-binding segment in BoNT/A2 rotates SV2C in two dimensions giving insight into the dynamic behavior of the interaction. Small differences in key residues at the binding interface may influence the binding to different SV2 isoforms, which may contribute to the differences between BoNT/A1 and BoNT/A2 observed in the clinic.

A monomeric copper-phosphoramide complex: synthesis, structure, and electronic properties

Czech Academy of Sciences Publication Activity Database

Henriques, Margarida Isabel Sousa; Gorbunov, D.I.; Ponomaryov, A.Y.; Saneei, A.; Pourayoubi, M.; Dušek, Michal; Zvyagin, S.; Uhlarz, M.; Wosnitza, J.

2016-01-01

Roč. 118, Nov (2016), s. 154-158 ISSN 0277-5387 R&D Projects: GA ČR(CZ) GA14-03276S; GA MŠk LO1603 EU Projects: European Commission(XE) CZ.2.16/3.1.00/24510 Institutional support: RVO:68378271 Keywords : phosphoramide * magnetization * EPR * mononuclear copper complex * crystal structure Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.926, year: 2016

Structure of valinomycin and its complexes

Czech Academy of Sciences Publication Activity Database

Hašek, Jindřich; Makrlík, E.; Dušek, Michal; Císařová, I.; Dohnálek, Jan; Dušková, Jarmila; Skálová, Tereza

2009-01-01

Roč. 16, 2a (2009), s. 30-31 ISSN 1211-5894. [Struktura - Colloquium of Czech and Slovak Crystallographic Association. Hluboká nad Vltavou, 22.06.2009-25.06.2009] R&D Projects: GA ČR GA305/07/1073; GA AV ČR IAA500500701 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z10100521 Keywords : valinomycin * complex * structure 8 hydration Subject RIV: CD - Macromolecular Chemistry

Structural insight into the UNC-45–myosin complex

DEFF Research Database (Denmark)

Fratev, Filip; Jonsdottir, Svava Osk; Pajeva, Ilza

2013-01-01

The UNC-45 chaperone protein interacts with and affects the folding, stability, and the ATPase activity of myosins. It plays a critical role in the cardiomyopathy development and in the breast cancer tumor growth. Here we propose the first structural model of the UNC-45–myosin complex using various...... is mainly stabilized by electrostatic interactions. Remarkably, the contact surface area is similar to that of the myosinactin complex. A significant interspecies difference in the myosin binding epitope is observed. Our results reveal the structural basis of MYH7 exons 15–16 hypertrophic cardiomyopathy...... mutations and provide directions for drug targeting. © 2013 Wiley Periodicals, Inc....

Synthesis, structures, and luminescent properties of lanthanide complexes with triphenylphospine oxide

Energy Technology Data Exchange (ETDEWEB)

Ma, Yan; Xu, Shan; Wang, Xin; Li, Yue-Xue; Jin, Qiong-Hua [Department of Chemistry, Capital Normal University, Beijing (China); Liu, Min [The College of Materials Science and Engineering, Beijing University of Technology (China); Xin, Xiu-Lan [School of Food and Chemical Engineering, Beijing Technology and Business University (China)

2017-07-03

Seven lanthanide complexes [Ln(OPPh{sub 3}){sub 3}(NO{sub 3}){sub 3}] (1-3) (OPPh{sub 3} = triphenylphosphine oxide, Ln = Nd, Sm, Gd), [Dy(OPPh{sub 3}){sub 4}(NO{sub 3}){sub 2}](NO{sub 3}) (4), [Ln(OPPh{sub 3}){sub 3}(NO{sub 3}){sub 3}]{sub 2} (5-7) (Ln = Pr, Eu, Gd) were synthesized by the reactions of different lanthanide salts and OPPh{sub 3} ligand in the air. These complexes were characterized by single-crystal X-ray diffraction analysis, elemental analysis, IR and fluorescence spectra. Structure analysis shows that complexes 1-4 are mononuclear complexes formed by OPPh{sub 3} ligands and nitrates. The asymmetric units of complexes 5-7 consist of two crystallographic-separate molecules. Complex 1 is self-assembled to construct a 2D layer-structure of (4,4) net topology by hydrogen bond interactions. The other complexes show a 1D chain-like structure that was assembled by OPPh{sub 3} ligands and nitrate ions through C-H..O interactions. Solid emission spectra of compounds 4 and 6 are assigned to the characteristic fluorescence of Tb{sup 3+} (λ{sub em} = 480, 574 nm) and Eu{sup 3+} (λ{sub em} = 552, 593, 619, 668 nm). (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Coupling Analysis of Low-Speed Multiphase Flow and High-Frequency Electromagnetic Field in a Complex Pipeline Structure

Directory of Open Access Journals (Sweden)

Xiaokai Huo

2014-01-01

Full Text Available Accurate estimation of water content in an oil-water mixture is a key technology in oil exploration and production. Based on the principles of the microwave transmission line (MTL, the logging probe is an important water content measuring apparatus. However, the effects of mixed fluid flow on the measurement of electromagnetic field parameters are rarely considered. This study presents the coupling model for low-speed multiphase flow and high-frequency electromagnetic field in a complex pipeline structure. We derived the S-parameter equations for the stratified oil/water flow model. The corresponding relationship between the S-parameters and water holdup is established. Evident coupling effects of the fluid flow and the electromagnetic field are confirmed by comparing the calculated S-parameters for both stratified and homogeneous flow patterns. In addition, a multiple-solution problem is analyzed for the inversion of dielectric constant from the S-parameters. The most sensitive phase angle range is determined to improve the detection of variation in the dielectric constant. Suggestions are proposed based on the influence of the oil/water layer on measurement sensitivity to optimize the geometric parameters of a device structure. The method proposed elucidates how accuracy and sensitivity can be improved in water holdup measurements under high water content conditions.

EM structure of a helicase-loader complex depicting a 6:2 binding sub-stoichiometry from Geobacillus kaustophilus HTA426

International Nuclear Information System (INIS)

Lin, Yen-Chen; Naveen, Vankadari; Hsiao, Chwan-Deng

2016-01-01

During DNA replication, bacterial helicase is recruited as a complex in association with loader proteins to unwind the parental duplex. Previous structural studies have reported saturated 6:6 helicase-loader complexes with different conformations. However, structural information on the sub-stoichiometric conformations of these previously-documented helicase-loader complexes remains elusive. Here, with the aid of single particle electron-microscopy (EM) image reconstruction, we present the Geobacillus kaustophilus HTA426 helicase-loader (DnaC-DnaI) complex with a 6:2 binding stoichiometry in the presence of ATPγS. In the 19 Å resolution EM map, the undistorted and unopened helicase ring holds a robust loader density above the C-terminal RecA-like domain. Meanwhile, the path of the central DNA binding channel appears to be obstructed by the reconstructed loader density, implying its potential role as a checkpoint conformation to prevent the loading of immature complex onto DNA. Our data also reveals that the bound nucleotides and the consequently induced conformational changes in the helicase hexamer are essential for active association with loader proteins. These observations provide fundamental insights into the formation of the helicase-loader complex in bacteria that regulates the DNA replication process. - Highlights: • Helicase-loader complex structure with 6:2 sub-stoichiometry is resolved by EM. • Helicase hexamer in 6:2 sub-stoichiometry is constricted and un-opened. • 6:2 binding ratio of helicase-loader complex could act as a DNA loading checkpoint. • Nucleotides stabilize helicase-loader complex at low protein concentrations.

EM structure of a helicase-loader complex depicting a 6:2 binding sub-stoichiometry from Geobacillus kaustophilus HTA426

Energy Technology Data Exchange (ETDEWEB)

Lin, Yen-Chen [Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan (China); Naveen, Vankadari [Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan (China); Molecular Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica, and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan (China); Hsiao, Chwan-Deng, E-mail: hsiao@gate.sinica.edu.tw [Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan (China); Molecular Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica, and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan (China)

2016-04-22

During DNA replication, bacterial helicase is recruited as a complex in association with loader proteins to unwind the parental duplex. Previous structural studies have reported saturated 6:6 helicase-loader complexes with different conformations. However, structural information on the sub-stoichiometric conformations of these previously-documented helicase-loader complexes remains elusive. Here, with the aid of single particle electron-microscopy (EM) image reconstruction, we present the Geobacillus kaustophilus HTA426 helicase-loader (DnaC-DnaI) complex with a 6:2 binding stoichiometry in the presence of ATPγS. In the 19 Å resolution EM map, the undistorted and unopened helicase ring holds a robust loader density above the C-terminal RecA-like domain. Meanwhile, the path of the central DNA binding channel appears to be obstructed by the reconstructed loader density, implying its potential role as a checkpoint conformation to prevent the loading of immature complex onto DNA. Our data also reveals that the bound nucleotides and the consequently induced conformational changes in the helicase hexamer are essential for active association with loader proteins. These observations provide fundamental insights into the formation of the helicase-loader complex in bacteria that regulates the DNA replication process. - Highlights: • Helicase-loader complex structure with 6:2 sub-stoichiometry is resolved by EM. • Helicase hexamer in 6:2 sub-stoichiometry is constricted and un-opened. • 6:2 binding ratio of helicase-loader complex could act as a DNA loading checkpoint. • Nucleotides stabilize helicase-loader complex at low protein concentrations.

Advances in the understanding of the BBSome complex structure and function

Directory of Open Access Journals (Sweden)

Hernandez-Hernandez V

2015-10-01

Full Text Available Victor Hernandez-Hernandez, Dagan JenkinsGenetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UKAbstract: Bardet–Biedl syndrome (BBS is an autosomal recessive condition characterized by important clinical features, including obesity, blindness, renal cystic disease, and intellectual disability. BBS is caused by mutations in >20 genes, a subset of which form the so-called BBSome. The BBSome is a complex that coats intracellular vesicles and interacts with key proteins, such as small GTPases, that regulate the trafficking of these vesicles to the base of cilia. Cilia are microtubular protusions present on the surface of most cells that are defective in a key group of disorders known as ciliopathies, of which BBS is one. BBSome components particularly localize to the basal body of cilia, and also centrosomes, where they interact with pericentriolar material proteins that regulate their function. The BBSome also facilitates the transport of key cargo within cilia by acting as an adaptor protein for intraflagellar transport complexes, and as such BBS mutations lead to a variety of functional defects in cilia in a tissue- and cell-type-specific manner. This might include defects in photoreceptor trafficking linked to the connecting cilium, abnormal hedgehog signaling within bone, and aberrant calcium signaling in response to fluid flow along renal tubules, although the precise mechanisms are still not completely understood. Taken together, the BBSome is an important complex that may be targeted for treatment of a variety of common and important disorders, and understanding the precise function of the BBSome will be essential to capitalize on this translationally.Keywords: retinitis pigmentosa GTPase regulator, polycystin, disrupted in schizophrenia 1, Hedgehog signaling, calcium signaling, photoreceptors

Thermodynamics and Structure of Actinide(IV) Complexes with Nitrilotriacetic Acid

Energy Technology Data Exchange (ETDEWEB)

Bonin, L.; Guillaumont, D.; Jeanson, A.; Den Auwer, C.; Moisy, Ph. [CEA Marcoule, DEN, DRCP, SCPS, F-30207 Bagnols Sur Ceze (France); Grigoriev, M. [RAS, AN Frumkin Inst Phys Chem and Electrochem, Moscow 119991 (Russian Federation); Berthet, J.C. [CEA Saclay, DSM, IRAMIS, URA 331, Serv Chim Mol, CNRS, F-91191 Gif Sur Yvette (France); Hennig, C.; Scheinost, A. [Forschungszentrum Dresden Rossendorf, Inst Radiochem, D-01314 Dresden (Germany)

2009-05-15

Nitrilotriacetic acid, commonly known as NITA (N(CH{sub 2}CO{sub 2}H){sub 3}), can be considered a representative of the polyamino-carboxylic family. The results presented in this paper describe the thermodynamical complexation and structural investigation of An(IV) complexes with NTA in aqueous solution. In the first part, the stability constants of the An(IV) complexes (An = Pu, Np, U, and Th) have been determined by spectrophotometry. In the second part, the coordination spheres of the actinide cation in these complexes have been described using extended X-ray absorption fine structure spectroscopy and compared to the solid-state structure of (Hpy){sub 2}[U(NTA){sub 2}].H{sub 2}O. These data are further compared to quantum chemical calculations, and their evolution across the actinide series is discussed. In particular, an interpretation of the role of the nitrogen atom in the coordination mode is proposed. These results are considered to be model behavior of polyamino-carboxylic ligands such as diethylenetriamine pentaacetic acid, which is nowadays the best candidate for a chelating agent in the framework of actinide decorporation for the human body. (authors)

Electronic structure of the [MNH2]+ (M = Sc-Cu) complexes.

Science.gov (United States)

Hendrickx, Marc F A; Clima, Sergiu

2006-11-23

B3LYP geometry optimizations for the [MNH2]+ complexes of the first-row transition metal cations (Sc+-Cu+) were performed. Without any exception the ground states of these unsaturated amide complexes were calculated to possess planar geometries. CASPT2 binding energies that were corrected for zero-point energies and including relativistic effects show a qualitative trend across the series that closely resembles the experimental observations. The electronic structures for the complexes of the early and middle transition metal cations (Sc+-Co+) differ from the electronic structures derived for the complexes of the late transition metal cations (Ni+ and Cu+). For the former complexes the relative higher position of the 3d orbitals above the singly occupied 2p(pi) HOMO of the uncoordinated NH2 induces an electron transfer from the 3d shell to 2p(pi). The stabilization of the 3d orbitals from the left to the right along the first-row transition metal series causes these orbitals to become situated below the HOMO of the NH2 ligand for Ni+ and Cu+, preventing a transfer from occurring in the [MNH2]+ complexes of these metal cations. Analysis of the low-lying states of the amide complexes revealed a rather unique characteristic of their electronic structures that was found across the entire series. Rather exceptionally for the whole of chemistry, pi-type interactions were calculated to be stronger than the corresponding sigma-type interactions. The origin of this extraordinary behavior can be ascribed to the low-lying sp2 lone pair orbital of the NH2 ligand with respect to the 3d level.

NMR study of structure of lanthanide complexes in solution

International Nuclear Information System (INIS)

Choppin, G.R.

1976-01-01

The diagnostic value PMR studies of diamagnetic lanthanide complexes to define the nature of the species in the lanthanide-pyruvate system is discussed. The use of NMR spectra of both diamagnetic and paramagnetic lanthanide complexes to obtain detailed structural information is reviewed

Spatial Patterns in Herbivory on a Coral Reef Are Influenced by Structural Complexity but Not by Algal Traits

Science.gov (United States)

Vergés, Adriana; Vanderklift, Mathew A.; Doropoulos, Christopher; Hyndes, Glenn A.

2011-01-01

Background Patterns of herbivory can alter the spatial structure of ecosystems, with important consequences for ecosystem functions and biodiversity. While the factors that drive spatial patterns in herbivory in terrestrial systems are well established, comparatively less is known about what influences the distribution of herbivory in coral reefs. Methodology and Principal Findings We quantified spatial patterns of macroalgal consumption in a cross-section of Ningaloo Reef (Western Australia). We used a combination of descriptive and experimental approaches to assess the influence of multiple macroalgal traits and structural complexity in establishing the observed spatial patterns in macroalgal herbivory, and to identify potential feedback mechanisms between herbivory and macroalgal nutritional quality. Spatial patterns in macroalgal consumption were best explained by differences in structural complexity among habitats. The biomass of herbivorous fish, and rates of herbivory were always greater in the structurally-complex coral-dominated outer reef and reef flat habitats, which were also characterised by high biomass of herbivorous fish, low cover and biomass of macroalgae and the presence of unpalatable algae species. Macroalgal consumption decreased to undetectable levels within 75 m of structurally-complex reef habitat, and algae were most abundant in the structurally-simple lagoon habitats, which were also characterised by the presence of the most palatable algae species. In contrast to terrestrial ecosystems, herbivory patterns were not influenced by the distribution, productivity or nutritional quality of resources (macroalgae), and we found no evidence of a positive feedback between macroalgal consumption and the nitrogen content of algae. Significance This study highlights the importance of seascape-scale patterns in structural complexity in determining spatial patterns of macroalgal consumption by fish. Given the importance of herbivory in maintaining the

Spatial patterns in herbivory on a coral reef are influenced by structural complexity but not by algal traits.

Directory of Open Access Journals (Sweden)

Adriana Vergés

2011-02-01

Full Text Available Patterns of herbivory can alter the spatial structure of ecosystems, with important consequences for ecosystem functions and biodiversity. While the factors that drive spatial patterns in herbivory in terrestrial systems are well established, comparatively less is known about what influences the distribution of herbivory in coral reefs.We quantified spatial patterns of macroalgal consumption in a cross-section of Ningaloo Reef (Western Australia. We used a combination of descriptive and experimental approaches to assess the influence of multiple macroalgal traits and structural complexity in establishing the observed spatial patterns in macroalgal herbivory, and to identify potential feedback mechanisms between herbivory and macroalgal nutritional quality. Spatial patterns in macroalgal consumption were best explained by differences in structural complexity among habitats. The biomass of herbivorous fish, and rates of herbivory were always greater in the structurally-complex coral-dominated outer reef and reef flat habitats, which were also characterised by high biomass of herbivorous fish, low cover and biomass of macroalgae and the presence of unpalatable algae species. Macroalgal consumption decreased to undetectable levels within 75 m of structurally-complex reef habitat, and algae were most abundant in the structurally-simple lagoon habitats, which were also characterised by the presence of the most palatable algae species. In contrast to terrestrial ecosystems, herbivory patterns were not influenced by the distribution, productivity or nutritional quality of resources (macroalgae, and we found no evidence of a positive feedback between macroalgal consumption and the nitrogen content of algae.This study highlights the importance of seascape-scale patterns in structural complexity in determining spatial patterns of macroalgal consumption by fish. Given the importance of herbivory in maintaining the ability of coral reefs to reorganise and

Bim Automation: Advanced Modeling Generative Process for Complex Structures

Science.gov (United States)

Banfi, F.; Fai, S.; Brumana, R.

2017-08-01

The new paradigm of the complexity of modern and historic structures, which are characterised by complex forms, morphological and typological variables, is one of the greatest challenges for building information modelling (BIM). Generation of complex parametric models needs new scientific knowledge concerning new digital technologies. These elements are helpful to store a vast quantity of information during the life cycle of buildings (LCB). The latest developments of parametric applications do not provide advanced tools, resulting in time-consuming work for the generation of models. This paper presents a method capable of processing and creating complex parametric Building Information Models (BIM) with Non-Uniform to NURBS) with multiple levels of details (Mixed and ReverseLoD) based on accurate 3D photogrammetric and laser scanning surveys. Complex 3D elements are converted into parametric BIM software and finite element applications (BIM to FEA) using specific exchange formats and new modelling tools. The proposed approach has been applied to different case studies: the BIM of modern structure for the courtyard of West Block on Parliament Hill in Ottawa (Ontario) and the BIM of Masegra Castel in Sondrio (Italy), encouraging the dissemination and interaction of scientific results without losing information during the generative process.

Preparation and structural studies on organotin(IV) complexes with flavonoids

International Nuclear Information System (INIS)

Nagy, L.; Christy, A.A.; Sletten, E.; Andersen, Q.M.; Edelmann, F.T.

1998-01-01

Fourteen complexes of di-n-butyltin(IV) 2+ cations with flavonoid glycosides (rutin, hesperidin, 2',4',3-trihydroxy-5',4-dimetoxychalkone 4-rutinoside) and flavonoid aglycones (quercetin, morin, hesperitin and sorte flavones) were prepared. The composition of the complexes was determined by standard analytical methods. The results showed that complexes containing diorganotin(IV) 2+ moiety and the ligand in 1:1, 2:1 or 3:1 ratio are formed. The FTIR spectra were consistent with the presence of Sn-O (phenol or carbohydrate) vibration in the compounds. The structure of the complexes was measured by Moessbauer spectroscopy. Comparison of the experimental quadrupole splitting with those calculated on the basis of partial quadrupole splitting concept revealed that the complexes are of four types: with the central tin atoms surrounded by donor atoms in a purely trigonal-bipyramidal, octahedral+trigonal-bipyramidal, trigonal-bipyramidal+tetrahedral and octahedral+tetrahedral arrangement. This procedure also distinguished between the different structural isomers of both trigonal-bipyramidal and octahedral complexes. Conclusions could therefore be drawn on the factors determining which of the isomers are formed in the systems. The Moessbauer parameters obtained for organotin(IV)-flavonoid complexes were compared with those measured for organotin(IV)-carbohydrate complexes. (author)

Is Phenomenal Consciousness a Complex Structure?

OpenAIRE

Stieg, Chuck

2004-01-01

Evolutionary explanations of psychological phenomena have become widespread. This paper examines a recent attempt by Nichols and Grantham (2000) to circumvent the problem of epiphenomenalism in establishing the selective status of consciousness. Nichols and Grantham (2000) argue that a case can be made for the view that consciousness is an adaptation based on its complexity. I set out this argument and argue that it fails to establish that phenomenal consciousness is a complex system. It ...

Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries

Energy Technology Data Exchange (ETDEWEB)

Pröpper, Kevin [University of Göttingen, (Germany); Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Meindl, Kathrin; Sammito, Massimo [Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Dittrich, Birger; Sheldrick, George M. [University of Göttingen, (Germany); Pohl, Ehmke, E-mail: ehmke.pohl@durham.ac.uk [Durham University, (United Kingdom); Usón, Isabel, E-mail: ehmke.pohl@durham.ac.uk [Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), (Spain); University of Göttingen, (Germany)

2014-06-01

The structure solution of DNA-binding protein structures and complexes based on the combination of location of DNA-binding protein motif fragments with density modification in a multi-solution frame is described. Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.

Uncertainty Quantification for Complex RF-structures Using the State-space Concatenation Approach

CERN Document Server

Heller, Johann; Schmidt, Christian; Van Rienen, Ursula

2015-01-01

as well as to employ robust optimizations, a so-called uncertainty quantification (UQ) is applied. For large and complex structures such computations are heavily demanding and cannot be carried out using standard brute-force approaches. In this paper, we propose a combination of established techniques to perform UQ for long and complex structures, where the uncertainty is located only in parts of the structure. As exemplary structure, we investigate the third-harmonic cavity, which is being used at the FLASH accelerator at DESY, assuming an uncertain...

The spectra of type IIB flux compactifications at large complex structure

International Nuclear Information System (INIS)

Brodie, Callum; Marsh, M.C. David

2016-01-01

We compute the spectra of the Hessian matrix, H, and the matrix M that governs the critical point equation of the low-energy effective supergravity, as a function of the complex structure and axio-dilaton moduli space in type IIB flux compactifications at large complex structure. We find both spectra analytically in an h − 1,2 +3 real-dimensional subspace of the moduli space, and show that they exhibit a universal structure with highly degenerate eigenvalues, independently of the choice of flux, the details of the compactification geometry, and the number of complex structure moduli. In this subspace, the spectrum of the Hessian matrix contains no tachyons, but there are also no critical points. We show numerically that the spectra of H and M remain highly peaked over a large fraction of the sampled moduli space of explicit Calabi-Yau compactifications with 2 to 5 complex structure moduli. In these models, the scale of the supersymmetric contribution to the scalar masses is strongly linearly correlated with the value of the superpotential over almost the entire moduli space, with particularly strong correlations arising for g s <1. We contrast these results with the expectations from the much-used continuous flux approximation, and comment on the applicability of Random Matrix Theory to the statistical modelling of the string theory landscape.

Analysis on complex structure stability under different bar angle with BIM technology

Directory of Open Access Journals (Sweden)

Wang Xiongjue

2016-03-01

Full Text Available Sun Valley, the landmark building of World Expo in Shanghai, which has free surface with single-layer reticulated shell structure, is a typical complex structure. CAD/CAM integrated information system to design is used for the complex structure; however, it is a very rigorous process to be used widely. The relevant technology of the Sun Valley is not open to the public at present, so we try to use BIM technology to model the Sun Valley, including architecture modelling and structure analysis. By analysis of the Sun Valley structure using this method, it is proved that the problems in modelling may be solved by writing some script codes in Rhino software and the stability of the model can also be analyzed. The new approach is viable and effective in combination with different softwares such as Rhino, Revit, and Midas in solution of the complex shaped surfaces’ structure for modelling and calculation.

Electronic structure and driving forces in β-cyclodextrin: Diclofenac inclusion complexes

International Nuclear Information System (INIS)

Bogdan, Diana; Morari, C.

2007-01-01

We investigate the geometry and electronic structure for complexes of β-cyclodextrin with diclofenac using DFT calculations. The effect of solvent is explicitly taken into account. This investigation allows us to draw meaningful conclusions upon the stability of the complex and the nature of the driving forces leading to the complexation process. In particular we emphasize the role of the water, by pointing out the changes in the solvent's electronic structure for different docking geometries

Structure identification and adaptive synchronization of uncertain general complex dynamical networks

International Nuclear Information System (INIS)

Xu Yuhua; Zhou Wuneng; Fang Jian'an; Lu Hongqian

2009-01-01

This Letter proposes an approach to identify the topological structure and unknown parameters for uncertain general complex networks simultaneously. By designing effective adaptive controllers, we achieve synchronization between two complex networks. The unknown network topological structure and system parameters of uncertain general complex dynamical networks are identified simultaneously in the process of synchronization. Several useful criteria for synchronization are given. Finally, an illustrative example is presented to demonstrate the application of the theoretical results.

Structure identification and adaptive synchronization of uncertain general complex dynamical networks

Energy Technology Data Exchange (ETDEWEB)

Xu Yuhua, E-mail: yuhuaxu2004@163.co [College of Information Science and Technology, Donghua University, Shanghai 201620 (China) and Department of Maths, Yunyang Teacher' s College, Hubei 442000 (China); Zhou Wuneng, E-mail: wnzhou@163.co [College of Information Science and Technology, Donghua University, Shanghai 201620 (China); Fang Jian' an [College of Information Science and Technology, Donghua University, Shanghai 201620 (China); Lu Hongqian [Shandong Institute of Light Industry, Shandong Jinan 250353 (China)

2009-12-28

This Letter proposes an approach to identify the topological structure and unknown parameters for uncertain general complex networks simultaneously. By designing effective adaptive controllers, we achieve synchronization between two complex networks. The unknown network topological structure and system parameters of uncertain general complex dynamical networks are identified simultaneously in the process of synchronization. Several useful criteria for synchronization are given. Finally, an illustrative example is presented to demonstrate the application of the theoretical results.

Synthesis and structure determination of a stable organometallic uranium(V) imine complex and its isolobal anionic U(IV)-ate complex

Energy Technology Data Exchange (ETDEWEB)

Sharma, M.; Botoshanskii, M.; Eisen, M.S. [Schulich Faculty of Chemistry, and Institute of Catalysis Science and Technology, Technion Israel Institute of Technology, Haifa (Israel); Bannenberg, Th.; Tamm, M. [Institut fur Anorganische und Analytische Chemie, Technische Universitat Braunschweig (Germany)

2010-06-15

The reaction of one equivalent of Cp*{sub 2}UCl{sub 2} with 2-(trimethylsilyl-imino)-1,3-di-tert-butyl-imidazoline in boiling toluene afforded a one electron oxidation of the uranium metal and the opening of the N-heterocyclic ring, resulting in the formation of an organometallic uranium(V) imine complex. This complex crystallized with one molecule of toluene in the unit cell, and its solid-state structure was determined by X-ray diffraction analysis. When the same reaction was performed in perdeuterated toluene, a myriad of organometallic complexes were obtained, however, when equimolar amounts of water were used in toluene, the same complex was obtained, and its solid state characterization shows two independent molecules in the unit cell with an additional water molecule. For comparison of the geometric parameters, the corresponding isolobal anionic uranium(IV) complex [Cp*{sub 2}UCl{sub 3}]{sup -} was synthesized by the reaction of Cp*{sub 2}UCl{sub 2} with 1,3-di-tert-butyl-imidazolium chloride, and the resulting U(IV)-ate complex was characterized by X-ray diffraction analysis. (authors)

Information structure and reference tracking in complex sentences

CERN Document Server

Gijn, Rik van; Matic, Dejan

2014-01-01

This paper discusses argument marking and reference tracking in Mekens complex clauses and their correlation to information structure. The distribution of pronominal arguments in Mekens simple clauses follows an absolutive pattern with main verbs. Complex clauses maintain the morphological absolutive argument marking, but show a nominative pattern with respect to argument reference tracking, since transitive and intransitive subjects function as syntactic pivots. The language extends the use of argument-marking verb morphology to control the reference of discourse participants across clauses.

Crystal Structures of Murine Carnitine Acetyltransferase in Ternary Complexes with Its Substrates

Energy Technology Data Exchange (ETDEWEB)

Hsiao,Y.; Jogl, G.; Tong, L.

2006-01-01

Carnitine acyltransferases catalyze the reversible exchange of acyl groups between coenzyme A (CoA) and carnitine. They have important roles in many cellular processes, especially the oxidation of long-chain fatty acids in the mitochondria for energy production, and are attractive targets for drug discovery against diabetes and obesity. To help define in molecular detail the catalytic mechanism of these enzymes, we report here the high resolution crystal structure of wild-type murine carnitine acetyltransferase (CrAT) in a ternary complex with its substrates acetyl-CoA and carnitine, and the structure of the S554A/M564G double mutant in a ternary complex with the substrates CoA and hexanoylcarnitine. Detailed analyses suggest that these structures may be good mimics for the Michaelis complexes for the forward and reverse reactions of the enzyme, representing the first time that such complexes of CrAT have been studied in molecular detail. The structural information provides significant new insights into the catalytic mechanism of CrAT and possibly carnitine acyltransferases in general.

Isolation and X-ray structures of four Rh(PCP) complexes including a Rh(I) dioxygen complex with a short O-O bond

KAUST Repository

Hayashi, Yukiko

2013-07-01

The reaction of RhCl3·H2O with tBu2P(CH2)5PtBu 2 afforded several complexes including [RhIII(H)Cl{ tBu2- P(CH2)2CH(CH2) 2PtBu2}] (1), [RhIIIHCl 2{tBu2P(CH2)5P tBu2}]2 (2), [RhICl{ tBu2P(CH2)2CH=CHCH2P tBu2}] (3) and [RhICl{tBu 2PCH2C(O)CH=CHCH2PtBu2}] (4). X-ray crystal structures of 3 and 4 showed that the C=C bond on the C 5 unit of tBu2P(CH2) 5PtBu2 is bound to Rh(I) in a η2 configuration. In 4, the Rh atom has a trigonal pyramidal coordination geometry. The X-ray crystal structure of 2 consists of two rhodium( III) centers bridged by two tBu2P(CH2)5P tBu2 ligands with two phosphorus atoms, one from each ligand, trans to one another. The crystal structure of the rhodium oxygen adduct with 1,3-bis(di-t-butylphosphinomethyl) benzene [RhO2{ tBu2PCH2(C6H3)CH 2PtBu2}] (5) was also investigated. In this species the O2 is η2 coordinated to the Rh(I) center with asymmetric Rh-O bond lengths (2.087(7) and 1.998(8) Å). The O-O bond distance is short (1.337(11) Å) with νO-O of 990.5 cm -1. DFT calculations on complex 5 yielded two η2- O2 structures that differed in energy by only 0.76 kcal/mol. The lower energy one (5a) had near C2 symmetry, and had nearly equal Rh-O bond lengths, while the higher energy structure (5b) had near Cs symmetry and generally good agreement with the experimental structure. The calculated UV-Vis and IR spectra of complex 5 are in excellent agreement with experiment. © 2012 Elsevier Ltd. All rights reserved.

Isolation and X-ray structures of four Rh(PCP) complexes including a Rh(I) dioxygen complex with a short O-O bond

KAUST Repository

Hayashi, Yukiko; Szalda, David J.; Grills, David C.; Hanson, Jonathan C.; Huang, Kuo-Wei; Muckerman, James T.; Fujita, Etsuko

2013-01-01

The reaction of RhCl3·H2O with tBu2P(CH2)5PtBu 2 afforded several complexes including [RhIII(H)Cl{ tBu2- P(CH2)2CH(CH2) 2PtBu2}] (1), [RhIIIHCl 2{tBu2P(CH2)5P tBu2}]2 (2), [RhICl{ tBu2P(CH2)2CH=CHCH2P tBu2}] (3) and [RhICl{tBu 2PCH2C(O)CH=CHCH2PtBu2}] (4). X-ray crystal structures of 3 and 4 showed that the C=C bond on the C 5 unit of tBu2P(CH2) 5PtBu2 is bound to Rh(I) in a η2 configuration. In 4, the Rh atom has a trigonal pyramidal coordination geometry. The X-ray crystal structure of 2 consists of two rhodium( III) centers bridged by two tBu2P(CH2)5P tBu2 ligands with two phosphorus atoms, one from each ligand, trans to one another. The crystal structure of the rhodium oxygen adduct with 1,3-bis(di-t-butylphosphinomethyl) benzene [RhO2{ tBu2PCH2(C6H3)CH 2PtBu2}] (5) was also investigated. In this species the O2 is η2 coordinated to the Rh(I) center with asymmetric Rh-O bond lengths (2.087(7) and 1.998(8) Å). The O-O bond distance is short (1.337(11) Å) with νO-O of 990.5 cm -1. DFT calculations on complex 5 yielded two η2- O2 structures that differed in energy by only 0.76 kcal/mol. The lower energy one (5a) had near C2 symmetry, and had nearly equal Rh-O bond lengths, while the higher energy structure (5b) had near Cs symmetry and generally good agreement with the experimental structure. The calculated UV-Vis and IR spectra of complex 5 are in excellent agreement with experiment. © 2012 Elsevier Ltd. All rights reserved.

Crystal structure of the human 4-1BB/4-1BBL complex.

Science.gov (United States)

Gilbreth, Ryan N; Oganesyan, Vaheh Y; Amdouni, Hamza; Novarra, Shabazz; Grinberg, Luba; Barnes, Arnita; Baca, Manuel

2018-05-02

4-1BBL is a member of the TNF superfamily and is the ligand for the TNFRsuperfamily receptor, 4-1BB. 4-1BB plays an immunomodulatory role in T cells and NK cells and agonists of this receptor have garnered strong attention as potentialimmunotherapy agents. Broadly speaking, the structural features of TNF superfamilymembers, their receptors and ligand/receptor complexes are similar. However, apublished crystal structure of human 4-1BBL suggests that it may be unique in thisregard, exhibiting a three-bladed propeller-like trimer assembly that is distinctly different from that observed in other family members. This unusual structure also suggests that the human 4-1BB/4-1BBL complex may be structurally unique within the TNF/TNFR superfamily, but to date no structural data have been reported. Here we report the crystal structure of the human 4-1BB/4-1BBL complex at 2.4 Å resolution. In this structure, 4-1BBL does not adopt the unusual trimer assembly previously reported, but instead forms a canonical bell-shaped trimer typical of other TNF superfamily members. The structure of 4-1BB is also largely canonical as is the 4-1BB/4-1BBL complex. Mutational data support the 4-1BBL structure reported here as being biologically relevant, suggesting that the previously reported structure is not. Together, the data presented here offer insight into structure/function relationships in the 4-1BB/4-1BBL system and improve our structural understanding of the TNF/TNFR superfamily more broadly. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Wave propagation in complex structures with LEGO

NARCIS (Netherlands)

Lancellotti, V.; Hon, de B.P.; Tijhuis, A.G.

2012-01-01

We present the extension of the linear embedding via Green's operators (LEGO) scheme to problems that involve elementary sources localized inside complex structures made of different dielectric media with inclusions. We show how this new feature allows solving problems of wave propagation within,

Three-dimensional bioprinting of complex cell laden alginate hydrogel structures.

Science.gov (United States)

Tabriz, Atabak Ghanizadeh; Hermida, Miguel A; Leslie, Nicholas R; Shu, Wenmiao

2015-12-21

Different bioprinting techniques have been used to produce cell-laden alginate hydrogel structures, however these approaches have been limited to 2D or simple three-dimension (3D) structures. In this study, a new extrusion based bioprinting technique was developed to produce more complex alginate hydrogel structures. This was achieved by dividing the alginate hydrogel cross-linking process into three stages: primary calcium ion cross-linking for printability of the gel, secondary calcium cross-linking for rigidity of the alginate hydrogel immediately after printing and tertiary barium ion cross-linking for long-term stability of the alginate hydrogel in culture medium. Simple 3D structures including tubes were first printed to ensure the feasibility of the bioprinting technique and then complex 3D structures such as branched vascular structures were successfully printed. The static stiffness of the alginate hydrogel after printing was 20.18 ± 1.62 KPa which was rigid enough to sustain the integrity of the complex 3D alginate hydrogel structure during the printing. The addition of 60 mM barium chloride was found to significantly extend the stability of the cross-linked alginate hydrogel from 3 d to beyond 11 d without compromising the cellular viability. The results based on cell bioprinting suggested that viability of U87-MG cells was 93 ± 0.9% immediately after bioprinting and cell viability maintained above 88% ± 4.3% in the alginate hydrogel over the period of 11 d.

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

KAUST Repository

Guturu, H.

2013-11-11

Mapping the DNA-binding preferences of transcription factor (TF) complexes is critical for deciphering the functions of cis-regulatory elements. Here, we developed a computational method that compares co-occurring motif spacings in conserved versus unconserved regions of the human genome to detect evolutionarily constrained binding sites of rigid TF complexes. Structural data were used to estimate TF complex physical plausibility, explore overlapping motif arrangements seldom tackled by non-structure-aware methods, and generate and analyse three-dimensional models of the predicted complexes bound to DNA. Using this approach, we predicted 422 physically realistic TF complex motifs at 18% false discovery rate, the majority of which (326, 77%) contain some sequence overlap between binding sites. The set of mostly novel complexes is enriched in known composite motifs, predictive of binding site configurations in TF-TF-DNA crystal structures, and supported by ChIP-seq datasets. Structural modelling revealed three cooperativity mechanisms: direct protein-protein interactions, potentially indirect interactions and \\'through-DNA\\' interactions. Indeed, 38% of the predicted complexes were found to contain four or more bases in which TF pairs appear to synergize through overlapping binding to the same DNA base pairs in opposite grooves or strands. Our TF complex and associated binding site predictions are available as a web resource at http://bejerano.stanford.edu/complex.

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

KAUST Repository

Guturu, H.; Doxey, A. C.; Wenger, A. M.; Bejerano, G.

2013-01-01

Mapping the DNA-binding preferences of transcription factor (TF) complexes is critical for deciphering the functions of cis-regulatory elements. Here, we developed a computational method that compares co-occurring motif spacings in conserved versus unconserved regions of the human genome to detect evolutionarily constrained binding sites of rigid TF complexes. Structural data were used to estimate TF complex physical plausibility, explore overlapping motif arrangements seldom tackled by non-structure-aware methods, and generate and analyse three-dimensional models of the predicted complexes bound to DNA. Using this approach, we predicted 422 physically realistic TF complex motifs at 18% false discovery rate, the majority of which (326, 77%) contain some sequence overlap between binding sites. The set of mostly novel complexes is enriched in known composite motifs, predictive of binding site configurations in TF-TF-DNA crystal structures, and supported by ChIP-seq datasets. Structural modelling revealed three cooperativity mechanisms: direct protein-protein interactions, potentially indirect interactions and 'through-DNA' interactions. Indeed, 38% of the predicted complexes were found to contain four or more bases in which TF pairs appear to synergize through overlapping binding to the same DNA base pairs in opposite grooves or strands. Our TF complex and associated binding site predictions are available as a web resource at http://bejerano.stanford.edu/complex.

Resolving complex chromosome structures during meiosis: versatile deployment of Smc5/6

NARCIS (Netherlands)

Verver, Dideke E.; Hwang, Grace H.; Jordan, Philip W.; Hamer, Geert

2016-01-01

The Smc5/6 complex, along with cohesin and condensin, is a member of the structural maintenance of chromosome (SMC) family, large ring-like protein complexes that are essential for chromatin structure and function. Thanks to numerous studies of the mitotic cell cycle, Smc5/6 has been implicated to

Solution structure of the Grb2 SH2 domain complexed with a high-affinity inhibitor

International Nuclear Information System (INIS)

Ogura, Kenji; Shiga, Takanori; Yokochi, Masashi; Yuzawa, Satoru; Burke, Terrence R.; Inagaki, Fuyuhiko

2008-01-01

The solution structure of the growth factor receptor-bound protein 2 (Grb2) SH2 domain complexed with a high-affinity inhibitor containing a non-phosphorus phosphate mimetic within a macrocyclic platform was determined by nuclear magnetic resonance (NMR) spectroscopy. Unambiguous assignments of the bound inhibitor and intermolecular NOEs between the Grb2 SH2 domain and the inhibitor was accomplished using perdeuterated Grb2 SH2 protein. The well-defined solution structure of the complex was obtained and compared to those by X-ray crystallography. Since the crystal structure of the Grb2 SH2 domain formed a domain-swapped dimer and several inhibitors were bound to a hinge region, there were appreciable differences between the solution and crystal structures. Based on the binding interactions between the inhibitor and the Grb2 SH2 domain in solution, we proposed a design of second-generation inhibitors that could be expected to have higher affinity

Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.

Science.gov (United States)

Martin, Juliette; Regad, Leslie; Etchebest, Catherine; Camproux, Anne-Claude

2008-11-15

Interresidue protein contacts in proteins structures and at protein-protein interface are classically described by the amino acid types of interacting residues and the local structural context of the contact, if any, is described using secondary structures. In this study, we present an alternate analysis of interresidue contact using local structures defined by the structural alphabet introduced by Camproux et al. This structural alphabet allows to describe a 3D structure as a sequence of prototype fragments called structural letters, of 27 different types. Each residue can then be assigned to a particular local structure, even in loop regions. The analysis of interresidue contacts within protein structures defined using Voronoï tessellations reveals that pairwise contact specificity is greater in terms of structural letters than amino acids. Using a simple heuristic based on specificity score comparison, we find that 74% of the long-range contacts within protein structures are better described using structural letters than amino acid types. The investigation is extended to a set of protein-protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. We then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter-based pairing functions.

Electronic structure and driving forces in {beta}-cyclodextrin: Diclofenac inclusion complexes

Energy Technology Data Exchange (ETDEWEB)

Bogdan, Diana [National Institute for Research and Development of Isotopic and Molecular Technologies, Donath street 71-103, 400293 Cluj-Napoca (Romania); Morari, C. [National Institute for Research and Development of Isotopic and Molecular Technologies, Donath street 71-103, 400293 Cluj-Napoca (Romania)]. E-mail: cristim@s3.itim-cj.ro

2007-07-02

We investigate the geometry and electronic structure for complexes of {beta}-cyclodextrin with diclofenac using DFT calculations. The effect of solvent is explicitly taken into account. This investigation allows us to draw meaningful conclusions upon the stability of the complex and the nature of the driving forces leading to the complexation process. In particular we emphasize the role of the water, by pointing out the changes in the solvent's electronic structure for different docking geometries.

Estimating the complexity of 3D structural models using machine learning methods

Science.gov (United States)

Mejía-Herrera, Pablo; Kakurina, Maria; Royer, Jean-Jacques

2016-04-01

Quantifying the complexity of 3D geological structural models can play a major role in natural resources exploration surveys, for predicting environmental hazards or for forecasting fossil resources. This paper proposes a structural complexity index which can be used to help in defining the degree of effort necessary to build a 3D model for a given degree of confidence, and also to identify locations where addition efforts are required to meet a given acceptable risk of uncertainty. In this work, it is considered that the structural complexity index can be estimated using machine learning methods on raw geo-data. More precisely, the metrics for measuring the complexity can be approximated as the difficulty degree associated to the prediction of the geological objects distribution calculated based on partial information on the actual structural distribution of materials. The proposed methodology is tested on a set of 3D synthetic structural models for which the degree of effort during their building is assessed using various parameters (such as number of faults, number of part in a surface object, number of borders, ...), the rank of geological elements contained in each model, and, finally, their level of deformation (folding and faulting). The results show how the estimated complexity in a 3D model can be approximated by the quantity of partial data necessaries to simulated at a given precision the actual 3D model without error using machine learning algorithms.

Heteroprotein Complex Formation of Bovine Lactoferrin and Pea Protein Isolate: A Multiscale Structural Analysis.

Science.gov (United States)

Adal, Eda; Sadeghpour, Amin; Connell, Simon; Rappolt, Michael; Ibanoglu, Esra; Sarkar, Anwesha

2017-02-13

Associative electrostatic interactions between two oppositely charged globular proteins, lactoferrin (LF) and pea protein isolate (PPI), the latter being a mixture of vicilin, legumin, and convicilin, was studied with a specific PPI/LF molar ratio at room temperature. Structural aspects of the electrostatic complexes probed at different length scales were investigated as a function of pH by means of different complementary techniques, namely, with dynamic light scattering, small-angle X-ray scattering (SAXS), turbidity measurements, and atomic force microscopy (AFM). Irrespective of the applied techniques, the results consistently displayed that complexation between LF and PPI did occur. In an optimum narrow range of pH 5.0-5.8, a viscous liquid phase of complex coacervate was obtained upon mild centrifugation of the turbid LF-PPI mixture with a maximum R h , turbidity and the ζ-potential being close to zero observed at pH 5.4. In particular, the SAXS data demonstrated that the coacervates were densely assembled with a roughly spherical size distribution exhibiting a maximum extension of ∼80 nm at pH 5.4. Equally, AFM image analysis showed size distributions containing most frequent cluster sizes around 40-80 nm with spherical to elliptical shapes (axis aspect ratio ≤ 2) as well as less frequent elongated to chainlike structures. The most frequently observed compact complexes, we identify as mainly leading to LF-PPI coacervation, whereas for the less frequent chain-like aggregates, we hypothesize that additionally PPI-PPI facilitated complexes exist.

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

Science.gov (United States)

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.

A thermodynamical and structural study on the complexation of trivalent lanthanides with a polycarboxylate based concrete superplasticizer.

Science.gov (United States)

Fröhlich, Daniel R; Maiwald, Martin M; Taube, Franziska; Plank, Johann; Panak, Petra J

2017-03-21

The complexation of trivalent lanthanides with a commercial polycarboxylate based concrete superplasticizer (Glenium® 51) is investigated using different spectroscopic techniques. Time-resolved laser fluorescence spectroscopy (TRLFS) in combination with a charge neutralization model is used to determine temperature dependent conditional stability constants (log β'(T)) for the complexation of Eu(iii) with Glenium® 51 in 0.1 mol kg -1 NaCl solution in the temperature range of 20-90 °C. Only one complex species is observed, and log β'(T) (given in kg per mol eq) shows a very slight increase with temperature from 7.5 to 7.9. The related conditional molar reaction enthalpy (Δ r H' m ) and entropy (Δ r S' m ) obtained using the Van't Hoff equation show that the complexation reaction is slightly endothermic and entropy driven. The thermodynamic investigations are complemented by structural data for complexes formed with Gd(iii) or Tb(iii) and Glenium® 51 using extended X-ray absorption fine structure (EXAFS) spectroscopy. The results imply a non-chelate coordination of the trivalent metals through approximately three carboxylic functions of the polycarboxylate comb polymer which are attached predominantly in a bidentate fashion to the lanthanide under the given experimental conditions.

Statistical inference approach to structural reconstruction of complex networks from binary time series

Science.gov (United States)

Ma, Chuang; Chen, Han-Shuang; Lai, Ying-Cheng; Zhang, Hai-Feng

2018-02-01

Complex networks hosting binary-state dynamics arise in a variety of contexts. In spite of previous works, to fully reconstruct the network structure from observed binary data remains challenging. We articulate a statistical inference based approach to this problem. In particular, exploiting the expectation-maximization (EM) algorithm, we develop a method to ascertain the neighbors of any node in the network based solely on binary data, thereby recovering the full topology of the network. A key ingredient of our method is the maximum-likelihood estimation of the probabilities associated with actual or nonexistent links, and we show that the EM algorithm can distinguish the two kinds of probability values without any ambiguity, insofar as the length of the available binary time series is reasonably long. Our method does not require any a priori knowledge of the detailed dynamical processes, is parameter-free, and is capable of accurate reconstruction even in the presence of noise. We demonstrate the method using combinations of distinct types of binary dynamical processes and network topologies, and provide a physical understanding of the underlying reconstruction mechanism. Our statistical inference based reconstruction method contributes an additional piece to the rapidly expanding "toolbox" of data based reverse engineering of complex networked systems.

Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage and Metal Binding Specificity.

Science.gov (United States)

Wahba, Haytham M; Lecoq, Lauriane; Stevenson, Michael; Mansour, Ahmed; Cappadocia, Laurent; Lafrance-Vanasse, Julien; Wilkinson, Kevin J; Sygusch, Jurgen; Wilcox, Dean E; Omichinski, James G

2016-02-23

In bacterial resistance to mercury, the organomercurial lyase (MerB) plays a key role in the detoxification pathway through its ability to cleave Hg-carbon bonds. Two cysteines (C96 and C159; Escherichia coli MerB numbering) and an aspartic acid (D99) have been identified as the key catalytic residues, and these three residues are conserved in all but four known MerB variants, where the aspartic acid is replaced with a serine. To understand the role of the active site serine, we characterized the structure and metal binding properties of an E. coli MerB mutant with a serine substituted for D99 (MerB D99S) as well as one of the native MerB variants containing a serine residue in the active site (Bacillus megaterium MerB2). Surprisingly, the MerB D99S protein copurified with a bound metal that was determined to be Cu(II) from UV-vis absorption, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, and electron paramagnetic resonance studies. X-ray structural studies revealed that the Cu(II) is bound to the active site cysteine residues of MerB D99S, but that it is displaced following the addition of either an organomercurial substrate or an ionic mercury product. In contrast, the B. megaterium MerB2 protein does not copurify with copper, but the structure of the B. megaterium MerB2-Hg complex is highly similar to the structure of the MerB D99S-Hg complexes. These results demonstrate that the active site aspartic acid is crucial for both the enzymatic activity and metal binding specificity of MerB proteins and suggest a possible functional relationship between MerB and its only known structural homologue, the copper-binding protein NosL.

Significance tests for functional data with complex dependence structure.

Science.gov (United States)

Staicu, Ana-Maria; Lahiri, Soumen N; Carroll, Raymond J

2015-01-01

We propose an L 2 -norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.

Significance tests for functional data with complex dependence structure

KAUST Repository

Staicu, Ana-Maria

2015-01-01

We propose an L (2)-norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.

Synthesis, Structure and Catalytic Activity of NHC-AgICarboxylate Complexes

KAUST Repository

Wong, Valerie H. L.; Vummaleti, Sai V. C.; Cavallo, Luigi; White, Andrew J. P.; Nolan, Steven P.; Hii, King Kuok Mimi

2016-01-01

A general synthetic route was used to prepare 15 new N-heterocyclic carbene (NHC)–AgI complexes bearing anionic carboxylate ligands [Ag(NHC)(O2CR)], including a homologous series of complexes of sterically flexible ITent ligands, which permit a systematic spectroscopic and theoretical study of the structural and electronic features of these compounds. The complexes displayed a significant ligand-accelerated effect in the intramolecular cyclisation of propargylic amides to oxazolidines. The substrate scope is highly complementary to that previously achieved by NHC–Au and pyridyl–AgI complexes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Synthesis, Structure and Catalytic Activity of NHC-AgICarboxylate Complexes

KAUST Repository

Wong, Valerie H. L.

2016-08-03

A general synthetic route was used to prepare 15 new N-heterocyclic carbene (NHC)–AgI complexes bearing anionic carboxylate ligands [Ag(NHC)(O2CR)], including a homologous series of complexes of sterically flexible ITent ligands, which permit a systematic spectroscopic and theoretical study of the structural and electronic features of these compounds. The complexes displayed a significant ligand-accelerated effect in the intramolecular cyclisation of propargylic amides to oxazolidines. The substrate scope is highly complementary to that previously achieved by NHC–Au and pyridyl–AgI complexes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Polyacrylic acids–bovine serum albumin complexation: Structure and dynamics

International Nuclear Information System (INIS)

Othman, Mohamed; Aschi, Adel; Gharbi, Abdelhafidh

2016-01-01

The study of the mixture of BSA with polyacrylic acids at different masses versus pH allowed highlighting the existence of two regimes of weak and strong complexation. These complexes were studied in diluted regime concentration, by turbidimetry, dynamic light scattering (DLS), zeta-potential measurements and nuclear magnetic resonance (NMR). We have followed the pH effect on the structure and properties of the complex. This allowed refining the interpretation of the phase diagram and understanding the observed phenomena. The NMR measurements allowed probing the dynamics of the constituents versus the pH. The computational method was used to precisely determine the electrostatic potential of BSA and how the polyelectrolyte binds to it at different pH. - Highlights: • Influence of physico-chemical parameters on the electrostatic interactions in the complex system (polyelectrolyte/protein). • Stabilization and encapsulation of biological macromolecules solution by mean of polyelectrolyte. • Properties and structure of mixture obtained by screening the charges of globular protein and at different masses of polyacrylic acids. • Dynamic of the constituents formed by complexes particles. • Evaluation of the electrostatic properties of bovine serum albumin versus pH through solution of the Poisson-Boltzmann equation.

Complex structure of type VI peptidoglycan muramidase effector and a cognate immunity protein

International Nuclear Information System (INIS)

Wang, Tianyu; Ding, Jinjing; Zhang, Ying; Wang, Da-Cheng; Liu, Wei

2013-01-01

The structure of the Tse3–Tsi3 complex associated with the bacterial type VI secretion system of P. aeruginosa has been solved and refined at 1.9 Å resolution. The structural basis of the recognition of the muramidase effector and its inactivation by its cognate immunity protein is revealed. The type VI secretion system (T6SS) is a bacterial protein-export machine that is capable of delivering virulence effectors between Gram-negative bacteria. The T6SS of Pseudomonas aeruginosa transports two lytic enzymes, Tse1 and Tse3, to degrade cell-wall peptidoglycan in the periplasm of rival bacteria that are competing for niches via amidase and muramidase activities, respectively. Two cognate immunity proteins, Tsi1 and Tsi3, are produced by the bacterium to inactivate the two antibacterial effectors, thereby protecting its siblings from self-intoxication. Recently, Tse1–Tsi1 has been structurally characterized. Here, the structure of the Tse3–Tsi3 complex is reported at 1.9 Å resolution. The results reveal that Tse3 contains a C-terminal catalytic domain that adopts a soluble lytic transglycosylase (SLT) fold in which three calcium-binding sites were surprisingly observed close to the catalytic Glu residue. The electrostatic properties of the substrate-binding groove are also distinctive from those of known structures with a similar fold. All of these features imply that a unique catalytic mechanism is utilized by Tse3 in cleaving glycosidic bonds. Tsi3 comprises a single domain showing a β-sandwich architecture that is reminiscent of the immunoglobulin fold. Three loops of Tsi3 insert deeply into the groove of Tse3 and completely occlude its active site, which forms the structural basis of Tse3 inactivation. This work is the first crystallographic report describing the three-dimensional structure of the Tse3–Tsi3 effector–immunity pair

Complex structure of type VI peptidoglycan muramidase effector and a cognate immunity protein

Energy Technology Data Exchange (ETDEWEB)

Wang, Tianyu [Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Ding, Jinjing; Zhang, Ying; Wang, Da-Cheng, E-mail: dcwang@ibp.ac.cn [Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Liu, Wei, E-mail: dcwang@ibp.ac.cn [The Third Military Medical University, Chongqing 400038 (China); Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

2013-10-01

The structure of the Tse3–Tsi3 complex associated with the bacterial type VI secretion system of P. aeruginosa has been solved and refined at 1.9 Å resolution. The structural basis of the recognition of the muramidase effector and its inactivation by its cognate immunity protein is revealed. The type VI secretion system (T6SS) is a bacterial protein-export machine that is capable of delivering virulence effectors between Gram-negative bacteria. The T6SS of Pseudomonas aeruginosa transports two lytic enzymes, Tse1 and Tse3, to degrade cell-wall peptidoglycan in the periplasm of rival bacteria that are competing for niches via amidase and muramidase activities, respectively. Two cognate immunity proteins, Tsi1 and Tsi3, are produced by the bacterium to inactivate the two antibacterial effectors, thereby protecting its siblings from self-intoxication. Recently, Tse1–Tsi1 has been structurally characterized. Here, the structure of the Tse3–Tsi3 complex is reported at 1.9 Å resolution. The results reveal that Tse3 contains a C-terminal catalytic domain that adopts a soluble lytic transglycosylase (SLT) fold in which three calcium-binding sites were surprisingly observed close to the catalytic Glu residue. The electrostatic properties of the substrate-binding groove are also distinctive from those of known structures with a similar fold. All of these features imply that a unique catalytic mechanism is utilized by Tse3 in cleaving glycosidic bonds. Tsi3 comprises a single domain showing a β-sandwich architecture that is reminiscent of the immunoglobulin fold. Three loops of Tsi3 insert deeply into the groove of Tse3 and completely occlude its active site, which forms the structural basis of Tse3 inactivation. This work is the first crystallographic report describing the three-dimensional structure of the Tse3–Tsi3 effector–immunity pair.

Factors influencing efficient structure of fuel and energy complex

Science.gov (United States)

Sidorova, N. G.; Novikova, S. A.

2017-10-01

The development of the Russian fuel-energy complex is a priority for the national economic policy, and the Far East is a link between Russia and the Asia-Pacific region. Large-scale engineering of numerous resources of the Far East will force industrial development, increase living standard and strengthen Russia’s position in the global energy market. So, revealing the factors which influence rational structure of the fuel-energy complex is very urgent nowadays. With the use of depth analysis of development tendencies of the complex and its problems the authors show ways of its efficiency improvement.

Structure of the Deactive State of Mammalian Respiratory Complex I.

Science.gov (United States)

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.

Parasites affect food web structure primarily through increased diversity and complexity.

Directory of Open Access Journals (Sweden)

Jennifer A Dunne

Full Text Available Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity, particularly when including concomitant links (links from predators to parasites of their prey. However, we clarify prior claims that parasites "dominate" food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites' roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites' feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic

Novel polymeric potassium complex: Its synthesis, structural characterization, photoluminescence and electrochemical properties

Energy Technology Data Exchange (ETDEWEB)

Ceyhan, Goekhan [Chemistry Department, K.Maras Suetcue Imam University, 46100 K.Maras (Turkey); Tuemer, Mehmet, E-mail: mtumer@ksu.edu.tr [Chemistry Department, K.Maras Suetcue Imam University, 46100 K.Maras (Turkey); Koese, Muhammet; McKee, Vickie [Chemistry Department, Loughborough University, LE11 3TU Leicestershire (United Kingdom)

2012-03-15

In this paper, we obtained a novel poly(vanillinato potassium) complex (PVP) as a single crystal and characterized by analytical and spectroscopic methods. A single crystal of the PVP was obtained from the acetone solution. X-ray structural data show that crystals contain polymeric K{sup +} complex of vanillin. Each potassium ion in the polymeric structure is identical and seven-coordinate, bonded to two methoxy, two phenoxy and three aldehyde oxygen atoms from four vaniline molecules. Two aldehyde oxygen atoms are bridging between potassium ions. It crystallizes in the monoclinic system, space group P2{sub 1}/c, with lattice parameters a=9.6215(10) A, b=17.4139(19) A, c=9.6119(10) A, {beta}=100.457(2) Degree-Sign and Z=4. Thermal properties of the PVP were investigated by TGA, DTA and DSC methods. The electrochemical properties of the complex were studied in different solvents and at various scan rates. The luminescence properties of the complex in different solvents and at different pH values have been investigated. The results show that the complex exhibits more efficient luminescence property in CH{sub 3}CN and n-butanol. - Highlights: Black-Right-Pointing-Pointer Novel polymeric potassium complex was prepared and fully characterized. Black-Right-Pointing-Pointer X-ray crystal structure of complex was reported. Black-Right-Pointing-Pointer Electrochemical properties of compound were investigated. Black-Right-Pointing-Pointer Thermal and DSC measurements of complex were examined.

Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits

Science.gov (United States)

2016-01-01

Ions regulate the assembly and mechanical properties of actin filaments. Recent work using structural bioinformatics and site-specific mutagenesis favors the existence of two discrete and specific divalent cation binding sites on actin filaments, positioned in the long axis between actin subunits. Cation binding at one site drives polymerization, while the other modulates filament stiffness and plays a role in filament severing by the regulatory protein, cofilin. Existing structural methods have not been able to resolve filament-associated cations, and so in this work we turn to molecular dynamics simulations to suggest a candidate binding pocket geometry for each site and to elucidate the mechanism by which occupancy of the “stiffness site” affects filament mechanical properties. Incorporating a magnesium ion in the “polymerization site” does not seem to require any large-scale change to an actin subunit’s conformation. Binding of a magnesium ion in the “stiffness site” adheres the actin DNase-binding loop (D-loop) to its long-axis neighbor, which increases the filament torsional stiffness and bending persistence length. Our analysis shows that bound D-loops occupy a smaller region of accessible conformational space. Cation occupancy buries key conserved residues of the D-loop, restricting accessibility to regulatory proteins and enzymes that target these amino acids. PMID:27146246

Synthesis and X-ray crystal structure of a novel organometallic (µ(3)-oxido)(µ(3)-imido) trinuclear iridium complex

DEFF Research Database (Denmark)

Schau-Magnussen, Magnus; Malcho, Phillip; Herbst, Konrad

2011-01-01

Reaction of the organometallic aqua ion [Cp*Ir(H(2)O)(3)](2+) with tert-butyl(trimethylsilyl)amine in acetone yielded a novel trinuclear (µ(3)-oxido)(µ(3)-imido)pentamethylcyclopentadienyliridium(iii) complex, [(Cp*Ir)(3)(O)(N(t)Bu)](2+). Single crystal structure analyses show the complex can be ...... that a trinuclear (µ(3)-oxido)(µ(3)-imido) transition metal complex has been structurally characterized....

Complex metrology on 3D structures using multi-channel OCD

Science.gov (United States)

Kagalwala, Taher; Mahendrakar, Sridhar; Vaid, Alok; Isbester, Paul K.; Cepler, Aron; Kang, Charles; Yellai, Naren; Sendelbach, Matthew; Ko, Mihael; Ilgayev, Ovadia; Katz, Yinon; Tamam, Lilach; Osherov, Ilya

2017-03-01

Device scaling has not only driven the use of measurements on more complex structures, in terms of geometry, materials, and tighter ground rules, but also the need to move away from non-patterned measurement sites to patterned ones. This is especially of concern for very thin film layers that have a high thickness dependence on structure geometry or wafer pattern factor. Although 2-dimensional (2D) sites are often found to be sufficient for process monitoring and control of very thin films, sometimes 3D sites are required to further simulate structures within the device. The measurement of film thicknesses only a few atoms thick on complex 3D sites, however, are very challenging. Apart from measuring thin films on 3D sites, there is also a critical need to measure parameters on 3D sites, which are weak and less sensitive for OCD (Optical Critical Dimension) metrology, with high accuracy and precision. Thus, state-ofthe-art methods are needed to address such metrology challenges. This work introduces the concept of Enhanced OCD which uses various methods to improve the sensitivity and reduce correlations for weak parameters in a complex measurement. This work also describes how more channels of information, when used correctly, can improve the precision and accuracy of weak, non-sensitive or complex parameters of interest.

Structured analysis and modeling of complex systems

Science.gov (United States)

Strome, David R.; Dalrymple, Mathieu A.

1992-01-01

The Aircrew Evaluation Sustained Operations Performance (AESOP) facility at Brooks AFB, Texas, combines the realism of an operational environment with the control of a research laboratory. In recent studies we collected extensive data from the Airborne Warning and Control Systems (AWACS) Weapons Directors subjected to high and low workload Defensive Counter Air Scenarios. A critical and complex task in this environment involves committing a friendly fighter against a hostile fighter. Structured Analysis and Design techniques and computer modeling systems were applied to this task as tools for analyzing subject performance and workload. This technology is being transferred to the Man-Systems Division of NASA Johnson Space Center for application to complex mission related tasks, such as manipulating the Shuttle grappler arm.

Structuring and assessing large and complex decision problems using MCDA

DEFF Research Database (Denmark)

Barfod, Michael Bruhn

This paper presents an approach for the structuring and assessing of large and complex decision problems using multi-criteria decision analysis (MCDA). The MCDA problem is structured in a decision tree and assessed using the REMBRANDT technique featuring a procedure for limiting the number of pair...

VP-Nets : Efficient automatic localization of key brain structures in 3D fetal neurosonography.

Science.gov (United States)

Huang, Ruobing; Xie, Weidi; Alison Noble, J

2018-04-23

Three-dimensional (3D) fetal neurosonography is used clinically to detect cerebral abnormalities and to assess growth in the developing brain. However, manual identification of key brain structures in 3D ultrasound images requires expertise to perform and even then is tedious. Inspired by how sonographers view and interact with volumes during real-time clinical scanning, we propose an efficient automatic method to simultaneously localize multiple brain structures in 3D fetal neurosonography. The proposed View-based Projection Networks (VP-Nets), uses three view-based Convolutional Neural Networks (CNNs), to simplify 3D localizations by directly predicting 2D projections of the key structures onto three anatomical views. While designed for efficient use of data and GPU memory, the proposed VP-Nets allows for full-resolution 3D prediction. We investigated parameters that influence the performance of VP-Nets, e.g. depth and number of feature channels. Moreover, we demonstrate that the model can pinpoint the structure in 3D space by visualizing the trained VP-Nets, despite only 2D supervision being provided for a single stream during training. For comparison, we implemented two other baseline solutions based on Random Forest and 3D U-Nets. In the reported experiments, VP-Nets consistently outperformed other methods on localization. To test the importance of loss function, two identical models are trained with binary corss-entropy and dice coefficient loss respectively. Our best VP-Net model achieved prediction center deviation: 1.8 ± 1.4 mm, size difference: 1.9 ± 1.5 mm, and 3D Intersection Over Union (IOU): 63.2 ± 14.7% when compared to the ground truth. To make the whole pipeline intervention free, we also implement a skull-stripping tool using 3D CNN, which achieves high segmentation accuracy. As a result, the proposed processing pipeline takes a raw ultrasound brain image as input, and output a skull-stripped image with five detected key brain

Coral identity underpins architectural complexity on Caribbean reefs.

Science.gov (United States)

Alvarez-Filip, Lorenzo; Dulvy, Nicholas K; Côte, Isabelle M; Watkinson, Andrew R; Gill, Jennifer A

2011-09-01

The architectural complexity of ecosystems can greatly influence their capacity to support biodiversity and deliver ecosystem services. Understanding the components underlying this complexity can aid the development of effective strategies for ecosystem conservation. Caribbean coral reefs support and protect millions of livelihoods, but recent anthropogenic change is shifting communities toward reefs dominated by stress-resistant coral species, which are often less architecturally complex. With the regionwide decline in reef fish abundance, it is becoming increasingly important to understand changes in coral reef community structure and function. We quantify the influence of coral composition, diversity, and morpho-functional traits on the architectural complexity of reefs across 91 sites at Cozumel, Mexico. Although reef architectural complexity increases with coral cover and species richness, it is highest on sites that are low in taxonomic evenness and dominated by morpho-functionally important, reef-building coral genera, particularly Montastraea. Sites with similar coral community composition also tend to occur on reefs with very similar architectural complexity, suggesting that reef structure tends to be determined by the same key species across sites. Our findings provide support for prioritizing and protecting particular reef types, especially those dominated by key reef-building corals, in order to enhance reef complexity.

Structural motifs of diiodine complexes with amides and thioamides.

Science.gov (United States)

Parigoridi, Ioanna-Efpraxia; Corban, Ghada J; Hadjikakou, Sotiris K; Hadjiliadis, Nick; Kourkoumelis, Nikolaos; Kostakis, George; Psycharis, Vassilis; Raptopoulou, Catherine P; Kubicki, Maciej

2008-10-14

The reaction of 2-pyrimidone hydrochloride ([C(4)H(5)N(2)O](+)[Cl](-) or [PMOH(2)](+)[Cl](-)) with diiodine in a dichloromethane-methanol solution resulted in the formation of ([C(4)H(5)N(2)O](+))(2)[I(2)Cl(2)](2-) (1) complex. The compound was characterized by elemental analysis, FT-IR, DTA-TG and conductivity titrations. The crystal structure of 1 was also determined by X-ray diffraction at 294(1) K. Compound 1 is monoclinic, space group P2(1)/n, consisting of two cationic [PMOH(2)](+) species and a [I(2)Cl(2)](2-) counter dianion. The cation is in its keto form. Direct reaction of thiazolidine-2-thione (tzdtH), with diiodine in dichloromethane solution, on the other hand, led to the formation of a crystalline solid which contained two complexes of formulae [(tzdtH)(2)I](+)[I(3)](-).2I(2) (2) and [(tzdtH)I(2)](2).I(2) (2a) in a ratio of 90 to 10%. Complex 2a was characterized by X-ray analysis at 180(2) K. Compound is monoclinic, space group C2/c and contains two units of [(tzdtH)I(2)] "spoke" structures. Compound 1, as well as the known species iodonium salt [(tzdtH)(2)I](+)[I(3)](-).2I(2) (2) and the charge transfer (CT) iodine complexes of formulae [(bztzdtH)I(2)] (3) and [(bztzdtH)I(2)].I(2) (4) (bztzdtH = 2-mercaptobenzothiazole) with "spoke" and extended "spoke" structures respectively, were tested for their oxidizing activity towards 3,5-di-tert-butylcatechol to 3,5-di-tert-butyl-o-benzoquinone.

Insight to structural subsite recognition in plant thiol protease-inhibitor complexes : Understanding the basis of differential inhibition and the role of water

Directory of Open Access Journals (Sweden)

Mukhopadhayay Bishnu P

2001-09-01

Full Text Available Abstract Background This work represents an extensive MD simulation / water-dynamics studies on a series of complexes of inhibitors (leupeptin, E-64, E-64-C, ZPACK and plant cysteine proteases (actinidin, caricain, chymopapain, calotropin DI of papain family to understand the various interactions, water binding mode, factors influencing it and the structural basis of differential inhibition. Results The tertiary structure of the enzyme-inhibitor complexes were built by visual interactive modeling and energy minimization followed by dynamic simulation of 120 ps in water environment. DASA study with and without the inhibitor revealed the potential subsite residues involved in inhibition. Though the interaction involving main chain atoms are similar, critical inspection of the complexes reveal significant differences in the side chain interactions in S2-P2 and S3-P3 pairs due to sequence differences in the equivalent positions of respective subsites leading to differential inhibition. Conclusion The key finding of the study is a conserved site of a water molecule near oxyanion hole of the enzyme active site, which is found in all the modeled complexes and in most crystal structures of papain family either native or complexed. Conserved water molecules at the ligand binding sites of these homologous proteins suggest the structural importance of the water, which changes the conventional definition of chemical geometry of inhibitor binding domain, its shape and complimentarity. The water mediated recognition of inhibitor to enzyme subsites (Pn...H2O....Sn of leupeptin acetyl oxygen to caricain, chymopapain and calotropinDI is an additional information and offer valuable insight to potent inhibitor design.

Structural characterization and Hirshfeld surface analysis of a CoII complex with imidazo[1,2-a]pyridine

Directory of Open Access Journals (Sweden)

Saikat Kumar Seth

2018-05-01

Full Text Available A new mononuclear tetrahedral CoII complex, dichloridobis(imidazo[1,2-a]pyridine-κN1cobalt(II, [CoCl2(C7H6N22], has been synthesized using a bioactive imidazopyridine ligand. X-ray crystallography reveals that the solid-state structure of the title complex exhibits both C—H...Cl and π–π stacking interactions in building supramolecular assemblies. Indeed, the molecules are linked by C—H...Cl interactions into a two-dimensional framework, with finite zero-dimensional dimeric units as building blocks, whereas π–π stacking plays a crucial role in building a supramolecular layered network. An exhaustive investigation of the diverse intermolecular interactions via Hirshfeld surface analysis enables contributions to the crystal packing of the title complex to be quantified. The fingerprint plots associated with the Hirshfeld surface clearly display each significant interaction involved in the structure, by quantifying them in an effective visual manner.

A 3D complex containing novel 2D CuII-azido layers: Structure, magnetic properties and effects of “Non-innocent” reagent

International Nuclear Information System (INIS)

Gao, Xue-Miao; Guo, Qian; Zhao, Jiong-Peng; Liu, Fu-Chen

2012-01-01

A novel copper-azido coordination polymer, [Cu 2 (N 3 ) 3 (L)] n (1, HL=pyrazine-2-carboxylic acid), has been synthesized by hydrothermal reaction with “Non-innocent” reagent in the aqueous solution. In the reaction system, Cu II ions are avoided to reduce to Cu I ions due to the existence of Nd III . It is found that the complex is a 3D structure based on two double EO azido bridged trimmers and octahedron Cu II ions, in which the azide ligands take on EO and μ 1,1,3 mode to form Cu II -azido 2D layers, furthermore L ligands pillar 2D layers into an infinite 3D framework with the Schläfli symbol of {4;6 2 }4{4 2 ;6 12 ;8 10 ;10 4 }{4 2 ;6 4 }. Magnetic studies revealed that the interactions between the Cu II ions in the trimmer are ferromagnetic for the Cu–N–Cu angle nearly 98°, while the interactions between the trimmer and octahedron Cu II ion are antiferromgantic and result in an antiferromagnetic state. - Graphical abstract: A 3D complex containing novel 2D Cu II -azido layers, [Cu 2 (N 3 ) 3 (L)] n (HL=pyrazine-2-carboxylic acid), was synthesized by hydrothermal reaction and exhibit interesting structure and magnetic properties. Highlights: ► “Non-innocent” reagents plays a key role in the process of formation of this complex. ► 2D layer is formed only by Cu II ions and azido ligands. ► Pyrazine-2-carboxylate ligands reinforce 2D layers and pillar them into an infinite 3D framework. ► Magnetic study indicates that alternating FM–AF coupling exists in the complex.

Structure, Behavior, Function as a Framework For Teaching and Learning about Complexity In Ecosystems: Lessons from Middle School Classrooms (Invited)

Science.gov (United States)

Hmelo-Silver, C.; Gray, S.; Jordan, R.

2010-12-01

Complex systems surround us, and as Sabelli (2006) has argued, understanding complex systems is a critical component of science literacy. Understanding natural and designed systems are also prominent in the new draft science standards (NRC, 2010) and therefore of growing importance in the science classroom. Our work has focused on promoting an understanding of one complex natural system, aquatic ecosystems, which given current events, is fast becoming a requisite for informed decision-making as citizens (Jordan et al. 2008). Learners have difficulty understanding many concepts related to complex natural systems (e.g., Hmelo-Silver, Marathe, & Liu, 2007; Jordan, Gray, Liu, Demeter, & Hmelo-Silver, 2009). Studies of how students think about complex ecological systems (e.g; Hmelo-Silver, Marathe, & Liu, 2007; Hogan, 2000, Hogan & Fisherkeller, 1996: Covitt & Gunkel, 2008) have revealed difficulties in thinking beyond linear flow, single causality, and visible structure. Helping students to learn about ecosystems is a complex task that requires providing opportunities for students to not only engage directly with ecosystems but also with resources that provide relevant background knowledge and opportunities for learners to make their thinking visible. Both tasks can be difficult given the large spatial and temporal scales on which ecosystems operate. Additionally, visible components interact with often invisible components which can obscure ecosystem processes for students. Working in the context of aquatic ecosystems, we sought to provide learners with representations and simulations that make salient the relationship between system components. In particular, we provided learners with opportunities to experience both the micro-level and macro-level phenomena that are key to understanding ecosystems (Hmelo-Silver, Liu, Gray, & Jordan, submitted; Liu & Hmelo-Silver, 2008; Jacobson & Wilensky, 2006). To accomplish this, we needed to help learners make connections across

Structural and Electronic Investigations of Complex Intermetallic Compounds

Energy Technology Data Exchange (ETDEWEB)

Ko, Hyunjin [Iowa State Univ., Ames, IA (United States)

2008-01-01

In solid state chemistry, numerous investigations have been attempted to address the relationships between chemical structure and physical properties. Such questions include: (1) How can we understand the driving forces of the atomic arrangements in complex solids that exhibit interesting chemical and physical properties? (2) How do different elements distribute themselves in a solid-state structure? (3) Can we develop a chemical understanding to predict the effects of valence electron concentration on the structures and magnetic ordering of systems by both experimental and theoretical means? Although these issues are relevant to various compound classes, intermetallic compounds are especially interesting and well suited for a joint experimental and theoretical effort. For intermetallic compounds, the questions listed above are difficult to answer since many of the constituent atoms simply do not crystallize in the same manner as in their separate, elemental structures. Also, theoretical studies suggest that the energy differences between various structural alternatives are small. For example, Al and Ga both belong in the same group on the Periodic Table of Elements and share many similar chemical properties. Al crystallizes in the fcc lattice with 4 atoms per unit cell and Ga crystallizes in an orthorhombic unit cell lattice with 8 atoms per unit cell, which are both fairly simple structures (Figure 1). However, when combined with Mn, which itself has a very complex cubic crystal structure with 58 atoms per unit cell, the resulting intermetallic compounds crystallize in a completely different fashion. At the 1:1 stoichiometry, MnAl forms a very simple tetragonal lattice with two atoms per primitive unit cell, while MnGa crystallizes in a complicated rhombohedral unit cell with 26 atoms within the primitive unit cell. The mechanisms influencing the arrangements of atoms in numerous crystal structures have been studied theoretically by calculating electronic

Thermal properties of composite materials with a complex fractal structure

International Nuclear Information System (INIS)

Cervantes-Álvarez, F; Reyes-Salgado, J J; Dossetti, V; Carrillo, J L

2014-01-01

In this work, we report the thermal characterization of platelike composite samples made of polyester resin and magnetite inclusions. By means of photoacoustic spectroscopy and thermal relaxation, the thermal diffusivity, conductivity and volumetric heat capacity of the samples were experimentally measured. The volume fraction of the inclusions was systematically varied in order to study the changes in the effective thermal conductivity of the composites. For some samples, a static magnetic field was applied during the polymerization process, resulting in anisotropic inclusion distributions. Our results show a decrease in the thermal conductivity of some of the anisotropic samples, compared to the isotropic randomly distributed ones. Our analysis indicates that the development of elongated inclusion structures leads to the formation of magnetite and resin domains, causing this effect. We correlate the complexity of the inclusion structure with the observed thermal response through a multifractal and lacunarity analysis. All the experimental data are contrasted with the well known Maxwell–Garnett effective media approximation for composite materials. (paper)

Architecture of the human mTORC2 core complex.

Science.gov (United States)

Stuttfeld, Edward; Aylett, Christopher Hs; Imseng, Stefan; Boehringer, Daniel; Scaiola, Alain; Sauer, Evelyn; Hall, Michael N; Maier, Timm; Ban, Nenad

2018-02-09

The mammalian target of rapamycin (mTOR) is a key protein kinase controlling cellular metabolism and growth. It is part of the two structurally and functionally distinct multiprotein complexes mTORC1 and mTORC2. Dysregulation of mTOR occurs in diabetes, cancer and neurological disease. We report the architecture of human mTORC2 at intermediate resolution, revealing a conserved binding site for accessory proteins on mTOR and explaining the structural basis for the rapamycin insensitivity of the complex. © 2018, Stuttfeld et al.

Structure of N-acetyl-[beta]-D-glucosaminidase (GcnA) from the Endocarditis Pathogen Streptococcus gordonii and its Complex with the Mechanism-based Inhibitor NAG-thiazoline

Energy Technology Data Exchange (ETDEWEB)

Langley, David B.; Harty, Derek W.S.; Jacques, Nicholas A.; Hunter, Neil; Guss, J. Mitchell; Collyer, Charles A. (Sydney); (Westmead)

2008-09-17

The crystal structure of GcnA, an N-acetyl-{beta}-D-glucosaminidase from Streptococcus gordonii, was solved by multiple wavelength anomalous dispersion phasing using crystals of selenomethionine-substituted protein. GcnA is a homodimer with subunits each comprised of three domains. The structure of the C-terminal {alpha}-helical domain has not been observed previously and forms a large dimerization interface. The fold of the N-terminal domain is observed in all structurally related glycosidases although its function is unknown. The central domain has a canonical ({beta}/{alpha}){sub 8} TIM-barrel fold which harbours the active site. The primary sequence and structure of this central domain identifies the enzyme as a family 20 glycosidase. Key residues implicated in catalysis have different conformations in two different crystal forms, which probably represent active and inactive conformations of the enzyme. The catalytic mechanism for this class of glycoside hydrolase, where the substrate rather than the enzyme provides the cleavage-inducing nucleophile, has been confirmed by the structure of GcnA complexed with a putative reaction intermediate analogue, N-acetyl-{beta}-D-glucosamine-thiazoline. The catalytic mechanism is discussed in light of these and other family 20 structures.

Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides

Energy Technology Data Exchange (ETDEWEB)

Abdur, Rob; Gerlits, Oksana O.; Gan, Jianhua; Jiang, Jiansheng; Salon, Jozef; Kovalevsky, Andrey Y.; Chumanevich, Alexander A.; Weber, Irene T.; Huang, Zhen, E-mail: huang@gsu.edu [Georgia State University, Atlanta, GA 30303 (United States)

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 scissile 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.

Is the largest aqueous gold cluster a superatom complex? Electronic structure & optical response of the structurally determined Au146(p-MBA)57.

Science.gov (United States)

López-Lozano, Xóchitl; Plascencia-Villa, G; Calero, G; Whetten, R L; Weissker, Hans-Christian

2017-12-07

The new water-soluble gold cluster Au 146 (p-MBA) 57 , the structure of which has been recently determined at sub-atomic resolution by Vergara et al., is the largest aqueous gold cluster ever structurally determined and likewise the smallest cluster with a stacking fault. The core presents a twinned truncated octahedron, while additional peripheral gold atoms follow a C 2 rotational symmetry. According to the usual counting rules of the superatom complex (SAC) model, the compound attains a number of 92 SAC electrons if the overall net charge is 3- (three additional electrons). As this is the number of electrons required for a major shell closing, the question arises of whether Au 146 (p-MBA) 57 should be regarded as a superatom complex. Starting from the experimental coordinates we have analyzed the structure using density-functional theory. The optimized (relaxed) structure retains all the connectivity of the experimental coordinates, while removing much of its irregularities in interatomic distances, thereby enhancing the C 2 -symmetry feature. On analyzing the angular-momentum-projected states, we show that, despite a small gap, the electronic structure does not exhibit SAC model character. In addition, optical absorption spectra are found to be relatively smooth compared to the example of the Au 144 (SR) 60 cluster. The Au 146 (SR) 57 does not derive its stability from SAC character; it cannot be considered as a superatom complex.

The guanidinium group as a key part of water-soluble polymer carriers for siRNA complexation and protection against degradation.

Science.gov (United States)

Tabujew, Ilja; Freidel, Christoph; Krieg, Bettina; Helm, Mark; Koynov, Kaloian; Müllen, Klaus; Peneva, Kalina

2014-07-01

Here, the preparation of a novel block copolymer consisting of a statistical copolymer N-(2-hydroxypropyl) methacrylamide-s-N-(3-aminopropyl) methacrylamide and a short terminal 3-guanidinopropyl methacrylamide block is reported. This polymer structure forms neutral but water-soluble nanosized complexes with siRNA. The siRNA block copolymer complexes are first analyzed using agarose gel electrophoresis and their size is determined with fluorescence correlation spectroscopy. The protective properties of the polymer against RNA degradation are investigated by treating the siRNA block copolymer complexes with RNase V1. Heparin competition assays confirm the efficient release of the cargo in vitro. In addition, the utilization of microscale thermophoresis is demonstrated for the determination of the binding strength between a fluorescently labeled polyanion and a polymer molecule. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Developing a framework for qualitative engineering: Research in design and analysis of complex structural systems

Science.gov (United States)

Franck, Bruno M.

1990-01-01

The research is focused on automating the evaluation of complex structural systems, whether for the design of a new system or the analysis of an existing one, by developing new structural analysis techniques based on qualitative reasoning. The problem is to identify and better understand: (1) the requirements for the automation of design, and (2) the qualitative reasoning associated with the conceptual development of a complex system. The long-term objective is to develop an integrated design-risk assessment environment for the evaluation of complex structural systems. The scope of this short presentation is to describe the design and cognition components of the research. Design has received special attention in cognitive science because it is now identified as a problem solving activity that is different from other information processing tasks (1). Before an attempt can be made to automate design, a thorough understanding of the underlying design theory and methodology is needed, since the design process is, in many cases, multi-disciplinary, complex in size and motivation, and uses various reasoning processes involving different kinds of knowledge in ways which vary from one context to another. The objective is to unify all the various types of knowledge under one framework of cognition. This presentation focuses on the cognitive science framework that we are using to represent the knowledge aspects associated with the human mind's abstraction abilities and how we apply it to the engineering knowledge and engineering reasoning in design.

On the structure of thorium and americium adenosine triphosphate complexes

International Nuclear Information System (INIS)

Mostapha, Sarah; Berton, Laurence; Boubals, Nathalie; Zorz, Nicole; Charbonnel, Marie-Christine; Fontaine-Vive, Fabien; Den Auwer, Christophe; Solari, Pier Lorenzo

2014-01-01

The actinides are chemical poisons and radiological hazards. One challenge to better appraise their toxicity and develop countermeasures in case of exposure of living organisms is to better assess pathways of contamination. Because of the high chemical affinity of those actinide elements for phosphate groups and the ubiquity of such chemical functions in biochemistry, nucleotides and in particular adenosine triphosphate nucleotide (ATP) may be considered critical target building blocks for actinides. Combinations of spectroscopic techniques (Fourier transformed Infra Red [FTIR], Electro-spray Ionization Mass Spectrometry [ESI-MS], and Extended X-ray Absorption Fine Structure [EXAFS]) with quantum chemical calculations have been implemented in order to assess the actinides coordination arrangement with ATP. We describe and compare herein the interaction of ATP with thorium and americium; thorium(IV) as a representative of actinide(IV) like plutonium(IV) and americium(III) as a representative of all heavier actinides. In the case of thorium, an insoluble complex is readily formed. In the case of americium, a behavior identical to that described previously for lutetium has been observed with insoluble and soluble complexes. The comparative study of ATP complexation with Th(IV) and Am(III) shows their ability to form insoluble complexes for which a structural model has been proposed by analogy with previously described Lu(III) complexes. (authors)

On the structure of thorium and americium adenosine triphosphate complexes.

Science.gov (United States)

Mostapha, Sarah; Fontaine-Vive, Fabien; Berthon, Laurence; Boubals, Nathalie; Zorz, Nicole; Solari, Pier Lorenzo; Charbonnel, Marie Christine; Den Auwer, Christophe

2014-11-01

The actinides are chemical poisons and radiological hazards. One challenge to better appraise their toxicity and develop countermeasures in case of exposure of living organisms is to better assess pathways of contamination. Because of the high chemical affinity of those actinide elements for phosphate groups and the ubiquity of such chemical functions in biochemistry, nucleotides and in particular adenosine triphosphate nucleotide (ATP) may be considered critical target building blocks for actinides. Combinations of spectroscopic techniques (Fourier transformed Infra Red [FTIR], Electrospray Ionization Mass Spectrometry [ESI-MS], and Extended X-ray Absorption Fine Structure [EXAFS]) with quantum chemical calculations have been implemented in order to assess the actinides coordination arrangement with ATP. We describe and compare herein the interaction of ATP with thorium and americium; thorium(IV) as a representative of actinide(IV) like plutonium(IV) and americium(III) as a representative of all heavier actinides. In the case of thorium, an insoluble complex is readily formed. In the case of americium, a behavior identical to that described previously for lutetium has been observed with insoluble and soluble complexes. The comparative study of ATP complexation with Th(IV) and Am(III) shows their ability to form insoluble complexes for which a structural model has been proposed by analogy with previously described Lu(III) complexes.

Copper-based metal coordination complexes with Voriconazole ligand: Syntheses, structures and antimicrobial properties

Science.gov (United States)

Zhao, Yan-Ming; Tang, Gui-Mei; Wang, Yong-Tao; Cui, Yue-Zhi; Ng, Seik Weng

2018-03-01

Three new chiral metal coordination complexes, namely, [Cu(FZ)2(CH3COO)2(H2O)]·2H2O (1), [Cu(FZ)2(NO3)2] (2), and [Cu2(FZ)2 (H2O)8](SO4)2·4H2O (3) [FZ = (2R,3S)-2-(2,4-difluorophenyl)-3-(5-fluoro-4-pyrimidiny)-1-(1H-1,2,4-triazol-1-yl)-2-butanol) (Voriconazole)] have been obtained by the reaction of Cu(II) salts and the free ligand FZ at room temperature. Complexes 1-3 were structurally characterized by X-ray single-crystal diffraction, IR, UV-vis, powder X-ray diffraction (PXRD), and thermogravimetric analysis (TGA). Complex 1 crystallizes in the chiral space group C2, which exhibits a mono-nuclear structure. Both complexes 2 and 3 display a one-dimensional (1D) tape structure, which crystallize in chiral space group P21212 and P212121, respectively. Among these complexes, there exist a variety of hydrogen bonds and stacking interactions, through which a three-dimensional supramolecular architecture will be generated. Compared with the standard (Voriconazole), these Cu-based complexes show the more potent inhibiting efficiency against the species of Candida and Aspergillus. Moreover, among these complexes, complex 1 shows the most excellent efficiency.

Typological diversity of tall buildings and complexes in relation to their functional structure

Science.gov (United States)

Generalov, Viktor P.; Generalova, Elena M.; Kalinkina, Nadezhda A.; Zhdanova, Irina V.

2018-03-01

The paper focuses on peculiarities of tall buildings and complexes, their typology and its formation in relation to their functional structure. The research is based on the analysis of tall buildings and complexes and identifies the following main functional elements of their formation: residential, administrative (office), hotel elements. The paper also considers the following services as «disseminated» in the space-planning structure: shops, medicine, entertainment, kids and sports facilities, etc., their location in the structure of the total bulk of the building and their impact on typological diversity. Research results include suggestions to add such concepts as «single-function tall buildings» and «mixed-use tall buildings and complexes» into the classification of tall buildings. In addition, if a single-function building or complex performs serving functions, it is proposed to add such concepts as «a residential tall building (complex) with provision of services», «an administrative (public) tall building (complex) with provision of services» into the classification of tall buildings. For mixed-use buildings and complexes the following terms are suggested: «a mixed-use tall building with provision of services», «a mixed-use tall complex with provision of services».

The kinesin–tubulin complex: considerations in structural and functional complexity

Directory of Open Access Journals (Sweden)

Olmsted ZT

2015-02-01

Full Text Available Zachary T Olmsted, Andrew G Colliver, Janet L Paluh State University of New York Polytechnic Institute, Colleges of Nanoscale Science and Engineering, College of Nanoscale Science, Nanobioscience Constellation, Albany, NY, USA Abstract: The ability of cells to respond to external cues by appropriately manipulating their internal environment requires a dynamic microtubule cytoskeleton that is facilitated by associated kinesin motor interactions. The evolutionary adaptations of kinesins and tubulins when merged generate a highly adaptable communication and infrastructure cellular network that is important to understanding specialized cell functions, human disease, and disease therapies. Here, we review the state of the field in the complex relationship of kinesin–tubulin interactions. We propose 12 mechanistic specializations of kinesins. In one category, referred to as sortability, we describe how kinesin interactions with tubulin isoforms, isotypes, or posttranslationally modified tubulins contribute to diverse cellular roles. Fourteen kinesin families have previously been described. Here, we illustrate the great depth of functional complexity that is possible in members within a single kinesin family by mechanistic specialization through discussion of the well-studied Kinesin-14 family. This includes new roles of Kinesin-14 in regulating supramolecular structures such as the microtubule-organizing center γ-tubulin ring complex of centrosomes. We next explore the value of an improved mechanistic understanding of kinesin–tubulin interactions in regard to human development, disease mechanisms, and improving treatments that target kinesin–tubulin complexes. The ability to combine the current kinesin nomenclature along with a more precisely defined kinesin and tubulin molecular toolbox is needed to support more detailed exploration of kinesin–tubulin interaction mechanisms including functional uniqueness, redundancy, or adaptations to new

Coherent wavepackets in the Fenna-Matthews-Olson complex are robust to excitonic-structure perturbations caused by mutagenesis

Science.gov (United States)

Maiuri, Margherita; Ostroumov, Evgeny E.; Saer, Rafael G.; Blankenship, Robert E.; Scholes, Gregory D.

2018-02-01

Femtosecond pulsed excitation of light-harvesting complexes creates oscillatory features in their response. This phenomenon has inspired a large body of work aimed at uncovering the origin of the coherent beatings and possible implications for function. Here we exploit site-directed mutagenesis to change the excitonic level structure in Fenna-Matthews-Olson (FMO) complexes and compare the coherences using broadband pump-probe spectroscopy. Our experiments detect two oscillation frequencies with dephasing on a picosecond timescale—both at 77 K and at room temperature. By studying these coherences with selective excitation pump-probe experiments, where pump excitation is in resonance only with the lowest excitonic state, we show that the key contributions to these oscillations stem from ground-state vibrational wavepackets. These experiments explicitly show that the coherences—although in the ground electronic state—can be probed at the absorption resonances of other bacteriochlorophyll molecules because of delocalization of the electronic excitation over several chromophores.

Photoelectron spectra and electronic structure of some spiroborate complexes

Energy Technology Data Exchange (ETDEWEB)

Vovna, V.I.; Tikhonov, S.A.; Lvov, I.B., E-mail: lvov.ib@dvfu.ru; Osmushko, I.S.; Svistunova, I.V.; Shcheka, O.L.

2014-12-15

Highlights: • The electronic structure of three spiroborate complexes—boron 1,2-dioxyphenylene β-diketonates has been investigated. • UV and X-ray photoelectron spectra have been interpreted. • DFT calculations have been used for interpretation of spectral bands. • The binding energy of nonequivalent carbon and oxygen atoms were measured. • The structure of X-ray photoelectron spectra of the valence electrons is in good agreement with the energies and composition of Kohn–Sham orbitals. - Abstract: The electronic structure of the valence and core levels of three spiroborate complexes – boron 1,2-dioxyphenylene β-diketonates – has been investigated by methods of UV and X-ray photoelectron spectroscopy and quantum chemical density functional theory. The ionization energy of π- and n-orbitals of the dioxyphenylene fragment and β-diketonate ligand were measured from UV photoelectron spectra. This made it possible to determine the effect of substitution of one or two methyl groups by the phenyl in diketone on the electronic structure of complexes. The binding energy of nonequivalent carbon and oxygen atoms were measured from X-ray photoelectron spectra. The results of calculations of the energy of the valence orbitals of complexes allowed us to refer bands observed in the spectra of the valence electrons to the 2s-type levels of carbon and oxygen.

Analysis of the structure of complex networks at different resolution levels

Energy Technology Data Exchange (ETDEWEB)

Arenas, A.; Fernandez, A.; Gomez, S.

2008-02-28

Modular structure is ubiquitous in real-world complex networks, and its detection is important because it gives insights in the structure-functionality relationship. The standard approach is based on the optimization of a quality function, modularity, which is a relative quality measure for a partition of a network into modules. Recently some authors have pointed out that the optimization of modularity has a fundamental drawback: the existence of a resolution limit beyond which no modular structure can be detected even though these modules might have own entity. The reason is that several topological descriptions of the network coexist at different scales, which is, in general, a fingerprint of complex systems. Here we propose a method that allows for multiple resolution screening of the modular structure. The method has been validated using synthetic networks, discovering the predefined structures at all scales. Its application to two real social networks allows to find the exact splits reported in the literature, as well as the substructure beyond the actual split.

Cellulose synthase complex organization and cellulose microfibril structure.

Science.gov (United States)

Turner, Simon; Kumar, Manoj

2018-02-13

Cellulose consists of linear chains of β-1,4-linked glucose units, which are synthesized by the cellulose synthase complex (CSC). In plants, these chains associate in an ordered manner to form the cellulose microfibrils. Both the CSC and the local environment in which the individual chains coalesce to form the cellulose microfibril determine the structure and the unique physical properties of the microfibril. There are several recent reviews that cover many aspects of cellulose biosynthesis, which include trafficking of the complex to the plasma membrane and the relationship between the movement of the CSC and the underlying cortical microtubules (Bringmann et al. 2012 Trends Plant Sci. 17 , 666-674 (doi:10.1016/j.tplants.2012.06.003); Kumar & Turner 2015 Phytochemistry 112 , 91-99 (doi:10.1016/j.phytochem.2014.07.009); Schneider et al. 2016 Curr. Opin. Plant Biol. 34 , 9-16 (doi:10.1016/j.pbi.2016.07.007)). In this review, we will focus on recent advances in cellulose biosynthesis in plants, with an emphasis on our current understanding of the structure of individual catalytic subunits together with the local membrane environment where cellulose synthesis occurs. We will attempt to relate this information to our current knowledge of the structure of the cellulose microfibril and propose a model in which variations in the structure of the CSC have important implications for the structure of the cellulose microfibril produced.This article is part of a discussion meeting issue 'New horizons for cellulose nanotechnology'. © 2017 The Author(s).

Imaging and structural studies of DNA–protein complexes and membrane ion channels

KAUST Repository

Marini, Monica; Limongi, Tania; Falqui, Andrea; Genovese, Alessandro; Allione, Marco; Moretti, Manola; Lopatin, Sergei; Tirinato, Luca; Das, Gobind; Torre, Bruno; Giugni, Andrea; Cesca, F.; Benfenati, F.; Di Fabrizio, Enzo M.

2017-01-01

In bio-imaging by electron microscopy, damage of the sample and limited contrast are the two main hurdles for reaching high image quality. We extend a new preparation method based on nanofabrication and super-hydrophobicity to the imaging and structural studies of nucleic acids, nucleic acid-protein complexes (DNA/Rad51 repair protein complex) and neuronal ion channels (gap-junction, K+ and GABA(A) channels) as paradigms of biological significance and increasing complexity. The preparation method is based on the liquid phase and is compatible with physiological conditions. Only in the very last stage, samples are dried for TEM analysis. Conventional TEM and high-resolution TEM (HRTEM) were used to achieve a resolution of 3.3 and 1.5 angstrom, respectively. The EM dataset quality allows the determination of relevant structural and metrological information on the DNA structure, DNA-protein interactions and ion channels, allowing the identification of specific macromolecules and their structure.

Imaging and structural studies of DNA–protein complexes and membrane ion channels

KAUST Repository

Marini, Monica

2017-01-17

In bio-imaging by electron microscopy, damage of the sample and limited contrast are the two main hurdles for reaching high image quality. We extend a new preparation method based on nanofabrication and super-hydrophobicity to the imaging and structural studies of nucleic acids, nucleic acid-protein complexes (DNA/Rad51 repair protein complex) and neuronal ion channels (gap-junction, K+ and GABA(A) channels) as paradigms of biological significance and increasing complexity. The preparation method is based on the liquid phase and is compatible with physiological conditions. Only in the very last stage, samples are dried for TEM analysis. Conventional TEM and high-resolution TEM (HRTEM) were used to achieve a resolution of 3.3 and 1.5 angstrom, respectively. The EM dataset quality allows the determination of relevant structural and metrological information on the DNA structure, DNA-protein interactions and ion channels, allowing the identification of specific macromolecules and their structure.

KEY ASPECTS OF ENSURING ENERGY EFFICIENCY OF BUILDINGS AND STRUCTURES

Directory of Open Access Journals (Sweden)

S.G. Abramyan

2017-06-01

Full Text Available The paper is based on the review of the foreign and national academic literature and intended to emphasize the issues of ensuring energy efficiency of buildings and structures applicable to all the countries as for reconstruction of existing buildings as for erection of new ones . The author highlights the key aspects of the provision of energy efficiency of buildings and structures in some foreign countries. The conclusion is made that the studies are mainly aimed at discovering new heat insulation materials, whereby polystyrene insulation is found to be the most widespread wall insulation material in a number of countries. At the same time, it is observed that the ongoing research is focused on solutions to optimize the structure of walling systems in terms of both insulant thickness and the number and sequence of insulation layers in the walling structure. A conclusion is made that hyper insulation of external walls leads to considerable expenses arising due to cooling during the summer season. The use of prefabricated vacuum panels as a heat insulation layer and off-the-shelf single-layer structures, subject to their heat insulation characteristics, appears a more constructive way to meet the energy efficiency requirements, as the arrangement of ideal air space in multilayered walls proves a significant challenge today. One of the most promising ways to ensure energy efficiency is the use of multifunctional polyvalent walls and provision of polyvalent heat supply from renewable energy sources. Since energy efficiency depends on the spatial arrangement of buildings, construction must ensure a minimum ratio of the area of enclosing structures to the overall building volume (by adding on new facilities in case of reconstruction. It is noted that a systemic approach to ensuring energy efficiency of buildings is impossible without proper regard to the environmental parameters of heat insulation materials.

Simple Web-based interactive key development software (WEBiKEY) and an example key for Kuruna (Poaceae: Bambusoideae).

Science.gov (United States)

Attigala, Lakshmi; De Silva, Nuwan I; Clark, Lynn G

2016-04-01

Programs that are user-friendly and freely available for developing Web-based interactive keys are scarce and most of the well-structured applications are relatively expensive. WEBiKEY was developed to enable researchers to easily develop their own Web-based interactive keys with fewer resources. A Web-based multiaccess identification tool (WEBiKEY) was developed that uses freely available Microsoft ASP.NET technologies and an SQL Server database for Windows-based hosting environments. WEBiKEY was tested for its usability with a sample data set, the temperate woody bamboo genus Kuruna (Poaceae). WEBiKEY is freely available to the public and can be used to develop Web-based interactive keys for any group of species. The interactive key we developed for Kuruna using WEBiKEY enables users to visually inspect characteristics of Kuruna and identify an unknown specimen as one of seven possible species in the genus.

A structural investigation of complex I and I+III2 supercomplex from Zea mays at 11-13 angstrom resolution : Assignment of the carbonic anhydrase domain and evidence for structural heterogeneity within complex I

NARCIS (Netherlands)

Peters, Katrin; Dudkina, Natalya V.; Jaensch, Lothar; Braun, Hans-Peter; Boekema, Egbert J.; Jänsch, Lothar

The projection structures of complex I and the I+III2 supercomplex from the C-4 plant Zea mays were determined by electron microscopy and single particle image analysis to a resolution of up to 11 angstrom. Maize complex I has a typical L-shape. Additionally, it has a large hydrophilic, extra-domain

Cationic liposome/DNA complexes: from structure to interactions with cellular membranes.

Science.gov (United States)

Caracciolo, Giulio; Amenitsch, Heinz

2012-10-01

Gene-based therapeutic approaches are based upon the concept that, if a disease is caused by a mutation in a gene, then adding back the wild-type gene should restore regular function and attenuate the disease phenotype. To deliver the gene of interest, both viral and nonviral vectors are used. Viruses are efficient, but their application is impeded by detrimental side-effects. Among nonviral vectors, cationic liposomes are the most promising candidates for gene delivery. They form stable complexes with polyanionic DNA (lipoplexes). Despite several advantages over viral vectors, the transfection efficiency (TE) of lipoplexes is too low compared with those of engineered viral vectors. This is due to lack of knowledge about the interactions between complexes and cellular components. Rational design of efficient lipoplexes therefore requires deeper comprehension of the interactions between the vector and the DNA as well as the cellular pathways and mechanisms involved. The importance of the lipoplex structure in biological function is revealed in the application of synchrotron small-angle X-ray scattering in combination with functional TE measurements. According to current understanding, the structure of lipoplexes can change upon interaction with cellular membranes and such changes affect the delivery efficiency. Recently, a correlation between the mechanism of gene release from complexes, the structure, and the physical and chemical parameters of the complexes has been established. Studies aimed at correlating structure and activity of lipoplexes are reviewed herein. This is a fundamental step towards rational design of highly efficient lipid gene vectors.

A new Kaempferol-based Ru(II) coordination complex, Ru(kaem)Cl(DMSO)3: Structure and absorption-emission spectroscopy study

International Nuclear Information System (INIS)

Shao, Ming Wei; Gang, Jong Back; Kim, Sang Ho; Yoon, Min Young

2016-01-01

Recent interest in developing a new anticancer drug with low side effects has led to the study of the combination of two new anticancer drugs. Although both kaempferol (kaem) and Ru-based metal complexes have not been proven as effective drugs, their unique anticancer activities with reduced side effects have drawn our attention to the need for further studies on their potential in anticancer application. Herein, we report the synthesis, characterization, structure, and spectroscopic properties of a kaem-based Ru (II) complex, RuCl(kaem)(DMSO) 3 (1). Because of the presence of a catechol-like functional group in its dihydropyran ring, kaem can strongly bind to the Ru(II) metal center in a basic medium. The molecular structure of the complex was characterized by spectroscopic studies and X-ray crystal structure analysis. In addition, the complex forms a molecular dimer as a result of the cooperative effect of H-bonding and π–π stacking interactions. Moreover, the molecular dimer forms a ladder-like one-dimensional network structure by water mediated H-bonding that further extended into a three-dimensional packing structure. UV–Vis spectroscopy studies of the complex demonstrated the appearance of a strong metal to ligand charge transfer (MLCT) band in the visible region with strong fluorescence emission derived from the MLCT. Further studies are now in progress to demonstrate synergetic anticancer activity

Structural Insights into HIV Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance

Energy Technology Data Exchange (ETDEWEB)

Das, Kalyan; Martinez, Sergio E.; Arnold, Eddy

2017-04-10

HIV-1 reverse transcriptase (RT) is targeted by multiple drugs. RT mutations that confer resistance to nucleoside RT inhibitors (NRTIs) emerge during clinical use. Q151M and four associated mutations, A62V, V75I, F77L, and F116Y, were detected in patients failing therapies with dideoxynucleosides (didanosine [ddI], zalcitabine [ddC]) and/or zidovudine (AZT). The cluster of the five mutations is referred to as the Q151M complex (Q151Mc), and an RT or virus containing Q151Mc exhibits resistance to multiple NRTIs. To understand the structural basis for Q151M and Q151Mc resistance, we systematically determined the crystal structures of the wild-type RT/double-stranded DNA (dsDNA)/dATP (complex I), wild-type RT/dsDNA/ddATP (complex II), Q151M RT/dsDNA/dATP (complex III), Q151Mc RT/dsDNA/dATP (complex IV), and Q151Mc RT/dsDNA/ddATP (complex V) ternary complexes. The structures revealed that the deoxyribose rings of dATP and ddATP have 3'-endo and 3'-exo conformations, respectively. The single mutation Q151M introduces conformational perturbation at the deoxynucleoside triphosphate (dNTP)-binding pocket, and the mutated pocket may exist in multiple conformations. The compensatory set of mutations in Q151Mc, particularly F116Y, restricts the side chain flexibility of M151 and helps restore the DNA polymerization efficiency of the enzyme. The altered dNTP-binding pocket in Q151Mc RT has the Q151-R72 hydrogen bond removed and has a switched conformation for the key conserved residue R72 compared to that in wild-type RT. On the basis of a modeled structure of hepatitis B virus (HBV) polymerase, the residues R72, Y116, M151, and M184 in Q151Mc HIV-1 RT are conserved in wild-type HBV polymerase as residues R41, Y89, M171, and M204, respectively; functionally, both Q151Mc HIV-1 and wild-type HBV are resistant to dideoxynucleoside analogs.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

Science.gov (United States)

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-04-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

Thermodynamical properties and thermoelastic coupling of complex macroscopic structure

International Nuclear Information System (INIS)

Fabbri, M.; Sacripanti, A.

1996-11-01

Gross qualitative/quantitative analysis about thermodynamical properties and thermoelastic coupling (or elastocaloric effect) of complex macroscopic structure (running shoes) is performed by infrared camera. The experimental results showed the achievability of a n industrial research project

Open-ringed structure of the Cdt1-Mcm2-7 complex as a precursor of the MCM double hexamer.

Science.gov (United States)

Zhai, Yuanliang; Cheng, Erchao; Wu, Hao; Li, Ningning; Yung, Philip Yuk Kwong; Gao, Ning; Tye, Bik-Kwoon

2017-03-01

The minichromosome maintenance complex (MCM) hexameric complex (Mcm2-7) forms the core of the eukaryotic replicative helicase. During G1 phase, two Cdt1-Mcm2-7 heptamers are loaded onto each replication origin by the origin-recognition complex (ORC) and Cdc6 to form an inactive MCM double hexamer (DH), but the detailed loading mechanism remains unclear. Here we examine the structures of the yeast MCM hexamer and Cdt1-MCM heptamer from Saccharomyces cerevisiae. Both complexes form left-handed coil structures with a 10-15-Å gap between Mcm5 and Mcm2, and a central channel that is occluded by the C-terminal domain winged-helix motif of Mcm5. Cdt1 wraps around the N-terminal regions of Mcm2, Mcm6 and Mcm4 to stabilize the whole complex. The intrinsic coiled structures of the precursors provide insights into the DH formation, and suggest a spring-action model for the MCM during the initial origin melting and the subsequent DNA unwinding.

The Influence of Fluorination on Structure of the Trifluoroacetonitrile Water Complex

Science.gov (United States)

Lin, Wei; Wu, Anan; Lu, Xin; Obenchain, Daniel A.; Novick, Stewart E.

2015-06-01

Acetonitrile, CH_3CN, and trifluoroacetonitrile, CF_3CN, are symmetric tops. In a recent study of the rotational spectrum of the acetonitrile and water complex, it was observed that the structure was also an effective symmetric top, with the external hydrogen freely rotating about the O-H bond aligned towards the nitrogen of the cyanide of CH_3CN. Unlike the CH_3CN-H_2O complex, the CH_3CN-Ar and CF_3CN-Ar complexes were observed to be asymmetric tops. Having a series of symmetric and asymmetric top complexes of acetonitrile and trifluoracetonitrile for comparison, we report the rotational spectrum of the weakly bound complex between trifluoroacetonitrile and water. Rotational constants and quadrupole coupling constants will be presented, and the structure of CF_3CN-H_2O will be revealed. Lovas, F.J.; Sobhanadri, J. Microwave rotational spectral study of CH_3CN-H_2O and Ar-CH_3CN. J. Mol. Spetrosc. 2015, 307, 59-64. SPOILER ALERT: It's an asymmetric top.

Key technological issues in LMFBR high-temperature structural design - the US perspective

International Nuclear Information System (INIS)