Three-dimensional distribution of polymorphs and magnesium in a calcified underwater attachment system by diffraction tomography

PubMed Central

Leemreize, Hanna; Almer, Jonathan D.; Stock, Stuart R.; Birkedal, Henrik

2013-01-01

Biological materials display complicated three-dimensional hierarchical structures. Determining these structures is essential in understanding the link between material design and properties. Herein, we show how diffraction tomography can be used to determine the relative placement of the calcium carbonate polymorphs calcite and aragonite in the highly mineralized holdfast system of the bivalve Anomia simplex. In addition to high fidelity and non-destructive mapping of polymorphs, we use detailed analysis of X-ray diffraction peak positions in reconstructed powder diffraction data to determine the local degree of Mg substitution in the calcite phase. These data show how diffraction tomography can provide detailed multi-length scale information on complex materials in general and of biomineralized tissues in particular. PMID:23804437

Protein structure determination by exhaustive search of Protein Data Bank derived databases.

PubMed

Stokes-Rees, Ian; Sliz, Piotr

2010-12-14

Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from Trichoplusia ni. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database.

The search for a structural basis for therapeutic intervention against the SARS coronavirus

NASA Astrophysics Data System (ADS)

Bartlam, M.; Xue, X.; Rao, Z.

2008-01-01

The severe acute respiratory syndrome (SARS) coronavirus outbreak in 2003 had profound social and economic impacts worldwide. This review highlights the importance of structural biology and shows that structures for drug design can be rapidly determined in the event of an emerging infectious disease.

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

Osipiuk, J.; Gornicki, P.; Maj, L.

The structure of the YlxR protein of unknown function from Streptococcus pneumonia was determined to 1.35 Angstroms. YlxR is expressed from the nusA/infB operon in bacteria and belongs to a small protein family (COG2740) that shares a conserved sequence motif GRGA(Y/W). The family shows no significant amino-acid sequence similarity with other proteins. Three-wavelength diffraction MAD data were collected to 1.7 Angstroms from orthorhombic crystals using synchrotron radiation and the structure was determined using a semi-automated approach. The YlxR structure resembles a two-layer {alpha}/{beta} sandwich with the overall shape of a cylinder and shows no structural homology to proteins of knownmore » structure. Structural analysis revealed that the YlxR structure represents a new protein fold that belongs to the {alpha}-{beta} plait superfamily. The distribution of the electrostatic surface potential shows a large positively charged patch on one side of the protein, a feature often found in nucleic acid-binding proteins. Three sulfate ions bind to this positively charged surface. Analysis of potential binding sites uncovered several substantial clefts, with the largest spanning 3/4 of the protein. A similar distribution of binding sites and a large sharply bent cleft are observed in RNA-binding proteins that are unrelated in sequence and structure. It is proposed that YlxR is an RNA-binding protein.« less

Data on crystal organization in the structure of the Fab fragment from the NIST reference antibody, RM 8671.

PubMed

Gallagher, D T; Karageorgos, I; Hudgens, J W; Galvin, C V

2018-02-01

The reported data describe the crystallization, crystal packing, structure determination and twinning of the unliganded Fab (antigen-binding fragment) from the NISTmAb (standard reference material 8671). The raw atomic coordinates are available as Protein Data Bank structure 5K8A and biological aspects are described in the article, (Karageorgos et al., 2017) [1]. Crystal data show that the packing is unique, and show the basis for the crystal's twinned growth. Twinning is a common and often serious problem in protein structure determination by x-ray crystallography [2]. In the present case the twinning is due to a small deviation (about 0.3 nm) from 4-fold symmetry in the primary intermolecular interface. The deviation produces pseudosymmetry, generating slightly different conformations of the protein, and alternating strong and weak forms of key packing interfaces throughout the lattice.

Epitope mapping of the domains of human angiotensin converting enzyme.

PubMed

Kugaevskaya, Elena V; Kolesanova, Ekaterina F; Kozin, Sergey A; Veselovsky, Alexander V; Dedinsky, Ilya R; Elisseeva, Yulia E

2006-06-01

Somatic angiotensin converting enzyme (sACE), contains in its single chain two homologous domains (called N- and C-domains), each bearing a functional zinc-dependent active site. The present study aims to define the differences between two sACE domains and to localize experimentally revealed antigenic determinants (B-epitopes) in the recently determined three-dimensional structure of testicular tACE. The predicted linear antigenic determinants of human sACE were determined by peptide scanning ("PEPSCAN") approach. Essential difference was demonstrated between locations of the epitopes in the N- and C-domains. Comparison of arrangement of epitopes in the human domains with the corresponding sequences of some mammalian sACEs enabled to classify the revealed antigenic determinants as variable or conserved areas. The location of antigenic determinants with respect to various structural elements and to functionally important sites of the human sACE C-domain was estimated. The majority of antigenic sites of the C-domain were located at the irregular elements and at the boundaries of secondary structure elements. The data show structural differences between the sACE domains. The experimentally revealed antigenic determinants were in agreement with the recently determined crystal tACE structure. New potential applications are open to successfully produce mono-specific and group-specific antipeptide antibodies.

Influence of water immersion on the mechanical properties of fiber posts.

PubMed

Komada, Wataru; Inagaki, Tasuku; Ueda, Yoji; Omori, Satoshi; Hosaka, Keiichi; Tagami, Junji; Miura, Hiroyuki

2017-01-01

The purpose of this study was to evaluate the influence of water immersion on the mechanical properties of three kinds of glass fiber posts and the fracture resistance of structures using resin composites with glass fiber posts. Each post was divided into three groups; a control group and two water immersion groups (30 and 90 days). Flexural strength was determined by three-point bending test. Each structure was divided into two groups; a control group and a water immersion group for 30 days. The fracture strength of structures was determined by a static loading test. In the flexural strength, two kinds of post in water immersion groups showed lower values than control groups. In the fracture strength, two kinds of structures in water immersion group showed lower values than control groups. The prefabricated glass fiber posts and structures using resin composites with glass fiber posts were affected by water immersion. Copyright © 2016 Japan Prosthodontic Society. Published by Elsevier Ltd. All rights reserved.

Structures of actin-like ParM filaments show architecture of plasmid-segregating spindles.

PubMed

Bharat, Tanmay A M; Murshudov, Garib N; Sachse, Carsten; Löwe, Jan

2015-07-02

Active segregation of Escherichia coli low-copy-number plasmid R1 involves formation of a bipolar spindle made of left-handed double-helical actin-like ParM filaments. ParR links the filaments with centromeric parC plasmid DNA, while facilitating the addition of subunits to ParM filaments. Growing ParMRC spindles push sister plasmids to the cell poles. Here, using modern electron cryomicroscopy methods, we investigate the structures and arrangements of ParM filaments in vitro and in cells, revealing at near-atomic resolution how subunits and filaments come together to produce the simplest known mitotic machinery. To understand the mechanism of dynamic instability, we determine structures of ParM filaments in different nucleotide states. The structure of filaments bound to the ATP analogue AMPPNP is determined at 4.3 Å resolution and refined. The ParM filament structure shows strong longitudinal interfaces and weaker lateral interactions. Also using electron cryomicroscopy, we reconstruct ParM doublets forming antiparallel spindles. Finally, with whole-cell electron cryotomography, we show that doublets are abundant in bacterial cells containing low-copy-number plasmids with the ParMRC locus, leading to an asynchronous model of R1 plasmid segregation.

Determination of the oxidative stability of perfluoropolyalkyl ethers and correlation with chemical structure

NASA Technical Reports Server (NTRS)

Helmick, Larry S.; Jones, William R., Jr.

1992-01-01

The oxidative stabilities of several perfluoropolyalkyl ethers (PFPAE) with related chemical structures were determined by thermal gravimetric analysis and correlated with their chemical structures. These results show that oxidative stability increases as the number of difluoroformal groups decreases and as trifluoromethyl substituents are added. They are also consistent with a recently proposed intramolecular disproportionation reaction mechanism involving coordination of successive ether oxygens to a Lewis acid. Since polytetrafluoroethylene contains no oxygen, it provides an indication of the upper limit to oxidative stability of PFPAE fluids. These results also show that oxidative decomposition of PFPAE fluids requires the presence of an active metal as well as air. Consequently, it may be possible to minimize decomposition and thus improve oxidative stability by passivating reactive metal surfaces.

Crystal structure of Au25(SePh)18 nanoclusters and insights into their electronic, optical and catalytic properties

NASA Astrophysics Data System (ADS)

Song, Yongbo; Zhong, Juan; Yang, Sha; Wang, Shuxin; Cao, Tiantian; Zhang, Jun; Li, Peng; Hu, Daqiao; Pei, Yong; Zhu, Manzhou

2014-10-01

The crystal structure of selenolate-capped Au25(SePh)18- nanoclusters has been unambiguously determined for the first time, and provides a solid basis for a deeper understanding of the structure-property relationships. The selenolate-capped Au25 cluster shows noticeable differences from the previously reported Au25(SCH2CH2Ph)18- counterpart, albeit both share the icosahedral Au13 core and semi-ring Au2(SeR)3 or Au2(SR)3 motifs. Distinct differences in the electronic structure and optical, catalytic and electrochemical properties are revealed by the coupling experiments with density functional theory (TD-DFT) calculations. Overall, the successful determination of the Au25(SePh)18- structure removes any ambiguity about its structure, and comparison with the thiolated Au25 counterpart helps us to further understand how the ligands affect the properties of the nanocluster.The crystal structure of selenolate-capped Au25(SePh)18- nanoclusters has been unambiguously determined for the first time, and provides a solid basis for a deeper understanding of the structure-property relationships. The selenolate-capped Au25 cluster shows noticeable differences from the previously reported Au25(SCH2CH2Ph)18- counterpart, albeit both share the icosahedral Au13 core and semi-ring Au2(SeR)3 or Au2(SR)3 motifs. Distinct differences in the electronic structure and optical, catalytic and electrochemical properties are revealed by the coupling experiments with density functional theory (TD-DFT) calculations. Overall, the successful determination of the Au25(SePh)18- structure removes any ambiguity about its structure, and comparison with the thiolated Au25 counterpart helps us to further understand how the ligands affect the properties of the nanocluster. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr04631e

A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory.

PubMed

Finke, John M; Cheung, Margaret S; Onuchic, José N

2004-09-01

Modeling the structure of natively disordered peptides has proved difficult due to the lack of structural information on these peptides. In this work, we use a novel application of the host-guest method, combining folding theory with experiments, to model the structure of natively disordered polyglutamine peptides. Initially, a minimalist molecular model (C(alpha)C(beta)) of CI2 is developed with a structurally based potential and captures many of the folding properties of CI2 determined from experiments. Next, polyglutamine "guest" inserts of increasing length are introduced into the CI2 "host" model and the polyglutamine is modeled to match the resultant change in CI2 thermodynamic stability between simulations and experiments. The polyglutamine model that best mimics the experimental changes in CI2 thermodynamic stability has 1), a beta-strand dihedral preference and 2), an attractive energy between polyglutamine atoms 0.75-times the attractive energy between the CI2 host Go-contacts. When free-energy differences in the CI2 host-guest system are correctly modeled at varying lengths of polyglutamine guest inserts, the kinetic folding rates and structural perturbation of these CI2 insert mutants are also correctly captured in simulations without any additional parameter adjustment. In agreement with experiments, the residues showing structural perturbation are located in the immediate vicinity of the loop insert. The simulated polyglutamine loop insert predominantly adopts extended random coil conformations, a structural model consistent with low resolution experimental methods. The agreement between simulation and experimental CI2 folding rates, CI2 structural perturbation, and polyglutamine insert structure show that this host-guest method can select a physically realistic model for inserted polyglutamine. If other amyloid peptides can be inserted into stable protein hosts and the stabilities of these host-guest mutants determined, this novel host-guest method may prove useful to determine structural preferences of these intractable but biologically relevant protein fragments.

The Structure of the Protonated Serine Octamer.

PubMed

Scutelnic, Valeriu; Perez, Marta A S; Marianski, Mateusz; Warnke, Stephan; Gregor, Aurelien; Rothlisberger, Ursula; Bowers, Michael T; Baldauf, Carsten; von Helden, Gert; Rizzo, Thomas R; Seo, Jongcheol

2018-06-20

The amino acid serine has long been known to form a protonated "magic-number" cluster containing eight monomer units that shows an unusually high abundance in mass spectra and has a remarkable homochiral preference. Despite many experimental and theoretical studies, there is no consensus on a Ser 8 H + structure that is in agreement with all experimental observations. Here, we present the structure of Ser 8 H + determined by a combination of infrared spectroscopy and ab initio molecular dynamics simulations. The three-dimensional structure that we determine is ∼25 kcal mol -1 more stable than the previous most stable published structure and explains both the homochiral preference and the experimentally observed facile replacement of two serine units.

Neutral Evolution of Multiple Quantitative Characters: A Genealogical Approach

PubMed Central

Griswold, Cortland K.; Logsdon, Benjamin; Gomulkiewicz, Richard

2007-01-01

The G matrix measures the components of phenotypic variation that are genetically heritable. The structure of G, that is, its principal components and their associated variances, determines, in part, the direction and speed of multivariate trait evolution. In this article we present a framework and results that give the structure of G under the assumption of neutrality. We suggest that a neutral expectation of the structure of G is important because it gives a null expectation for the structure of G from which the unique consequences of selection can be determined. We demonstrate how the processes of mutation, recombination, and drift shape the structure of G. Furthermore, we demonstrate how shared common ancestry between segregating alleles shapes the structure of G. Our results show that shared common ancestry, which manifests itself in the form of a gene genealogy, causes the structure of G to be nonuniform in that the variances associated with the principal components of G decline at an approximately exponential rate. Furthermore we show that the extent of the nonuniformity in the structure of G is enhanced with declines in mutation rates, recombination rates, and numbers of loci and is dependent on the pattern and modality of mutation. PMID:17339224

NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia.

PubMed

Serrano, Pedro; Dutta, Samit K; Proudfoot, Andrew; Mohanty, Biswaranjan; Susac, Lukas; Martin, Bryan; Geralt, Michael; Jaroszewski, Lukasz; Godzik, Adam; Elsliger, Marc; Wilson, Ian A; Wüthrich, Kurt

2016-11-01

For more than a decade, the Joint Center for Structural Genomics (JCSG; www.jcsg.org) worked toward increased three-dimensional structure coverage of the protein universe. This coordinated quest was one of the main goals of the four high-throughput (HT) structure determination centers of the Protein Structure Initiative (PSI; www.nigms.nih.gov/Research/specificareas/PSI). To achieve the goals of the PSI, the JCSG made use of the complementarity of structure determination by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy to increase and diversify the range of targets entering the HT structure determination pipeline. The overall strategy, for both techniques, was to determine atomic resolution structures for representatives of large protein families, as defined by the Pfam database, which had no structural coverage and could make significant contributions to biological and biomedical research. Furthermore, the experimental structures could be leveraged by homology modeling to further expand the structural coverage of the protein universe and increase biological insights. Here, we describe what could be achieved by this structural genomics approach, using as an illustration the contributions from 20 NMR structure determinations out of a total of 98 JCSG NMR structures, which were selected because they are the first three-dimensional structure representations of the respective Pfam protein families. The information from this small sample is representative for the overall results from crystal and NMR structure determination in the JCSG. There are five new folds, which were classified as domains of unknown functions (DUF), three of the proteins could be functionally annotated based on three-dimensional structure similarity with previously characterized proteins, and 12 proteins showed only limited similarity with previous deposits in the Protein Data Bank (PDB) and were classified as DUFs. © 2016 Federation of European Biochemical Societies.

Structural classification of CDR-H3 revisited: a lesson in antibody modeling.

PubMed

Kuroda, Daisuke; Shirai, Hiroki; Kobori, Masato; Nakamura, Haruki

2008-11-15

Among the six complementarity-determining regions (CDRs) in the variable domains of an antibody, the third CDR of the heavy chain (CDR-H3), which lies in the center of the antigen-binding site, plays a particularly important role in antigen recognition. CDR-H3 shows significant variability in its length, sequence, and structure. Although difficult, model building of this segment is the most critical step in antibody modeling. Since our first proposal of the "H3-rules," which classify CDR-H3 structure based on amino acid sequence, the number of experimentally determined antibody structures has increased. Here, we revise these H3-rules and propose an improved classification scheme for CDR-H3 structure modeling. In addition, we determine the common features of CDR-H3 in antibody drugs as well as discuss the concept of "antibody druggability," which can be applied as an indicator of antibody evaluation during drug discovery.

Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ

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

Barends, Thomas R. M., E-mail: thomas.barends@mpimf-heidelberg.mpg.de; Brosi, Richard W. W.; Steinmetz, Andrea

2013-08-01

The crystal structure of the N-terminal part of T. thermophilus DnaJ unexpectedly showed an ordered GF domain and guided the design of a construct enabling the first structure determination of a complete DnaJ cochaperone molecule. By combining the crystal structures with spin-labelling EPR and cross-linking in solution, a dynamic view of this flexible molecule was developed. Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein,more » but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ.« less

Quantification of the impact of PSI:Biology according to the annotations of the determined structures.

PubMed

DePietro, Paul J; Julfayev, Elchin S; McLaughlin, William A

2013-10-21

Protein Structure Initiative:Biology (PSI:Biology) is the third phase of PSI where protein structures are determined in high-throughput to characterize their biological functions. The transition to the third phase entailed the formation of PSI:Biology Partnerships which are composed of structural genomics centers and biomedical science laboratories. We present a method to examine the impact of protein structures determined under the auspices of PSI:Biology by measuring their rates of annotations. The mean numbers of annotations per structure and per residue are examined. These are designed to provide measures of the amount of structure to function connections that can be leveraged from each structure. One result is that PSI:Biology structures are found to have a higher rate of annotations than structures determined during the first two phases of PSI. A second result is that the subset of PSI:Biology structures determined through PSI:Biology Partnerships have a higher rate of annotations than those determined exclusive of those partnerships. Both results hold when the annotation rates are examined either at the level of the entire protein or for annotations that are known to fall at specific residues within the portion of the protein that has a determined structure. We conclude that PSI:Biology determines structures that are estimated to have a higher degree of biomedical interest than those determined during the first two phases of PSI based on a broad array of biomedical annotations. For the PSI:Biology Partnerships, we see that there is an associated added value that represents part of the progress toward the goals of PSI:Biology. We interpret the added value to mean that team-based structural biology projects that utilize the expertise and technologies of structural genomics centers together with biological laboratories in the community are conducted in a synergistic manner. We show that the annotation rates can be used in conjunction with established metrics, i.e. the numbers of structures and impact of publication records, to monitor the progress of PSI:Biology towards its goals of examining structure to function connections of high biomedical relevance. The metric provides an objective means to quantify the overall impact of PSI:Biology as it uses biomedical annotations from external sources.

Quantification of the impact of PSI:Biology according to the annotations of the determined structures

PubMed Central

2013-01-01

Background Protein Structure Initiative:Biology (PSI:Biology) is the third phase of PSI where protein structures are determined in high-throughput to characterize their biological functions. The transition to the third phase entailed the formation of PSI:Biology Partnerships which are composed of structural genomics centers and biomedical science laboratories. We present a method to examine the impact of protein structures determined under the auspices of PSI:Biology by measuring their rates of annotations. The mean numbers of annotations per structure and per residue are examined. These are designed to provide measures of the amount of structure to function connections that can be leveraged from each structure. Results One result is that PSI:Biology structures are found to have a higher rate of annotations than structures determined during the first two phases of PSI. A second result is that the subset of PSI:Biology structures determined through PSI:Biology Partnerships have a higher rate of annotations than those determined exclusive of those partnerships. Both results hold when the annotation rates are examined either at the level of the entire protein or for annotations that are known to fall at specific residues within the portion of the protein that has a determined structure. Conclusions We conclude that PSI:Biology determines structures that are estimated to have a higher degree of biomedical interest than those determined during the first two phases of PSI based on a broad array of biomedical annotations. For the PSI:Biology Partnerships, we see that there is an associated added value that represents part of the progress toward the goals of PSI:Biology. We interpret the added value to mean that team-based structural biology projects that utilize the expertise and technologies of structural genomics centers together with biological laboratories in the community are conducted in a synergistic manner. We show that the annotation rates can be used in conjunction with established metrics, i.e. the numbers of structures and impact of publication records, to monitor the progress of PSI:Biology towards its goals of examining structure to function connections of high biomedical relevance. The metric provides an objective means to quantify the overall impact of PSI:Biology as it uses biomedical annotations from external sources. PMID:24139526

The Structure of the Mouse Serotonin 5-HT3 Receptor in Lipid Vesicles.

PubMed

Kudryashev, Mikhail; Castaño-Díez, Daniel; Deluz, Cédric; Hassaine, Gherici; Grasso, Luigino; Graf-Meyer, Alexandra; Vogel, Horst; Stahlberg, Henning

2016-01-05

The function of membrane proteins is best understood if their structure in the lipid membrane is known. Here, we determined the structure of the mouse serotonin 5-HT3 receptor inserted in lipid bilayers to a resolution of 12 Å without stabilizing antibodies by cryo electron tomography and subtomogram averaging. The reconstruction reveals protein secondary structure elements in the transmembrane region, the extracellular pore, and the transmembrane channel pathway, showing an overall similarity to the available X-ray model of the truncated 5-HT3 receptor determined in the presence of a stabilizing nanobody. Structural analysis of the 5-HT3 receptor embedded in a lipid bilayer allowed the position of the membrane to be determined. Interactions between the densely packed receptors in lipids were visualized, revealing that the interactions were maintained by the short horizontal helices. In combination with methodological improvements, our approach enables the structural analysis of membrane proteins in response to voltage and ligand gating. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118.

PubMed

Lobley, Carina M C; Aller, Pierre; Douangamath, Alice; Reddivari, Yamini; Bumann, Mario; Bird, Louise E; Nettleship, Joanne E; Brandao-Neto, Jose; Owens, Raymond J; O'Toole, Paul W; Walsh, Martin A

2012-12-01

The structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC188 has been determined at 1.72 Å resolution. The structure was solved by molecular replacement, which identified the functional homodimer in the asymmetric unit. Despite only showing 57% sequence identity to its closest homologue, the structure adopted the typical α and β D-ribose 5-phosphate isomerase fold. Comparison to other related structures revealed high homology in the active site, allowing a model of the substrate-bound protein to be proposed. The determination of the structure was expedited by the use of in situ crystallization-plate screening on beamline I04-1 at Diamond Light Source to identify well diffracting protein crystals prior to routine cryocrystallography.

Neutron structure of human carbonic anhydrase II: a hydrogen-bonded water network "switch" is observed between pH 7.8 and 10.0.

PubMed

Fisher, Zoë; Kovalevsky, Andrey Y; Mustyakimov, Marat; Silverman, David N; McKenna, Robert; Langan, Paul

2011-11-08

The neutron structure of wild-type human carbonic anhydrase II at pH 7.8 has been determined to 2.0 Å resolution. Detailed analysis and comparison to the previously determined structure at pH 10.0 show important differences in the protonation of key catalytic residues in the active site as well as a rearrangement of the H-bonded water network. For the first time, a completed H-bonded network stretching from the Zn-bound solvent to the proton shuttling residue, His64, has been directly observed.

Schools, Skills and Risk

ERIC Educational Resources Information Center

Hartog, Joop; Vijverberg, Wim

2007-01-01

Skill development involves important choices for individuals and school designers: should individuals and schools specialize, or should they aim for an optimal combination of skills? We analyze this question by employing mean-standard deviation analysis and show how cost structure, benefit structure and risk attitudes jointly determine the optimal…

In-plane chemical pressure essential for superconductivity in BiCh2-based (Ch: S, Se) layered structure

PubMed Central

Mizuguchi, Yoshikazu; Miura, Akira; Kajitani, Joe; Hiroi, Takafumi; Miura, Osuke; Tadanaga, Kiyoharu; Kumada, Nobuhiro; Magome, Eisuke; Moriyoshi, Chikako; Kuroiwa, Yoshihiro

2015-01-01

BiCh2-based compounds (Ch: S, Se) are a new series of layered superconductors, and the mechanisms for the emergence of superconductivity in these materials have not yet been elucidated. In this study, we investigate the relationship between crystal structure and superconducting properties of the BiCh2-based superconductor family, specifically, optimally doped Ce1−xNdxO0.5F0.5BiS2 and LaO0.5F0.5Bi(S1−ySey)2. We use powder synchrotron X-ray diffraction to determine the crystal structures. We show that the structure parameter essential for the emergence of bulk superconductivity in both systems is the in-plane chemical pressure, rather than Bi-Ch bond lengths or in-plane Ch-Bi-Ch bond angle. Furthermore, we show that the superconducting transition temperature for all REO0.5F0.5BiCh2 superconductors can be determined from the in-plane chemical pressure. PMID:26447333

Rutile IrO2/TiO2 superlattices: A hyperconnected analog to the Ruddelsden-Popper structure

NASA Astrophysics Data System (ADS)

Kawasaki, Jason K.; Baek, David; Paik, Hanjong; Nair, Hari P.; Kourkoutis, Lena F.; Schlom, Darrell G.; Shen, Kyle M.

2018-05-01

Dimensionality and connectivity among octahedra play important roles in determining the properties, electronic structure, and phase transitions of transition-metal oxides. Here we demonstrate the epitaxial growth of (110)-oriented alternating layers of IrO2 and TiO2, both of which have the rutile structure. These (IrO2)n/(TiO2)2 superlattices consist of IrO6 and TiO6 octahedra tiled in a hyperconnected, edge- and corner-sharing network. Despite the large lattice mismatch between constituent layers (Δ d∥=-2.1 % and Δ c =+6.6 % ), our reactive molecular-beam epitaxy-grown superlattices show high structural quality as determined by x-ray diffraction and sharp interfaces as observed by transmission electron microscopy. The large strain at the interface is accommodated by an ordered interfacial reconstruction. The superlattices show persistent metallicity down to n =3 atomic layers, and angle-resolved photoemission spectroscopy measurements reveal quantized sub-bands with signatures of IrO2-IrO2 interlayer coupling.

Epidemic spreading on complex networks with community structures

PubMed Central

Stegehuis, Clara; van der Hofstad, Remco; van Leeuwaarden, Johan S. H.

2016-01-01

Many real-world networks display a community structure. We study two random graph models that create a network with similar community structure as a given network. One model preserves the exact community structure of the original network, while the other model only preserves the set of communities and the vertex degrees. These models show that community structure is an important determinant of the behavior of percolation processes on networks, such as information diffusion or virus spreading: the community structure can both enforce as well as inhibit diffusion processes. Our models further show that it is the mesoscopic set of communities that matters. The exact internal structures of communities barely influence the behavior of percolation processes across networks. This insensitivity is likely due to the relative denseness of the communities. PMID:27440176

What determines the spectrum of protein native state structures?

PubMed

Lezon, Timothy R; Banavar, Jayanth R; Lesk, Arthur M; Maritan, Amos

2006-05-01

We present a brief summary of the key factors underlying protein structure, as developed in the investigations of Pauling, Ramachandran, and Rose. We then outline a simplified physical model of proteins that focuses on geometry and symmetry. Although this model superficially appears unrelated to the detailed chemical descriptions commonly applied to proteins, we show that it captures the essential elements of the chemistry and provides a unified framework for understanding the common characteristics of folded proteins. We suggest that the spectrum of protein native state structures is determined by geometry and symmetry and the role of the sequence is to choose its native state structure from this predetermined menu. 2006 Wiley-Liss, Inc.

Determination of the Effects of Magnesium on the Structural Order of Amorphous Calcium Phosphate

NASA Astrophysics Data System (ADS)

Hoeher, A.; Michel, F. M.; Rakovan, J. F.; Borkiewicz, O.; Klysubun, W.

2016-12-01

Determining the pathways and mechanisms of calcium phosphate formation is important for understanding bone mineralization and advancing potential biological applications such as coatings on internal prosthetics. Studies show that amorphous calcium phosphate (ACP) is a precursor phase in the low temperature crystallization of hydroxylapatite, the primary mineral component found in bone and teeth of most modern vertebrates. ACP has been shown to have a structural order out to about 1 nm. Our recent extended x-ray absorption fine structure (EXAFS) spectroscopy analysis of synthetic ACP showed that the local structure of calcium in ACP differed from that in hydroxylapatite. Phosphorus EXAFS, however, indicated that the local structure in ACP is similar to hydroxylapatite (i.e., tetrahedrally coordinated with oxygen). EXAFS results were limited to only the first and second nearest neighbors in these samples, so the intermediate range order in ACP is yet unexplored. Furthermore, it remains unclear how ACP structure varies as a function of initial solution chemistry, how common impurities such as Mg are incorporated, and what role they play in determining the structural and physical characteristics of the final crystalline solid. We are using synchrotron x-ray total scattering for pair distribution function (PDF) analysis to investigate the influence of initial solution chemistry and Mg content on the structure of ACP. Magnesium is commonly used to stabilize the amorphous nature of the material, preventing crystallization. Ex situ samples synthesized at pH 10, with Ca:Mg ratios of 2:1, and freeze-dried are structurally similar to hydroxylapatite. Samples synthesized in identical conditions without Mg are structurally similar to another calcium phosphate mineral, brushite. In situ PDF measurements done at similar conditions in a custom mixed-flow reactor reveal that the short range order of ACP after 10 minutes of reacting is structurally different from ACP formed ex situ in the laboratory. Future analysis is aimed at quantifying the influence of these differences and to determine the validity of competing structural models proposed for ACP. This information is essential to further develop our understanding of the ACP transformation process into hydroxylapatite.

Metastable phases of silver and gold in hexagonal structure

NASA Astrophysics Data System (ADS)

Jona, F.; Marcus, P. M.

2004-07-01

Metastable phases of silver and gold in hexagonal close-packed structures are investigated by means of first-principles total-energy calculations. Two different methods are employed to find the equilibrium states: determination of the minima along the hexagonal epitaxial Bain path, and direct determination of minima of the total energy by a new minimum-path procedure. Both metals have two equilibrium states at different values of the hexagonal axial ratio c/a. For both metals, the elastic constants show that the high-c/a states are stable, hence, since the ground states are face-centred cubic, these states represent hexagonal close-packed metastable phases. The elastic constants of the low-c/a states show that they are unstable.

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination.

PubMed

Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

2013-11-01

The number of macromolecular structures deposited in the Protein Data Bank now approaches 100,000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. © 2013 FEBS.

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

PubMed Central

Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

2014-01-01

The number of macromolecular structures deposited in the Protein Data Bank now approaches 100 000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. PMID:24034303

a Study of the Synchrotron Laue Method for Quantitative Crystal Structure Analysis.

NASA Astrophysics Data System (ADS)

Gomez de Anderez, Dora M.

1990-01-01

Available from UMI in association with The British Library. Quantitative crystal structure analyses have been carried out on small molecule crystals using synchrotron radiation and the Laue method. A variety of single crystal structure determinations and associated refinements are used and compared with the monochromatic analyses. The new molecular structure of 7-amino-5-bromo -4-methyl-2-oxo-1,2,3,4-tetrahidro-1, 6 -naphthyridine-8-carbonitrile (C_{10 }H_9ON_4 Br.H_2O) has been determined, first using monochromatic Mo Kalpha radiation and a four-circle diffractometer, then using synchrotron Laue diffraction photography. The structure refinements showed a R-factor of 4.97 and 14.0% for the Mo Kalpha and Laue data respectively. The molecular structure of (S)-2-chloro-2-fluoro-N-((S)-1-phenylethyl) ethanamide, (C_{10}H _{11}ClFNO), has been determined using the same crystal throughout for X-ray monochromatic analyses (Mo Kalpha and Cu K alpha) followed by synchrotron Laue data collection. The Laue and monochromatic data compare favourably. The R -factors (on F) were 6.23, 6.45 and 8.19% for the Mo K alpha, Cu Kalpha and Laue data sets respectively. The molecular structure of 3-(5-hydroxy-3-methyl-1-phenylpyrazol-4-yl)-1,3-diphenyl -prop- 2-en-1-one, (C_{25 }H_{20}N _2O_2) has been determined using the synchrotron Laue method. The results compare very well with Mo Kalpha monochromatic data. The R-factors (on F) were 4.60 and 5.29% for Mo Kalpha and Laue analysis respectively. The Laue method is assessed in locating the 20 hydrogen atoms in this structure. The structure analysis of the benzil compound ((C_6H_5 O.CO_2)) is carried out using the synchrotron Laue method firstly at room temperature and secondly at low temperature -114 ^circC. The structure shows an R-factor (on F) of 13.06% and 6.85% for each data set respectively. The synchrotron Laue method was used to collect data for ergocalciferol (Vitamin D_2). The same crystal was also used to record oscillation data with the synchrotron radiation monochromatic beam. A new molecular structure of (Dinitrato-(N,N ^'-dimethylethylene-diamine)copper(II)) has been determined using Mo Kalpha radiation on a four circle diffractometer. The refinement resulted in an R-factor (on F) of 4.06%.

A Study of the Synchrotron Laue Method for Quantitative Crystal Structure Analysis

NASA Astrophysics Data System (ADS)

Gomez de Anderez, Dora M.

1990-01-01

Quantitative crystal structure analyses have been carried out on small molecule crystals using synchrotron radiation and the Laue method. A variety of single crystal structure determinations and associated refinements are used and compared with the monochromatic analyses. The new molecular structure of 7-amino-5-bromo -4-methyl-2-oxo-1,2,3,4 -tetrahidro-1,6 -naphthyridine-8-carbonitrile (C_{10 }H_9ON_4 BrcdotH_2O) has been determined, first using monochromatic Mo K alpha radiation and a four-circle diffractometer, then using synchrotron Laue diffraction photography. The structure refinements showed an R-factor of 4.97 and 14.0% for the Mo Kalpha and Laue data respectively. The molecular structure of (S)-2-chloro-2-fluoro-N-((S)-1-phenylethyl) ethanamide, (C_{10}H _{11}ClFNO), has been determined using the same crystal throughout for X-ray monochromatic analyses (Mo Kalpha and Cu K alpha) followed by synchrotron Laue data collection. The Laue and monochromatic data compare favourably. The R -factors (on F) were 6.23, 6.45 and 8.19% for the Mo K alpha, Cu Kalpha and Laue data sets respectively. The molecular structure of 3-(5-hydroxy-3-methyl-1-phenylpyrazol-4-yl)-1,3-diphenyl -prop-2-en-1-one, (C_{25}H _{20}N_2 O_2) has been determined using the synchrotron Laue method. The results compare very well with Mo Kalpha monochromatic data. The R-factors (on F) were 4.60 and 5.29% for Mo Kalpha and Laue analyses respectively. The Laue method is assessed in locating the 20 hydrogen atoms in this structure. The structure analyses of the benzil compound ((C_6H_5 OcdotCO_2)) is carried out using the synchrotron Laue method firstly at room temperature and secondly at low temperature. The structure shows an R-factor (on F) of 13.06% and 6.85% for each data set respectively. The synchrotron Laue method was used to collect data for ergocalciferol (Vitamin D_2). The same crystal was also used to record oscillation data with the synchrotron radiation monochromatic beam. A new molecular structure of (Dinitrato-(N,N ^'-dimethylethylene-diamine)copper(II)) has been determined using Mo Kalpha radiation on a four circle diffractometer. The refinement resulted in an R-factor (on F) of 4.06%.

The Self-Description Inventory+, Part 1: Factor Structure and Convergent Validity Analyses

DTIC Science & Technology

2013-07-01

measures 12 scales of personality. The current report examines the possibility of replacing the EQ with a Five Factor Model ( FFM ) measure of...Checklist. Our results show that the SDI + has scales that are intercorrelated in a manner consistent with the FFM (Experiment 1), a factor structure...met the criteria showing it to be an FFM instrument, we will conduct concurrent validity research to determine if the SDI+ has greater predictive

Crystal structure of a designed, thermostable, heterotrimeric coiled coil.

PubMed Central

Nautiyal, S.; Alber, T.

1999-01-01

Electrostatic interactions are often critical for determining the specificity of protein-protein complexes. To study the role of electrostatic interactions for assembly of helical bundles, we previously designed a thermostable, heterotrimeric coiled coil, ABC, in which charged residues were employed to drive preferential association of three distinct, 34-residue helices. To investigate the basis for heterotrimer specificity, we have used multiwavelength anomalous diffraction (MAD) analysis to determine the 1.8 A resolution crystal structure of ABC. The structure shows that ABC forms a heterotrimeric coiled coil with the intended arrangement of parallel chains. Over half of the ion pairs engineered to restrict helix associations were apparent in the experimental electron density map. As seen in other trimeric coiled coils, ABC displays acute knobs-into-holes packing and a buried anion coordinated by core polar amino acids. These interactions validate the design strategy and illustrate how packing and polar contacts determine structural uniqueness. PMID:10210186

Buried Man-made Structure Imaging using 2-D Resistivity Inversion

NASA Astrophysics Data System (ADS)

Anderson Bery, Andy; Nordiana, M. M.; El Hidayah Ismail, Noer; Jinmin, M.; Nur Amalina, M. K. A.

2018-04-01

This study is carried out with the objective to determine the suitable resistivity inversion method for buried man-made structure (bunker). This study was carried out with two stages. The first stage is suitable array determination using 2-D computerized modeling method. One suitable array is used for the infield resistivity survey to determine the dimension and location of the target. The 2-D resistivity inversion results showed that robust inversion method is suitable to resolve the top and bottom part of the buried bunker as target. In addition, the dimension of the buried bunker is successfully determined with height of 7 m and length of 20 m. The location of this target is located at -10 m until 10 m of the infield resistivity survey line. The 2-D resistivity inversion results obtained in this study showed that the parameters selection is important in order to give the optimum results. These parameters are array type, survey geometry and inversion method used in data processing.

Solution structure of an antifreeze protein CfAFP-501 from Choristoneura fumiferana.

PubMed

Li, Congmin; Guo, Xianrong; Jia, Zongchao; Xia, Bin; Jin, Changwen

2005-07-01

Antifreeze proteins (AFPs) are widely employed by various organisms as part of their overwintering survival strategy. AFPs have the unique ability to suppress the freezing point of aqueous solution and inhibit ice recrystallization through binding to the ice seed crystals and restricting their growth. The solution structure of CfAFP-501 from spruce budworm has been determined by NMR spectroscopy. Our result demonstrates that CfAFP-501 retains its rigid and highly regular structure in solution. Overall, the solution structure is similar to the crystal structure except the N- and C-terminal regions. NMR spin-relaxation experiments further indicate the overall rigidity of the protein and identify a collection of residues with greater flexibilities. Furthermore, Pro91 shows a cis conformation in solution instead of the trans conformation determined in the crystal structure.

The structure and dynamics in solution of Cu(I) pseudoazurin from Paracoccus pantotrophus.

PubMed Central

Thompson, G. S.; Leung, Y. C.; Ferguson, S. J.; Radford, S. E.; Redfield, C.

2000-01-01

The solution structure and backbone dynamics of Cu(I) pseudoazurin, a 123 amino acid electron transfer protein from Paracoccus pantotrophus, have been determined using NMR methods. The structure was calculated to high precision, with a backbone RMS deviation for secondary structure elements of 0.35+/-0.06 A, using 1,498 distance and 55 torsion angle constraints. The protein has a double-wound Greek-key fold with two alpha-helices toward its C-terminus, similar to that of its oxidized counterpart determined by X-ray crystallography. Comparison of the Cu(I) solution structure with the X-ray structure of the Cu(II) protein shows only small differences in the positions of some of the secondary structure elements. Order parameters S2, measured for amide nitrogens, indicate that the backbone of the protein is rigid on the picosecond to nanosecond timescale. PMID:10850794

The structure and host entry of an invertebrate parvovirus.

PubMed

Meng, Geng; Zhang, Xinzheng; Plevka, Pavel; Yu, Qian; Tijssen, Peter; Rossmann, Michael G

2013-12-01

The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (Acheta domesticus densovirus [AdDNV]) has been determined. Structural comparisons show that vertebrate and invertebrate parvoviruses have evolved independently, although there are common structural features among all parvovirus capsid proteins. It was shown that raising the temperature of the AdDNV particles caused a loss of their genomes. The structure of these emptied particles was determined by cryo-electron microscopy to 5.5-Å resolution, and the capsid structure was found to be the same as that for the full, mature virus except for the absence of the three ordered nucleotides observed in the crystal structure. The viral protein 1 (VP1) amino termini could be externalized without significant damage to the capsid. In vitro, this externalization of the VP1 amino termini is accompanied by the release of the viral genome.

The Structure and Host Entry of an Invertebrate Parvovirus

PubMed Central

Meng, Geng; Zhang, Xinzheng; Plevka, Pavel; Yu, Qian; Tijssen, Peter

2013-01-01

The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (Acheta domesticus densovirus [AdDNV]) has been determined. Structural comparisons show that vertebrate and invertebrate parvoviruses have evolved independently, although there are common structural features among all parvovirus capsid proteins. It was shown that raising the temperature of the AdDNV particles caused a loss of their genomes. The structure of these emptied particles was determined by cryo-electron microscopy to 5.5-Å resolution, and the capsid structure was found to be the same as that for the full, mature virus except for the absence of the three ordered nucleotides observed in the crystal structure. The viral protein 1 (VP1) amino termini could be externalized without significant damage to the capsid. In vitro, this externalization of the VP1 amino termini is accompanied by the release of the viral genome. PMID:24027306

Crystal Structure and Theoretical Analysis of Green Gold Au 30 (S- t Bu) 18 Nanomolecules and Their Relation to Au 30 S(S- t Bu) 18

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

Dass, Amala; Jones, Tanya; Rambukwella, Milan

We report the complete X-ray crystallographic structure as determined through single crystal X-ray diffraction and a thorough theoretical analysis of the green gold Au30(S-tBu)18. While the structure of Au30S(S-tBu)18 with 19 sulfur atoms has been reported, the crystal structure of Au30(S-tBu)18 without the μ3-sulfur has remained elusive until now, though matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) and electrospray ionization mass spectrometry (ESI-MS) data unequivocally shows its presence in abundance. The Au30(S-tBu)18 nanomolecule is not only distinct in its crystal structure but has unique temperature dependent optical properties. Structure determination allows a rigorous comparison and an excellent agreement with theoreticalmore » predictions of structure, stability, and optical response.« less

Energetic domains and conformational analysis of human serum albumin upon co-incubation with sodium benzoate and glucose.

PubMed

Taghavi, F; Moosavi-Movahedi, A A; Bohlooli, M; Habibi-Rezaei, M; Hadi Alijanvand, H; Amanlou, M; Sheibani, N; Saboury, A A; Ahmad, F

2014-01-01

Sodium benzoate (SB), a powerful inhibitor of microbial growth, is one of the most commonly used food preservative. Here, we determined the effects of SB on human serum albumin (HSA) structure in the presence or absence of glucose after 35 days of incubation under physiological conditions. The biochemical, biophysical, and molecular approaches including free amine content assay (TNBSA assay), fluorescence, and circular dichroism spectroscopy (CD), differential scanning calorimetry (DSC), and molecular docking and LIGPLOT studies were utilized for structural studies. The TNBSA results indicated that SB has the ability to bind Lys residues in HSA through covalent bonds. The docking and LIGPLOT studies also determined another specific site via hydrophobic interactions. The CD results showed more structural helicity for HSA incubated with SB, while HSA incubated with glucose had the least, and HSA incubated with glucose + SB had medium helicity. Fluorescence spectrophotometry results demonstrated partial unfolding of HSA incubated with SB in the presence or absence of glucose, while maximum partial unfolding was observed in HSA incubated with glucose. These results were confirmed by DSC and its deconvoluted thermograms. The DSC results also showed significant changes in HSA energetic structural domains due to HSA incubation with SB in the presence or absence of glucose. Together, our studies showed the formation of three different intermediates and indicate that biomolecular investigation are effective in providing new insight into safety determinations especially in health-related conditions including diabetes.

Structure of p73 DNA-binding domain tetramer modulates p73 transactivation

PubMed Central

Ethayathulla, Abdul S.; Tse, Pui-Wah; Monti, Paola; Nguyen, Sonha; Inga, Alberto; Fronza, Gilberto; Viadiu, Hector

2012-01-01

The transcription factor p73 triggers developmental pathways and overlaps stress-induced p53 transcriptional pathways. How p53-family response elements determine and regulate transcriptional specificity remains an unsolved problem. In this work, we have determined the first crystal structures of p73 DNA-binding domain tetramer bound to response elements with spacers of different length. The structure and function of the adaptable tetramer are determined by the distance between two half-sites. The structures with zero and one base-pair spacers show compact p73 DNA-binding domain tetramers with large tetramerization interfaces; a two base-pair spacer results in DNA unwinding and a smaller tetramerization interface, whereas a four base-pair spacer hinders tetramerization. Functionally, p73 is more sensitive to spacer length than p53, with one base-pair spacer reducing 90% of transactivation activity and longer spacers reducing transactivation to basal levels. Our results establish the quaternary structure of the p73 DNA-binding domain required as a scaffold to promote transactivation. PMID:22474346

Structural analysis of determinants of histo-blood group antigen binding specificity in genogroup I noroviruses.

PubMed

Shanker, Sreejesh; Czako, Rita; Sankaran, Banumathi; Atmar, Robert L; Estes, Mary K; Prasad, B V Venkataram

2014-06-01

Human noroviruses (NoVs) cause acute epidemic gastroenteritis. Susceptibility to the majority of NoV infections is determined by genetically controlled secretor-dependent expression of histo-blood group antigens (HBGAs), which are also critical for NoV attachment to host cells. Human NoVs are classified into two major genogroups (genogroup I [GI] and GII), with each genogroup further divided into several genotypes. GII NoVs are more prevalent and exhibit periodic emergence of new variants, suggested to be driven by altered HBGA binding specificities and antigenic drift. Recent epidemiological studies show increased activity among GI NoVs, with some members showing the ability to bind nonsecretor HBGAs. NoVs bind HBGAs through the protruding (P) domain of the major capsid protein VP1. GI NoVs, similar to GII, exhibit significant sequence variations in the P domain; it is unclear how these variations affect HBGA binding specificities. To understand the determinants of possible strain-specific HBGA binding among GI NoVs, we determined the structure of the P domain of a GI.7 clinical isolate and compared it to the previously determined P domain structures of GI.1 and GI.2 strains. Our crystallographic studies revealed significant structural differences, particularly in the loop regions of the GI.7 P domain, altering its surface topography and electrostatic landscape and potentially indicating antigenic variation. The GI.7 strain bound to H- and A-type, Lewis secretor, and Lewis nonsecretor families of HBGAs, allowing us to further elucidate the structural determinants of nonsecretor HBGA binding among GI NoVs and to infer several contrasting and generalizable features of HBGA binding in the GI NoVs. Human noroviruses (NoVs) cause acute epidemic gastroenteritis. Recent epidemiological studies have shown increased prevalence of genogroup I (GI) NoVs. Although secretor-positive status is strongly correlated with NoV infection, cases of NoV infection associated with secretor-negative individuals are reported. Biochemical studies have shown that GI NoVs exhibit genotype-dependent binding to nonsecretor histo-blood group antigens (HBGAs). From our crystallographic studies of a GI.7 NoV, in comparison with previous studies on GI.1 and GI.2 NoVs, we show that genotypic differences translate to extensive structural changes in the loop regions that significantly alter the surface topography and electrostatic landscape of the P domain; these features may be indicative of antigenic variations contributing to serotypic differentiation in GI NoVs and also differential modulation of the HBGA binding characteristics. A significant finding is that the threshold length and the structure of one of the loops are critical determinants in the binding of GI NoVs to nonsecretor HBGAs.

Determination of elastic modulus of ceramics using ultrasonic testing

NASA Astrophysics Data System (ADS)

Sasmita, Firmansyah; Wibisono, Gatot; Judawisastra, Hermawan; Priambodo, Toni Agung

2018-04-01

Elastic modulus is important material property on structural ceramics application. However, bending test as a common method for determining this property require particular specimen preparation. Furthermore, elastic modulus of ceramics could vary because it depends on porosity content. For structural ceramics industry, such as ceramic tiles, this property is very important. This drives the development of new method to improve effectivity or verification method as well. In this research, ultrasonic testing was conducted to determine elastic modulus of soda lime glass and ceramic tiles. The experiment parameter was frequency of probe (1, 2, 4 MHz). Characterization of density and porosity were also done for analysis. Results from ultrasonic testing were compared with elastic modulus resulted from bending test. Elastic modulus of soda-lime glass based on ultrasonic testing showed excellent result with error 2.69% for 2 MHz probe relative to bending test result. Testing on red and white ceramic tiles were still contained error up to 41% and 158%, respectively. The results for red ceramic tile showed trend that 1 MHz probe gave better accuracy in determining elastic modulus. However, testing on white ceramic tile showed different trend. It was due to the presence of porosity and near field effect.

TALEs from a spring--superelasticity of Tal effector protein structures.

PubMed

Flechsig, Holger

2014-01-01

Transcription activator-like effectors (TALEs) are DNA-related proteins that recognise and bind specific target sequences to manipulate gene expression. Recently determined crystal structures show that their common architecture reveals a superhelical overall structure that may undergo drastic conformational changes. To establish a link between structure and dynamics in TALE proteins we have employed coarse-grained elastic-network modelling of currently available structural data and implemented a force-probe setup that allowed us to investigate their mechanical behaviour in computer experiments. Based on the measured force-extension curves we conclude that TALEs exhibit superelastic dynamical properties allowing for large-scale global conformational changes along their helical axis, which represents the soft direction in such proteins. For moderate external forcing the TALE models behave like linear springs, obeying Hooke's law, and the investigated structures can be characterised and compared by a corresponding spring constant. We show that conformational flexibility underlying the large-scale motions is not homogeneously distributed over the TALE structure, but instead soft spot residues around which strain is accumulated and which turn out to represent key agents in the transmission of conformational motions are identified. They correspond to the RVD loop residues that have been experimentally determined to play an eminent role in the binding process of target DNA.

TALEs from a Spring – Superelasticity of Tal Effector Protein Structures

PubMed Central

Flechsig, Holger

2014-01-01

Transcription activator-like effectors (TALEs) are DNA-related proteins that recognise and bind specific target sequences to manipulate gene expression. Recently determined crystal structures show that their common architecture reveals a superhelical overall structure that may undergo drastic conformational changes. To establish a link between structure and dynamics in TALE proteins we have employed coarse-grained elastic-network modelling of currently available structural data and implemented a force-probe setup that allowed us to investigate their mechanical behaviour in computer experiments. Based on the measured force-extension curves we conclude that TALEs exhibit superelastic dynamical properties allowing for large-scale global conformational changes along their helical axis, which represents the soft direction in such proteins. For moderate external forcing the TALE models behave like linear springs, obeying Hooke's law, and the investigated structures can be characterised and compared by a corresponding spring constant. We show that conformational flexibility underlying the large-scale motions is not homogeneously distributed over the TALE structure, but instead soft spot residues around which strain is accumulated and which turn out to represent key agents in the transmission of conformational motions are identified. They correspond to the RVD loop residues that have been experimentally determined to play an eminent role in the binding process of target DNA. PMID:25313859

The Economics of Structured Continuing Education in Selected Professional Journals.

ERIC Educational Resources Information Center

Sasmor, James C.

A study determined what business administration considerations were elements in the managerial decision making process to include structured continuing education in a professional journal and what the positive or negative results have been in terms of operating benefits and profits. An initial literature review showed the need for exploratory…

Evaluating the quality of NMR structures by local density of protons.

PubMed

Ban, Yih-En Andrew; Rudolph, Johannes; Zhou, Pei; Edelsbrunner, Herbert

2006-03-01

Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. 2005 Wiley-Liss, Inc.

Control Centrality and Hierarchical Structure in Complex Networks

PubMed Central

Liu, Yang-Yu; Slotine, Jean-Jacques; Barabási, Albert-László

2012-01-01

We introduce the concept of control centrality to quantify the ability of a single node to control a directed weighted network. We calculate the distribution of control centrality for several real networks and find that it is mainly determined by the network’s degree distribution. We show that in a directed network without loops the control centrality of a node is uniquely determined by its layer index or topological position in the underlying hierarchical structure of the network. Inspired by the deep relation between control centrality and hierarchical structure in a general directed network, we design an efficient attack strategy against the controllability of malicious networks. PMID:23028542

Molecular and crystal structure of 2-{( E)-[(4-Methylphenyl)imino]methyl}-4-nitrophenol: A redetermination

NASA Astrophysics Data System (ADS)

Kaynar, Nihal Kan; Tanak, Hasan; Şahin, Songul; Dege, Necmi; Ağar, Erbil; Yavuz, Metin

2016-03-01

The crystal structure of the title compound, C14H12N2O3, was recently determined as a mixture of its neutral (OH containing) and zwitterionic (NH containing) forms, in a 0.60 (4): 0.40 (4) ratio using the X-ray determination. In this study, the title compound has been characterized by FT-IR and X-ray diffraction. The redetermination showed that the title compound has only enol (OH) form because of lack of the NH stretching vibration in FT-IR spectrum. In addition, the molecular structure and tautomerism of the title compound have been discussed.

Automatic protein structure solution from weak X-ray data

NASA Astrophysics Data System (ADS)

Skubák, Pavol; Pannu, Navraj S.

2013-11-01

Determining new protein structures from X-ray diffraction data at low resolution or with a weak anomalous signal is a difficult and often an impossible task. Here we propose a multivariate algorithm that simultaneously combines the structure determination steps. In tests on over 140 real data sets from the protein data bank, we show that this combined approach can automatically build models where current algorithms fail, including an anisotropically diffracting 3.88 Å RNA polymerase II data set. The method seamlessly automates the process, is ideal for non-specialists and provides a mathematical framework for successfully combining various sources of information in image processing.

Molecular and crystal structure of 2-((E)-[(4-Methylphenyl)imino]methyl)-4-nitrophenol: A redetermination

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

Kaynar, Nihal Kan, E-mail: nihal-kan84@windowslive.com; Tanak, Hasan; Şahin, Songul

The crystal structure of the title compound, C{sub 14}H{sub 12}N{sub 2}O{sub 3}, was recently determined as a mixture of its neutral (OH containing) and zwitterionic (NH containing) forms, in a 0.60 (4): 0.40 (4) ratio using the X-ray determination. In this study, the title compound has been characterized by FT-IR and X-ray diffraction. The redetermination showed that the title compound has only enol (OH) form because of lack of the NH stretching vibration in FT-IR spectrum. In addition, the molecular structure and tautomerism of the title compound have been discussed.

Thrust-wrench fault interference in a brittle medium: new insights from analogue modelling experiments

NASA Astrophysics Data System (ADS)

Rosas, Filipe; Duarte, Joao; Schellart, Wouter; Tomas, Ricardo; Grigorova, Vili; Terrinha, Pedro

2015-04-01

We present analogue modelling experimental results concerning thrust-wrench fault interference in a brittle medium, to try to evaluate the influence exerted by different prescribed interference angles in the formation of morpho-structural interference fault patterns. All the experiments were conceived to simulate simultaneous reactivation of confining strike-slip and thrust faults defining a (corner) zone of interference, contrasting with previously reported discrete (time and space) superposition of alternating thrust and strike-slip events. Different interference angles of 60°, 90° and 120° were experimentally investigated by comparing the specific structural configurations obtained in each case. Results show that a deltoid-shaped morpho-structural pattern is consistently formed in the fault interference (corner) zone, exhibiting a specific geometry that is fundamentally determined by the different prescribed fault interference angle. Such angle determines the orientation of the displacement vector shear component along the main frontal thrust direction, determining different fault confinement conditions in each case, and imposing a complying geometry and kinematics of the interference deltoid structure. Model comparison with natural examples worldwide shows good geometric and kinematic similarity, pointing to the existence of matching underlying dynamic process. Acknowledgments This work was sponsored by the Fundação para a Ciência e a Tecnologia (FCT) through project MODELINK EXPL/GEO-GEO/0714/2013.

Structure formation in Ag-X (X = Au, Cu) alloys synthesized far-from-equilibrium

NASA Astrophysics Data System (ADS)

Elofsson, V.; Almyras, G. A.; Lü, B.; Garbrecht, M.; Boyd, R. D.; Sarakinos, K.

2018-04-01

We employ sub-monolayer, pulsed Ag and Au vapor fluxes, along with deterministic growth simulations, and nanoscale probes to study structure formation in miscible Ag-Au films synthesized under far-from-equilibrium conditions. Our results show that nanoscale atomic arrangement is primarily determined by roughness build up at the film growth front, whereby larger roughness leads to increased intermixing between Ag and Au. These findings suggest a different structure formation pathway as compared to the immiscible Ag-Cu system for which the present study, in combination with previously published data, reveals that no significant roughness is developed, and the local atomic structure is predominantly determined by the tendency of Ag and Cu to phase-separate.

Antibacterial properties and atomic resolution X-ray complex crystal structure of a ruthenocene conjugated β-lactam antibiotic

DOE PAGES

Lewandowski, Eric M.; Skiba, Joanna; Torelli, Nicholas J.; ...

2015-03-02

We have determined a 1.18 Å resolution X-ray crystal structure of a novel ruthenocenyle-6-aminopenicillinic acid in complex with CTX-M β-lactamase, showing unprecedented details of interactions between ruthenocene and protein. As the first product complex with an intact catalytic serine, the structure also offers insights into β-lactamase catalysis and inhibitor design.

Transport induced by large scale convective structures in a dipole-confined plasma.

PubMed

Grierson, B A; Mauel, M E; Worstell, M W; Klassen, M

2010-11-12

Convective structures characterized by E×B motion are observed in a dipole-confined plasma. Particle transport rates are calculated from density dynamics obtained from multipoint measurements and the reconstructed electrostatic potential. The calculated transport rates determined from the large-scale dynamics and local probe measurements agree in magnitude, show intermittency, and indicate that the particle transport is dominated by large-scale convective structures.

Aqueous phase synthesis, crystal structure and biological study of isoxazole extensions of pyrazole-4-carbaldehyde derivatives

NASA Astrophysics Data System (ADS)

Wazalwar, Sachin S.; Banpurkar, Anita R.; Perdih, Franc

2017-12-01

A series of novel isoxazol derivatives was synthesized by green route in aqueous phase at room temperature by the reaction of 3-methyl-4H-isoxazol-5-one with 3-(substituted phenyl)-1-phenyl-1H-pyrazole-4-carbaldehyde by one-pot Knoevenagel condensation method using sodium benzoate as a catalyst. Compounds were characterized on the basis of IR, 1H NMR, mass spectroscopy and melting point determination. Crystal structures of five compounds were determined by X-ray diffraction. The compounds formed were screened for antibacterial and antifungal activity. Some compounds showed activity close to ampicillin against E. coli, S. aureus, and S. pyogenus. Two compounds showed antifungal activity against C. albicans close to standard greseofulvin.

Structure-based Markov random field model for representing evolutionary constraints on functional sites.

PubMed

Jeong, Chan-Seok; Kim, Dongsup

2016-02-24

Elucidating the cooperative mechanism of interconnected residues is an important component toward understanding the biological function of a protein. Coevolution analysis has been developed to model the coevolutionary information reflecting structural and functional constraints. Recently, several methods have been developed based on a probabilistic graphical model called the Markov random field (MRF), which have led to significant improvements for coevolution analysis; however, thus far, the performance of these models has mainly been assessed by focusing on the aspect of protein structure. In this study, we built an MRF model whose graphical topology is determined by the residue proximity in the protein structure, and derived a novel positional coevolution estimate utilizing the node weight of the MRF model. This structure-based MRF method was evaluated for three data sets, each of which annotates catalytic site, allosteric site, and comprehensively determined functional site information. We demonstrate that the structure-based MRF architecture can encode the evolutionary information associated with biological function. Furthermore, we show that the node weight can more accurately represent positional coevolution information compared to the edge weight. Lastly, we demonstrate that the structure-based MRF model can be reliably built with only a few aligned sequences in linear time. The results show that adoption of a structure-based architecture could be an acceptable approximation for coevolution modeling with efficient computation complexity.

Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry

PubMed Central

Walker, Peter

2017-01-01

Abstract The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures. We show that the XSI-based model of the TAR RNA ensemble closely resembles an independent model derived from NMR-RDC data. Further, we show how the TAR RNA ensemble changes shape at different salt concentrations. Finally, we demonstrate that a single hybrid model of the TAR RNA ensemble simultaneously fits both the XSI and NMR-RDC data set and show that XSI can be combined with NMR-RDC to further improve the quality of the determined ensemble. The results suggest that XSI-RNA will be a powerful approach for characterizing the solution conformational ensembles of RNAs and RNA-protein complexes under diverse solution conditions. PMID:28108663

Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

NASA Astrophysics Data System (ADS)

Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion

2016-04-01

The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

Development of a hybrid wave based-transfer matrix model for sound transmission analysis.

PubMed

Dijckmans, A; Vermeir, G

2013-04-01

In this paper, a hybrid wave based-transfer matrix model is presented that allows for the investigation of the sound transmission through finite multilayered structures placed between two reverberant rooms. The multilayered structure may consist of an arbitrary configuration of fluid, elastic, or poro-elastic layers. The field variables (structural displacements and sound pressures) are expanded in terms of structural and acoustic wave functions. The boundary and continuity conditions in the rooms determine the participation factors in the pressure expansions. The displacement of the multilayered structure is determined by the mechanical impedance matrix, which gives a relation between the pressures and transverse displacements at both sides of the structure. The elements of this matrix are calculated with the transfer matrix method. First, the hybrid model is numerically validated. Next a comparison is made with sound transmission loss measurements of a hollow brick wall and a sandwich panel. Finally, numerical simulations show the influence of structural damping, room dimensions and plate dimensions on the sound transmission loss of multilayered structures.

Crystal structure prediction supported by incomplete experimental data

NASA Astrophysics Data System (ADS)

Tsujimoto, Naoto; Adachi, Daiki; Akashi, Ryosuke; Todo, Synge; Tsuneyuki, Shinji

2018-05-01

We propose an efficient theoretical scheme for structure prediction on the basis of the idea of combining methods, which optimize theoretical calculation and experimental data simultaneously. In this scheme, we formulate a cost function based on a weighted sum of interatomic potential energies and a penalty function which is defined with partial experimental data totally insufficient for conventional structure analysis. In particular, we define the cost function using "crystallinity" formulated with only peak positions within the small range of the x-ray-diffraction pattern. We apply this method to well-known polymorphs of SiO2 and C with up to 108 atoms in the simulation cell and show that it reproduces the correct structures efficiently with very limited information of diffraction peaks. This scheme opens a new avenue for determining and predicting structures that are difficult to determine by conventional methods.

Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility.

PubMed

Mlýnský, Vojtěch; Bussi, Giovanni

2018-01-18

The function of RNA molecules usually depends on their overall fold and on the presence of specific structural motifs. Chemical probing methods are routinely used in combination with nearest-neighbor models to determine RNA secondary structure. Among the available methods, SHAPE is relevant due to its capability to probe all RNA nucleotides and the possibility to be used in vivo. However, the structural determinants for SHAPE reactivity and its mechanism of reaction are still unclear. Here molecular dynamics simulations and enhanced sampling techniques are used to predict the accessibility of nucleotide analogs and larger RNA structural motifs to SHAPE reagents. We show that local RNA reconformations are crucial in allowing reagents to reach the 2'-OH group of a particular nucleotide and that sugar pucker is a major structural factor influencing SHAPE reactivity.

SAD phasing of a structure based on cocrystallized iodides using an in-house Cu Kalpha X-ray source: effects of data redundancy and completeness on structure solution.

PubMed

Yogavel, Manickam; Gill, Jasmita; Mishra, Prakash Chandra; Sharma, Amit

2007-08-01

Superoxide dismutase (SOD) from Potentilla atrosanguinea (Wall. ex. Lehm.) was crystallized using 20% PEG 3350 and 0.2 M ammonium iodide and diffraction data were collected to 2.36 A resolution using an in-house Cu Kalpha X-ray source. Analyses show that data with a redundancy of 3.2 were sufficient to determine the structure by the SAD technique using the iodine anomalous signal. This redundancy is lower than that in previous cases in which protein structures were determined using iodines for phasing and in-house copper X-ray sources. Cocrystallization of proteins with halide salts such as ammonium iodide in combination with copper-anode X-ray radiation can therefore serve as a powerful and easy avenue for structure solution.

Pressure-Induced Structural Transition and Enhancement of Energy Gap of CuAlO2

NASA Astrophysics Data System (ADS)

Nakanishi, Akitaka

2011-02-01

By using first-principles calculations, we studied the stable crystal structures and energy gaps of CuAlO2 under high pressure. Our simulation shows that CuAlO2 transforms from a delafossite structure to a leaning delafossite structure. The critical pressure of the transition was determined to be 60 GPa. The energy gap of CuAlO2 increases through the structural transition due to the enhanced covalency of Cu 3d and O 2p states. We found that a chalcopyrite structure does not appear as a stable structure under high pressure.

Structure determination of an Fab fragment that neutralizes human rhinovirus 14 and analysis of the Fab-virus complex.

PubMed

Liu, H; Smith, T J; Lee, W M; Mosser, A G; Rueckert, R R; Olson, N H; Cheng, R H; Baker, T S

1994-07-08

The crystal structure of Fab17-IA, an antigen-binding fragment from a murine immunoglobulin that neutralizes human rhinovirus 14 (HRV14), has been solved to 2.7 A resolution. Fab17-IA crystallized into three different space groups depending upon the method used to purify the intact antibody. The structure was determined by use of molecular and isomorphous replacement methods. The current model has a crystallographic R-factor of approximately 19% for 10,192 independent reflections between 8 and 2.7 A. Correlation coefficient calculations showed that the Fab17-IA structure can be fit into the Fab17-IA/HRV14 image reconstruction density to within 5 A positional accuracy and to within a few degrees of rotation. The resulting interface of the docked antibody was examined and showed extensive charge and shape complementarity with the virus surface that was supported by site-directed mutagenesis experiments. The success of this approach validates the utility of combining X-ray crystallography with cryo-electron microscopy of complex macromolecular assemblies.

[Validity and internal consistency of the Maslach Burnout Inventory in Dental Students from Cartagena, Colombia].

PubMed

Simancas-Pallares, Miguel Angel; Fortich Mesa, Natalia; González Martínez, Farith Damián

To determine the internal consistency and content validity of the Maslach Burnout Inventory-Student Survey (MBI-SS) in dental students from Cartagena, Colombia. Scale validation study in 886 dental students from Cartagena, Colombia. Factor structure was determined through exploratory factor analysis (EFA) and confirmatory factor analysis (CFA). Internal consistency was measured using the Cronbach's alpha coefficient. Analyses were performed using the Stata v.13.2 for Windows (Statacorp., USA) and Mplus v.7.31 for Windows (Muthén & Muthén, USA) software. Internal consistency was α=.806. The factor structure showed three that accounted for the 56.6% of the variance. CFA revealed: χ 2 =926.036; df=85; RMSEA=.106 (90%CI, .100-.112); CFI=.947; TLI=.934. The MBI showed an adequate internal consistency and a factor structure being consistent with the original proposed structure with a poor fit, which does not reflect adequate content validity in this sample. Copyright © 2016 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Structural analysis of Herbaspirillum seropedicae lipid-A and of two mutants defective to colonize maize roots.

PubMed

Serrato, Rodrigo V; Balsanelli, Eduardo; Sassaki, Guilherme L; Carlson, Russell W; Muszynski, Artur; Monteiro, Rose A; Pedrosa, Fábio O; Souza, Emanuel M; Iacomini, Marcello

2012-11-01

Lipid-A was isolated by mild acid hydrolysis from lipopolysaccharides extracted from cells of Herbaspirillum seropedicae, strain SMR1, and from two mutants deficient in the biosynthesis of rhamnose (rmlB⁻ and rmlC⁻). Structural analyzes were carried out using MALDI-TOF and derivatization by per-O-trimethylsilylation followed by GC-MS in order to determine monosaccharide and fatty acid composition. De-O-acylation was also performed to determine the presence of N-linked fatty acids. Lipid-A from H. seropedicae SMR1 showed a major structure comprising 2-amino-2-deoxy-glucopyranose-(1→6)-2-amino-2-deoxy-glucopyranose phosphorylated at C4' and C1 positions, each carrying a unit of 4-amino-4-deoxy-arabinose. C2 and C2' positions were substituted by amide-linked 3-hydroxy-dodecanoic acids. Both rhamnose-defective mutants showed similar structure for their lipid-A moieties, except for the lack of 4-amino-4-deoxy-arabinose units attached to phosphoryl groups. Copyright © 2012 Elsevier B.V. All rights reserved.

Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.

PubMed

Spasic, Aleksandar; Berger, Kyle D; Chen, Jonathan L; Seetin, Matthew G; Turner, Douglas H; Mathews, David H

2018-06-01

RNA folding free energy change nearest neighbor parameters are widely used to predict folding stabilities of secondary structures. They were determined by linear regression to datasets of optical melting experiments on small model systems. Traditionally, the optical melting experiments are analyzed assuming a two-state model, i.e. a structure is either complete or denatured. Experimental evidence, however, shows that structures exist in an ensemble of conformations. Partition functions calculated with existing nearest neighbor parameters predict that secondary structures can be partially denatured, which also directly conflicts with the two-state model. Here, a new approach for determining RNA nearest neighbor parameters is presented. Available optical melting data for 34 Watson-Crick helices were fit directly to a partition function model that allows an ensemble of conformations. Fitting parameters were the enthalpy and entropy changes for helix initiation, terminal AU pairs, stacks of Watson-Crick pairs and disordered internal loops. The resulting set of nearest neighbor parameters shows a 38.5% improvement in the sum of residuals in fitting the experimental melting curves compared to the current literature set.

Rapid condition assessment of structural condition after a blast using state-space identification

NASA Astrophysics Data System (ADS)

Eskew, Edward; Jang, Shinae

2015-04-01

After a blast event, it is important to quickly quantify the structural damage for emergency operations. In order improve the speed, accuracy, and efficiency of condition assessments after a blast, the authors have previously performed work to develop a methodology for rapid assessment of the structural condition of a building after a blast. The method involved determining a post-event equivalent stiffness matrix using vibration measurements and a finite element (FE) model. A structural model was built for the damaged structure based on the equivalent stiffness, and inter-story drifts from the blast are determined using numerical simulations, with forces determined from the blast parameters. The inter-story drifts are then compared to blast design conditions to assess the structures damage. This method still involved engineering judgment in terms of determining significant frequencies, which can lead to error, especially with noisy measurements. In an effort to improve accuracy and automate the process, this paper will look into a similar method of rapid condition assessment using subspace state-space identification. The accuracy of the method will be tested using a benchmark structural model, as well as experimental testing. The blast damage assessments will be validated using pressure-impulse (P-I) diagrams, which present the condition limits across blast parameters. Comparisons between P-I diagrams generated using the true system parameters and equivalent parameters will show the accuracy of the rapid condition based blast assessments.

Facile synthesis of silicon nanowire-nanopillar superhydrophobic structures

NASA Astrophysics Data System (ADS)

Roy, Abhijit; Satpati, Biswarup

2018-04-01

We have used metal assisted chemical etching (MACE) method to produce silicon (Si) nanowire-nanopillar array. Nanowire-nanopillar combined structures show higher degree of hydrophobicity compared to its nanowire (Si-NW) counterparts. The rate of etching is depended on initial metal deposition. The structural analysis was carried out using scanning electron microscopy (SEM) in combination with transmission electron microscopy (TEM) to determine different parameters like etching direction, crystallinity etc.

Investigating Molecular Structures of Bio-Fuel and Bio-Oil Seeds as Predictors To Estimate Protein Bioavailability for Ruminants by Advanced Nondestructive Vibrational Molecular Spectroscopy.

PubMed

Ban, Yajing; L Prates, Luciana; Yu, Peiqiang

2017-10-18

This study was conducted to (1) determine protein and carbohydrate molecular structure profiles and (2) quantify the relationship between structural features and protein bioavailability of newly developed carinata and canola seeds for dairy cows by using Fourier transform infrared molecular spectroscopy. Results showed similarity in protein structural makeup within the entire protein structural region between carinata and canola seeds. The highest area ratios related to structural CHO, total CHO, and cellulosic compounds were obtained for carinata seeds. Carinata and canola seeds showed similar carbohydrate and protein molecular structures by multivariate analyses. Carbohydrate molecular structure profiles were highly correlated to protein rumen degradation and intestinal digestion characteristics. In conclusion, the molecular spectroscopy can detect inherent structural characteristics in carinata and canola seeds in which carbohydrate-relative structural features are related to protein metabolism and utilization. Protein and carbohydrate spectral profiles could be used as predictors of rumen protein bioavailability in cows.

Combined spectrophotometry and tensile measurements of human connective tissues: potentials and limitations.

PubMed

Ernstberger, Markus; Sichting, Freddy; Baselt, Tobias; Hartmann, Peter; Aust, Gabriela; Hammer, Niels

2013-06-01

Strain-dependent transmission data of nine iliotibial tract specimens are determined using a custom-built optical setup with a halogen light source and an industrial norm material testing machine. Polarized light microscopy and hematoxylin-eosin staining indicated that lateral contraction of collagen structures is responsible for total intensity variations during a 20-cycle preconditioning and a 5-cycle tensile test. Tensile force progress is opposite to total transmission progress. Due to dehydration, wavelength-specific radiation intensity shifting is determined during the test, primarily noticeable in a water absorption band between 1400 and 1500 nm. The results show the capability of integrating spectrophotometry technology into biomechanics for determining structural alterations of human collagen due to applied strain. Being more sensitive to drying, spectrophotometry may likely serve as a quality control in stress-strain testing of biological structures.

Young children's knowledge of the "determiner" and "adjective" categories.

PubMed

Kemp, Nenagh; Lieven, Elena; Tomasello, Michael

2005-06-01

Children's understanding of the grammatical categories of "determiner" and "adjective" was examined using 2 different methodologies. In Experiment 1, children heard novel nouns combined with either a or the. Few 2-year-olds, but nearly all 3- and 4-year-olds, subsequently produced the novel nouns with a different determiner from the modeled combination. Experiment 2 used a priming methodology. Children age 2, 3, 4, and 6 years repeated descriptions of pictures, before describing target pictures themselves. When the primes consisted of a varied determiner + noun, all age groups produced more determiner + noun descriptions. When the primes consisted of a determiner + adjective + noun, 2-year-olds showed no priming. Three- to 6-year-olds showed item-specific priming, but only 6-year-olds (and to a limited extent 4-year-olds) showed both item-specific and structural priming. These results suggest that children build an understanding of determiners and adjectives gradually, perhaps from individual lexical items, over a number of years, and that pragmatic correctness may be attained particularly late.

The Crystal Structure of Streptococcus pyogenes Uridine Phosphorylase Reveals a Distinct Subfamily of Nucleoside Phosphorylases

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

Tran, Timothy H.; Christoffersen, S.; Allan, Paula W.

2011-09-20

Uridine phosphorylase (UP), a key enzyme in the pyrimidine salvage pathway, catalyzes the reversible phosphorolysis of uridine or 2'-deoxyuridine to uracil and ribose 1-phosphate or 2'-deoxyribose 1-phosphate. This enzyme belongs to the nucleoside phosphorylase I superfamily whose members show diverse specificity for nucleoside substrates. Phylogenetic analysis shows Streptococcus pyogenes uridine phosphorylase (SpUP) is found in a distinct branch of the pyrimidine subfamily of nucleoside phosphorylases. To further characterize SpUP, we determined the crystal structure in complex with the products, ribose 1-phosphate and uracil, at 1.8 {angstrom} resolution. Like Escherichia coli UP (EcUP), the biological unit of SpUP is a hexamermore » with an ?/? monomeric fold. A novel feature of the active site is the presence of His169, which structurally aligns with Arg168 of the EcUP structure. A second active site residue, Lys162, is not present in previously determined UP structures and interacts with O2 of uracil. Biochemical studies of wild-type SpUP showed that its substrate specificity is similar to that of EcUP, while EcUP is {approx}7-fold more efficient than SpUP. Biochemical studies of SpUP mutants showed that mutations of His169 reduced activity, while mutation of Lys162 abolished all activity, suggesting that the negative charge in the transition state resides mostly on uracil O2. This is in contrast to EcUP for which transition state stabilization occurs mostly at O4.« less

Mycobacterium tuberculosis acyl carrier protein synthase adopts two different pH-dependent structural conformations

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

Gokulan, Kuppan; Aggarwal, Anup; Shipman, Lance

2011-09-20

The crystal structures of acyl carrier protein synthase (AcpS) from Mycobacterium tuberculosis (Mtb) and Corynebacterium ammoniagenes determined at pH 5.3 and pH 6.5, respectively, are reported. Comparison of the Mtb apo-AcpS structure with the recently reported structure of the Mtb AcpS-ADP complex revealed that AcpS adopts two different conformations: the orthorhombic and trigonal space-group structures show structural differences in the {alpha}2 helix and in the conformation of the {alpha}3-{alpha}4 connecting loop, which is in a closed conformation. The apo-AcpS structure shows electron density for the entire model and was obtained at lower pH values (4.4-6.0). In contrast, at a highermore » pH value (6.5) AcpS undergoes significant conformational changes, resulting in disordered regions that show no electron density in the AcpS model. The solved structures also reveal that C. ammoniagenes AcpS undergoes structural rearrangement in two regions, similar to the recently reported Mtb AcpS-ADP complex structure. In vitro reconstitution experiments show that AcpS has a higher post-translational modification activity between pH 4.4 and 6.0 than at pH values above 6.5, where the activity drops owing to the change in conformation. The results show that apo-AcpS and AcpS-ADP adopt different conformations depending upon the pH conditions of the crystallization solution.« less

Structural and Biophysical Characterization of Cajanus cajan Protease Inhibitor.

PubMed

Shamsi, Tooba Naz; Parveen, Romana; Ahamad, Shahzaib; Fatima, Sadaf

2017-01-01

A large number of studies have proven that Protease inhibitors (PIs), specifically serine protease inhibitors, show immense divergence in regulation of proteolysis by targeting their specific proteases and hence, they play a key role in healthcare. We aimed to access in-vitro anticancer potential of PI from Cajanus cajan (CCPI). Also, crystallization of CCPI was targetted alongwith structure determination and its structure-function relationship. CCPI was purified from Cajanus cajan seeds by chromatographic techniques. The purity and molecular mass was determined by SDS-PAGE. Anticancer potential of CCPI was determined by MTT assay in normal HEK and cancerous A549 cells. The crystallization screening of CCPI was performed by commercially available screens. CCPI sequence was subject to BLASTp with homologous PIs. Progressive multiple alignment was performed using clustalw2 and was modelled using ab initio protocol of I-TASSER. The results showed ~14kDa CCPI was purified in homogeneity. Also, CCPI showed low cytotoxic effects of in HEK i.e., 27% as compared with 51% cytotoxicity in A549 cells. CCPI crystallized at 16°C using 15% PEG 6000 in 0.1M potassium phosphate buffer (pH 6.0) in 2-3weeks as rod or needles visualized as clusters under the microscope. The molecular modelling revealed that it contains 3 beta sheets, 3 beta hairpins, 2 β-bulges, 6 strands, 3 helices, 1helix-helix interaction, 41 β-turns and 27 γ-turns. The results indicate that CCPI may help to treat cancer in vivo aswell. Also, this is the first report on preliminary crystallization and structural studies of CCPI.

Accurate protein structure modeling using sparse NMR data and homologous structure information.

PubMed

Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

2012-06-19

While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

Explaining gender differences in ill-health in South Korea: the roles of socio-structural, psychosocial, and behavioral factors.

PubMed

Chun, Heeran; Khang, Young-Ho; Kim, Il-Ho; Cho, Sung-Il

2008-09-01

This study examines and explains the gender disparity in health despite rapid modernization in South Korea where the social structure is still based on traditional gender relations. A nationally representative sample of 2897 men and 3286 women aged 25-64 from the 2001 Korean National Health and Nutrition Examination Survey was analyzed. Health indicators included self rated health and chronic disease. Age-adjusted prevalence was computed according to a gender and odds ratios (OR) derived from logistic regression. Percentage changes in OR by inclusion of determinant variables (socio-structural, psychosocial, and behavioral) into the base logistic regression model were used to estimate the contributions to the gender gap in two morbidity measures. Results showed a substantial female excess in ill-health in both measures, revealing an increasing disparity in the older age group. Group-specific age-adjusted prevalence of ill-health showed an inverse relationship to socioeconomic position. When adjusting for each determinant, employment status, education, and depression contributed the greatest to the gender gap. After adjusting for all suggested determinants, 78% for self rated health and 86% for chronic disease in excess OR could be explained. After stratifying for age, the full model provided a complete explanation for the female excess in chronic illness, but for self rated health a female excess was still evident for the younger age group. Socio-structural factors played a crucial role in accounting for female excess in ill-health. This result calls for greater attention to gender-based health inequality stemming from socio-structural determinants in South Korea. Cross-cultural validation studies are suggested for further discussion of the link between changing gender relations and the gender health gap in morbidity in diverse settings.

Porous calcium polyphosphate bone substitutes: additive manufacturing versus conventional gravity sinter processing-effect on structure and mechanical properties.

PubMed

Hu, Youxin; Shanjani, Yaser; Toyserkani, Ehsan; Grynpas, Marc; Wang, Rizhi; Pilliar, Robert

2014-02-01

Porous calcium polyphosphate (CPP) structures proposed as bone-substitute implants and made by sintering CPP powders to form bending test samples of approximately 35 vol % porosity were machined from preformed blocks made either by additive manufacturing (AM) or conventional gravity sintering (CS) methods and the structure and mechanical characteristics of samples so made were compared. AM-made samples displayed higher bending strengths (≈1.2-1.4 times greater than CS-made samples), whereas elastic constant (i.e., effective elastic modulus of the porous structures) that is determined by material elastic modulus and structural geometry of the samples was ≈1.9-2.3 times greater for AM-made samples. X-ray diffraction analysis showed that samples made by either method displayed the same crystal structure forming β-CPP after sinter annealing. The material elastic modulus, E, determined using nanoindentation tests also showed the same value for both sample types (i.e., E ≈ 64 GPa). Examination of the porous structures indicated that significantly larger sinter necks resulted in the AM-made samples which presumably resulted in the higher mechanical properties. The development of mechanical properties was attributed to the different sinter anneal procedures required to make 35 vol % porous samples by the two methods. A primary objective of the present study, in addition to reporting on bending strength and sample stiffness (elastic constant) characteristics, was to determine why the two processes resulted in the observed mechanical property differences for samples of equivalent volume percentage of porosity. An understanding of the fundamental reason(s) for the observed effect is considered important for developing improved processes for preparation of porous CPP implants as bone substitutes for use in high load-bearing skeletal sites. Copyright © 2013 Wiley Periodicals, Inc.

Structure of the buffalo secretory signalling glycoprotein at 2.8 Å resolution

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

Ethayathulla, Abdul S.; Srivastava, Devendra B.; Kumar, Janesh

2007-04-01

The crystal structure of a signalling glycoprotein isolated from buffalo dry secretions (SPB-40) has been determined at 2.8 Å resolution. Two unique residues, Tyr120 and Glu269, found in SPB-40 distort the shape of the sugar-binding groove considerably. The water structure in the groove is also different. The conformations of three flexible loops, His188–His197, Phe202–Arg212 and Tyr244–Pro260, also differ from those found in other structurally similar proteins. The crystal structure of a 40 kDa signalling glycoprotein from buffalo (SPB-40) has been determined at 2.8 Å resolution. SPB-40 acts as a protective signalling factor by binding to viable cells during the earlymore » phase of involution, during which extensive tissue remodelling occurs. It was isolated from the dry secretions of Murrah buffalo. It was purified and crystallized using the hanging-drop vapour-diffusion method with 19% ethanol as the precipitant. The protein was also cloned and its complete nucleotide and amino-acid sequences were determined. When compared with the sequences of other members of the family, the sequence of SPB-40 revealed two very important mutations in the sugar-binding region, in which Tyr120 changed to Trp120 and Glu269 changed to Trp269. The structure showed a significant distortion in the shape of the sugar-binding groove. The water structure in the groove is also drastically altered. The folding of the protein chain in the flexible region comprising segments His188–His197, Phe202–Arg212 and Tyr244–Pro260 shows large variations when compared with other proteins of the family.« less

Biomaterial-host interactions: consequences, determined by implant retrieval analysis.

PubMed

Kaplan, S S

1994-01-01

Prosthetic biomaterials have had a profound impact on reconstructive surgery but complete biocompatability remains illusive. This review considers the retrieval analysis of four common prosthetic structures: the hip, the knee, heart valves, and blood vessels. We show that despite a fine record of early success, deterioration due to mechanical failure or deleterious host responses to the implant may compromise long term function. The eventual retrieval and detailed analysis of implanted structures provides an invaluable opportunity to determine the characteristics of implant success or failure and to provoke the development of still better materials.

A Single-Site Platinum CO Oxidation Catalyst in Zeolite KLTL: Microscopic and Spectroscopic Determination of the Locations of the Platinum Atoms

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

Kistler, Joseph D.; Chotigkrai, Nutchapon; Xu, Pinghong

2014-07-01

A stable site-isolated mononuclear platinum catalyst with a well-defined structure is presented. Platinum complexes supported in zeolite KLTL were synthesized from [Pt(NH 3) 4](NO 3) 2, oxidized at 633 K, and used to catalyze CO oxidation. Finally, IR and X-ray absorption spectra and electron micrographs determine the structures and locations of the platinum complexes in the zeolite pores, demonstrate the platinum-support bonding, and show that the platinum remained site isolated after oxidation and catalysis.

G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures.

PubMed

Lee, Hui Sun; Im, Wonpil

2017-01-01

Recent advances in high-throughput structure determination and computational protein structure prediction have significantly enriched the universe of protein structure. However, there is still a large gap between the number of available protein structures and that of proteins with annotated function in high accuracy. Computational structure-based protein function prediction has emerged to reduce this knowledge gap. The identification of a ligand binding site and its structure is critical to the determination of a protein's molecular function. We present a computational methodology for predicting small molecule ligand binding site and ligand structure using G-LoSA, our protein local structure alignment and similarity measurement tool. All the computational procedures described here can be easily implemented using G-LoSA Toolkit, a package of standalone software programs and preprocessed PDB structure libraries. G-LoSA and G-LoSA Toolkit are freely available to academic users at http://compbio.lehigh.edu/GLoSA . We also illustrate a case study to show the potential of our template-based approach harnessing G-LoSA for protein function prediction.

Small-angle x-ray scattering study of polymer structure: Carbosilane dendrimers in hexane solution

NASA Astrophysics Data System (ADS)

Shtykova, E. V.; Feigin, L. A.; Volkov, V. V.; Malakhova, Yu. N.; Streltsov, D. R.; Buzin, A. I.; Chvalun, S. N.; Katarzhanova, E. Yu.; Ignatieva, G. M.; Muzafarov, A. M.

2016-09-01

The three-dimensional organization of monodisperse hyper-branched macromolecules of regular structure—carbosilane dendrimers of zero, third, and sixth generations—has been studied by small-angle X-ray scattering (SAXS) in solution. The use of modern methods of SAXS data interpretation, including ab initio modeling, has made it possible to determine the internal architecture of the dendrimers in dependence of the generation number and the number of cyclosiloxane end groups (forming the shell of dendritic macromolecules) and show dendrimers to be spherical. The structural results give grounds to consider carbosilane dendrimers promising objects for forming crystals with subsequent structural analysis and determining their structure with high resolution, as well as for designing new materials to be used in various dendrimer-based technological applications.

Synthesis, spectroscopic, and molecular structure characterizations of some azo derivatives of 2-hydroxyacetophenone

NASA Astrophysics Data System (ADS)

Albayrak, Çiğdem; Gümrükçüoğlu, İsmail E.; Odabaşoğlu, Mustafa; İskeleli, Nazan Ocak; Ağar, Erbil

2009-08-01

Some novel azo compounds were prepared by the reaction of 2-hydroxyacetophenone with aniline and its substituted derivatives. The structures of synthesized azo compounds were determined by IR, UV-Vis, 1H NMR and 13C NMR spectroscopic techniques and the structures of some of these compounds were also determined by X-ray diffraction studies. Structural analysis using IR in solid state shows that the azo form is favoured in the azo compounds whereas UV-Vis analysis of the azo compounds in solution has shown that there is a azo and ionic form. The azo compounds in the basic solvents dimethylformamide (DMF) and dimethylsulfoxide (DMSO) are both azo and ionic form while these compounds in ethyl alcohol (EtOH) and chloroform (CHCl 3) are only azo form.

Determinants of Literacy Proficiency: A Lifelong-Lifewide Learning Perspective

ERIC Educational Resources Information Center

Desjardins, Richard

2003-01-01

The aim of this article is to investigate the predictive capacity of major determinants of literacy proficiency that are associated with a variety of contexts including school, home, work, community and leisure. An identical structural model based on previous research is fitted to data for 18 countries. The results show that even after accounting…

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

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

Han, B.-G.; Dong, M.; Liu, H.

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,more » 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.« less

Relating structure with morphology: A comparative study of perfect Langmuir Blodgett multilayers

NASA Astrophysics Data System (ADS)

Mukherjee, Smita; Datta, Alokmay; Giglia, Angelo; Mahne, Nichole; Nannarone, Stefano

2008-01-01

Atomic force microscopy and X-ray reflectivity of metal-stearate (MSt) Langmuir-Blodgett films on hydrophilic Silicon (1 0 0), show dramatic reduction in 'pinhole' defects when metal M is changed from Cd to Co, along with excellent periodicity in multilayer, with hydrocarbon tails tilted 9.6° from vertical for CoSt (untilted for CdSt). Near edge X-ray absorption fine structure (NEXAFS) and Fourier transform infra-red (FTIR) spectroscopies indicate bidentate bridging metal-carboxylate coordination in CoSt (unidentate in CdSt), underscoring role of headgroup structure in determining morphology. FTIR studies also show increased packing density in CoSt, consistent with increased coverage.

Structural Conservation of the Myoviridae Phage Tail Sheath Protein Fold

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

Aksyuk, Anastasia A.; Kurochkina, Lidia P.; Fokine, Andrei

2012-02-21

Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 {angstrom} diameter icosahedral head and a 2000 {angstrom}-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 {angstrom} resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 {angstrom} resolution. Despite low sequence identity between these proteins, all ofmore » these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.« less

Network structure exploration in networks with node attributes

NASA Astrophysics Data System (ADS)

Chen, Yi; Wang, Xiaolong; Bu, Junzhao; Tang, Buzhou; Xiang, Xin

2016-05-01

Complex networks provide a powerful way to represent complex systems and have been widely studied during the past several years. One of the most important tasks of network analysis is to detect structures (also called structural regularities) embedded in networks by determining group number and group partition. Most of network structure exploration models only consider network links. However, in real world networks, nodes may have attributes that are useful for network structure exploration. In this paper, we propose a novel Bayesian nonparametric (BNP) model to explore structural regularities in networks with node attributes, called Bayesian nonparametric attribute (BNPA) model. This model does not only take full advantage of both links between nodes and node attributes for group partition via shared hidden variables, but also determine group number automatically via the Bayesian nonparametric theory. Experiments conducted on a number of real and synthetic networks show that our BNPA model is able to automatically explore structural regularities in networks with node attributes and is competitive with other state-of-the-art models.

Relation between native ensembles and experimental structures of proteins

PubMed Central

Best, Robert B.; Lindorff-Larsen, Kresten; DePristo, Mark A.; Vendruscolo, Michele

2006-01-01

Different experimental structures of the same protein or of proteins with high sequence similarity contain many small variations. Here we construct ensembles of “high-sequence similarity Protein Data Bank” (HSP) structures and consider the extent to which such ensembles represent the structural heterogeneity of the native state in solution. We find that different NMR measurements probing structure and dynamics of given proteins in solution, including order parameters, scalar couplings, and residual dipolar couplings, are remarkably well reproduced by their respective high-sequence similarity Protein Data Bank ensembles; moreover, we show that the effects of uncertainties in structure determination are insufficient to explain the results. These results highlight the importance of accounting for native-state protein dynamics in making comparisons with ensemble-averaged experimental data and suggest that even a modest number of structures of a protein determined under different conditions, or with small variations in sequence, capture a representative subset of the true native-state ensemble. PMID:16829580

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

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

Wan, William; Stubbs, Gerald

2014-05-01

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

Improved stud configurations for attaching laminated wood wind turbine blades

NASA Technical Reports Server (NTRS)

Fadoul, J. R.

1985-01-01

A series of bonded stud design configurations was screened on the basis of tension-tension cyclic tests to determine the structural capability of each configuration for joining a laminated wood structure (wind turbine blade) to a steel flange (wind turbine hub). Design parameters which affected the joint strength (ultimate and fatigue) were systematically varied and evaluated through appropriate testing. Two designs showing the most promise were used to fabricate addiate testing. Two designs showing the most promise were used to fabricate additional test specimens to determine ultimate strength and fatigue curves. Test results for the bonded stud designs demonstrated that joint strengths approaching the 10,000 to 12,000 psi ultimate strength and 5000 psi high cycle fatigue strength of the wood epoxy composite could be achieved.

Global search in photoelectron diffraction structure determination using genetic algorithms

NASA Astrophysics Data System (ADS)

Viana, M. L.; Díez Muiño, R.; Soares, E. A.; Van Hove, M. A.; de Carvalho, V. E.

2007-11-01

Photoelectron diffraction (PED) is an experimental technique widely used to perform structural determinations of solid surfaces. Similarly to low-energy electron diffraction (LEED), structural determination by PED requires a fitting procedure between the experimental intensities and theoretical results obtained through simulations. Multiple scattering has been shown to be an effective approach for making such simulations. The quality of the fit can be quantified through the so-called R-factor. Therefore, the fitting procedure is, indeed, an R-factor minimization problem. However, the topography of the R-factor as a function of the structural and non-structural surface parameters to be determined is complex, and the task of finding the global minimum becomes tough, particularly for complex structures in which many parameters have to be adjusted. In this work we investigate the applicability of the genetic algorithm (GA) global optimization method to this problem. The GA is based on the evolution of species, and makes use of concepts such as crossover, elitism and mutation to perform the search. We show results of its application in the structural determination of three different systems: the Cu(111) surface through the use of energy-scanned experimental curves; the Ag(110)-c(2 × 2)-Sb system, in which a theory-theory fit was performed; and the Ag(111) surface for which angle-scanned experimental curves were used. We conclude that the GA is a highly efficient method to search for global minima in the optimization of the parameters that best fit the experimental photoelectron diffraction intensities to the theoretical ones.

Chemical bath deposited and dip coating deposited CuS thin films - Structure, Raman spectroscopy and surface study

NASA Astrophysics Data System (ADS)

Tailor, Jiten P.; Khimani, Ankurkumar J.; Chaki, Sunil H.

2018-05-01

The crystal structure, Raman spectroscopy and surface microtopography study on as-deposited CuS thin films were carried out. Thin films deposited by two techniques of solution growth were studied. The thin films used in the present study were deposited by chemical bath deposition (CBD) and dip coating deposition techniques. The X-ray diffraction (XRD) analysis of both the as-deposited thin films showed that both the films possess covellite phase of CuS and hexagonal unit cell structure. The determined lattice parameters of both the films are in agreement with the standard JCPDS as well as reported data. The crystallite size determined by Scherrer's equation and Hall-Williamsons relation using XRD data for both the as-deposited thin films showed that the respective values were in agreement with each other. The ambient Raman spectroscopy of both the as-deposited thin films showed major emission peaks at 474 cm-1 and a minor emmision peaks at 265 cm-1. The observed Raman peaks matched with the covellite phase of CuS. The atomic force microscopy of both the as-deposited thin films surfaces showed dip coating thin film to be less rough compared to CBD deposited thin film. All the obtained results are presented and deliberated in details.

Radiation Heat Transfer Between Diffuse-Gray Surfaces Using Higher Order Finite Elements

NASA Technical Reports Server (NTRS)

Gould, Dana C.

2000-01-01

This paper presents recent work on developing methods for analyzing radiation heat transfer between diffuse-gray surfaces using p-version finite elements. The work was motivated by a thermal analysis of a High Speed Civil Transport (HSCT) wing structure which showed the importance of radiation heat transfer throughout the structure. The analysis also showed that refining the finite element mesh to accurately capture the temperature distribution on the internal structure led to very large meshes with unacceptably long execution times. Traditional methods for calculating surface-to-surface radiation are based on assumptions that are not appropriate for p-version finite elements. Two methods for determining internal radiation heat transfer are developed for one and two-dimensional p-version finite elements. In the first method, higher-order elements are divided into a number of sub-elements. Traditional methods are used to determine radiation heat flux along each sub-element and then mapped back to the parent element. In the second method, the radiation heat transfer equations are numerically integrated over the higher-order element. Comparisons with analytical solutions show that the integration scheme is generally more accurate than the sub-element method. Comparison to results from traditional finite elements shows that significant reduction in the number of elements in the mesh is possible using higher-order (p-version) finite elements.

Synchronisation and stability in river metapopulation networks.

PubMed

Yeakel, J D; Moore, J W; Guimarães, P R; de Aguiar, M A M

2014-03-01

Spatial structure in landscapes impacts population stability. Two linked components of stability have large consequences for persistence: first, statistical stability as the lack of temporal fluctuations; second, synchronisation as an aspect of dynamic stability, which erodes metapopulation rescue effects. Here, we determine the influence of river network structure on the stability of riverine metapopulations. We introduce an approach that converts river networks to metapopulation networks, and analytically show how fluctuation magnitude is influenced by interaction structure. We show that river metapopulation complexity (in terms of branching prevalence) has nonlinear dampening effects on population fluctuations, and can also buffer against synchronisation. We conclude by showing that river transects generally increase synchronisation, while the spatial scale of interaction has nonlinear effects on synchronised dynamics. Our results indicate that this dual stability - conferred by fluctuation and synchronisation dampening - emerges from interaction structure in rivers, and this may strongly influence the persistence of river metapopulations. © 2013 John Wiley & Sons Ltd/CNRS.

Crystal structure and ligand affinity of avidin in the complex with 4‧-hydroxyazobenzene-2-carboxylic acid

NASA Astrophysics Data System (ADS)

Strzelczyk, Paweł; Bujacz, Grzegorz

2016-04-01

Avidin is a protein found in egg white that binds numerous organic compounds with high affinity, especially biotin and its derivatives. Due to its extraordinary affinity for its ligands, avidin is extensively used in biotechnology. X-ray crystallography and fluorescence-based biophysical techniques were used to show that avidin binds the dye 4‧-hydroxyazobenzene-2-carboxylic acid (HABA) with a lower affinity than biotin. The apparent dissociation constant determined for the avidin complex with HABA by microscale thermophoresis (MST) is 4.12 μM. The crystal structure of avidin-HABA complex was determined at a resolution of 2.2 Å (PDB entry 5chk). The crystals belong to a hexagonal system, in the space group P6422. In that structure, the hydrazone tautomer of HABA is bound at the bottom part of the central calyx near the polar residues. We show interactions of the dye with avidin and compare them with the previously reported avidin-biotin complex.

Analysis of Protein Thermostability Enhancing Factors in Industrially Important Thermus Bacteria Species

PubMed Central

Kumwenda, Benjamin; Litthauer, Derek; Bishop, Özlem Tastan; Reva, Oleg

2013-01-01

Elucidation of evolutionary factors that enhance protein thermostability is a critical problem and was the focus of this work on Thermus species. Pairs of orthologous sequences of T. scotoductus SA-01 and T. thermophilus HB27, with the largest negative minimum folding energy (MFE) as predicted by the UNAFold algorithm, were statistically analyzed. Favored substitutions of amino acids residues and their properties were determined. Substitutions were analyzed in modeled protein structures to determine their locations and contribution to energy differences using PyMOL and FoldX programs respectively. Dominant trends in amino acid substitutions consistent with differences in thermostability between orthologous sequences were observed. T. thermophilus thermophilic proteins showed an increase in non-polar, tiny, and charged amino acids. An abundance of alanine substituted by serine and threonine, as well as arginine substituted by glutamine and lysine was observed in T. thermophilus HB27. Structural comparison showed that stabilizing mutations occurred on surfaces and loops in protein structures. PMID:24023508

Influences of Co doping on the structural and optical properties of ZnO nanostructured

NASA Astrophysics Data System (ADS)

Majeed Khan, M. A.; Wasi Khan, M.; Alhoshan, Mansour; Alsalhi, M. S.; Aldwayyan, A. S.

2010-07-01

Pure and Co-doped ZnO nanostructured samples have been synthesized by a chemical route. We have studied the structural and optical properties of the samples by using X-ray diffraction (XRD), field-emission scanning electron microscopy (FESEM), field-emission transmission electron microscope (FETEM), energy-dispersive X-ray (EDX) analysis and UV-VIS spectroscopy. The XRD patterns show that all the samples are hexagonal wurtzite structures. Changes in crystallite size due to mechanical activation were also determined from X-ray measurements. These results were correlated with changes in particle size followed by SEM and TEM. The average crystallite sizes obtained from XRD were between 20 to 25 nm. The TEM images showed the average particle size of undoped ZnO nanostructure was about 20 nm whereas the smallest average grain size at 3% Co was about 15 nm. Optical parameters such as absorption coefficient ( α), energy band gap ( E g ), the refractive index ( n), and dielectric constants ( σ) have been determined using different methods.

Application of Powder Diffraction Methods to the Analysis of the Atomic Structure of Nanocrystals: The Concept of the Apparent Lattice Parameter (ALP)

NASA Technical Reports Server (NTRS)

Palosz, B.; Grzanka, E.; Gierlotka, S.; Stelmakh, S.; Pielaszek, R.; Bismayer, U.; Weber, H.-P.; Palosz, W.; Curreri, Peter A. (Technical Monitor)

2002-01-01

The applicability of standard methods of elaboration of powder diffraction data for determination of the structure of nano-size crystallites is analysed. Based on our theoretical calculations of powder diffraction data we show, that the assumption of the infinite crystal lattice for nanocrystals smaller than 20 nm in size is not justified. Application of conventional tools developed for elaboration of powder diffraction data, like the Rietveld method, may lead to erroneous interpretation of the experimental results. An alternate evaluation of diffraction data of nanoparticles, based on the so-called 'apparent lattice parameter' (alp) is introduced. We assume a model of nanocrystal having a grain core with well-defined crystal structure, surrounded by a surface shell with the atomic structure similar to that of the core but being under a strain (compressive or tensile). The two structural components, the core and the shell, form essentially a composite crystal with interfering, inseparable diffraction properties. Because the structure of such a nanocrystal is not uniform, it defies the basic definitions of an unambiguous crystallographic phase. Consequently, a set of lattice parameters used for characterization of simple crystal phases is insufficient for a proper description of the complex structure of nanocrystals. We developed a method of evaluation of powder diffraction data of nanocrystals, which refers to a core-shell model and is based on the 'apparent lattice parameter' methodology. For a given diffraction pattem, the alp values are calculated for every individual Bragg reflection. For nanocrystals the alp values depend on the diffraction vector Q. By modeling different a0tomic structures of nanocrystals and calculating theoretically corresponding diffraction patterns using the Debye functions we showed, that alp-Q plots show characteristic shapes which can be used for evaluation of the atomic structure of the core-shell system. We show, that using a simple model of a nanocrystal with spherical shape and centro-symmetric strain at the surface shell we obtain theoretical alp-Q values which match very well the alp-Q plots determined experimentally for Sic, GaN, and diamond nanopowders. The theoretical models are defined by the lattice parameter of the grain core, thickness of the surface shell, and the magnitude and distribution of the strain field in the surface shell. According to our calculations, the part of the diffraction pattern measured at relatively low diffraction vectors Q (below 10/angstrom) provides information on the surface strain, whle determination of the lattice parameters in the grain core requires measurements at large Q-values (above 15 - 20/angstrom).

Binding in alkali and alkaline-earth tetrahydroborates: Special position of magnesium tetrahydroborate

NASA Astrophysics Data System (ADS)

Łodziana, Zbigniew; van Setten, Michiel J.

2010-01-01

Compounds of light elements and hydrogen are currently extensively studied due to their potential application in the field of hydrogen or energy storage. A number of new interesting tetrahydroborates that are especially promising due to their very high gravimetric hydrogen content were recently reported. However, the determination and understanding of their complex crystalline structures has created considerable debate. Metal tetrahydroborates, in general, form a large variety of structures ranging from simple for NaBH4 to very complex for Mg(BH4)2 . Despite the extensive discussion in the literature no clear explanation has been offered for this variety so far. In this paper we analyze the structural and electronic properties of a broad range of metal tetrahydroborates and reveal the factors that determine their structure: ionic bonding, the orientation of the BH4 groups, and the coordination number of the metal cation. We show, in a simple way, that the charge transfer in the metal tetrahydroborates rationally explains the structural diversity of these compounds. Being ionic systems, the metal tetrahydroborates fall into the classification of Linus Pauling. By using the ionic radius for the BH4 group as determined in this paper, this allows for structural predictions for new and mixed compounds.

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

Rodriguez, Jose A.; Ivanova, Magdalena I.; Sawaya, Michael R.

We report that the protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 Å resolution structure demonstrates thatmore » this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face β-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length α-synuclein. Finally, the NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils.« less

The hairpin resonator: A plasma density measuring technique revisited

NASA Astrophysics Data System (ADS)

Piejak, R. B.; Godyak, V. A.; Garner, R.; Alexandrovich, B. M.; Sternberg, N.

2004-04-01

A microwave resonator probe is a resonant structure from which the relative permittivity of the surrounding medium can be determined. Two types of microwave resonator probes (referred to here as hairpin probes) have been designed and built to determine the electron density in a low-pressure gas discharge. One type, a transmission probe, is a functional equivalent of the original microwave resonator probe introduced by R. L. Stenzel [Rev. Sci. Instrum. 47, 603 (1976)], modified to increase coupling to the hairpin structure and to minimize plasma perturbation. The second type, a reflection probe, differs from the transmission probe in that it requires only one coaxial feeder cable. A sheath correction, based on the fluid equations for collisionless ions in a cylindrical electron-free sheath, is presented here to account for the sheath that naturally forms about the hairpin structure immersed in plasma. The sheath correction extends the range of electron density that can be accurately measured with a particular wire separation of the hairpin structure. Experimental measurements using the hairpin probe appear to be highly reproducible. Comparisons with Langmuir probes show that the Langmuir probe determines an electron density that is 20-30% lower than the hairpin. Further comparisons, with both an interferometer and a Langmuir probe, show hairpin measurements to be in good agreement with the interferometer while Langmuir probe measurements again result in a lower electron density.

Comparative studies of industrial grade carbon black powders

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

Chawla, Komal, E-mail: komalchawla.rs@gmail.com; Chauhan, Alok P. S., E-mail: chauhan.alok@gmail.com, E-mail: alok.chauhan@alumni.stonybrook.edu

Comparative studies of two dissimilar industrial grade Carbon Black (CB) powders (N375 and N405) were conducted. The structure, surface area and particle size are the three important characteristics of CB powder that determine their processability and application as filler in preparing rubber compounds. The powders were characterized for their structure using dibutyl phthalate absorption (DBPA), particle size via laser particle size analyzer and surface area by nitrogen adsorption method. The structural characterization showed that N405 had lower DBPA in comparison to N375, confirming low structure of N405 grade CB powder. It was observed from the particle size analysis that N375more » was coarser than N405 grade CB. The total surface area values were determined by the BET method based on the cross sectional area of the nitrogen molecule. N375, a coarse grade CB powder with high structure, depicted less surface area as compared to N405.« less

Structural determinants of nuclear export signal orientation in binding to exportin CRM1

DOE PAGES

Fung, Ho Yee Joyce; Fu, Szu -Chin; Brautigam, Chad A.; ...

2015-09-08

The Chromosome Region of Maintenance 1 (CRM1) protein mediates nuclear export of hundreds of proteins through recognition of their nuclear export signals (NESs), which are highly variable in sequence and structure. The plasticity of the CRM1-NES interaction is not well understood, as there are many NES sequences that seem incompatible with structures of the NES-bound CRM1 groove. Crystal structures of CRM1 bound to two different NESs with unusual sequences showed the NES peptides binding the CRM1 groove in the opposite orientation (minus) to that of previously studied NESs (plus). A comparison of minus and plus NESs identified structural and sequencemore » determinants for NES orientation. The binding of NESs to CRM1 in both orientations results in a large expansion in NES consensus patterns and therefore a corresponding expansion of potential NESs in the proteome.« less

Structure-property relationships in hybrid dental nanocomposite resins containing monofunctional and multifunctional polyhedral oligomeric silsesquioxanes.

PubMed

Wang, Weiguo; Sun, Xiang; Huang, Li; Gao, Yu; Ban, Jinghao; Shen, Lijuan; Chen, Jihua

2014-01-01

Organic-inorganic hybrid materials, such as polyhedral oligomeric silsesquioxanes (POSS), have the potential to improve the mechanical properties of the methacrylate-based composites and resins used in dentistry. In this article, nanocomposites of methacryl isobutyl POSS (MI-POSS [bears only one methacrylate functional group]) and methacryl POSS (MA-POSS [bears eight methacrylate functional groups]) were investigated to determine the effect of structures on the properties of dental resin. The structures of the POSS-containing networks were determined by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, and Fourier transform infrared spectroscopy. Monofunctional POSS showed a strong tendency toward aggregation and crystallization, while multifunctional POSS showed higher miscibility with the dimethacrylate monomer. The mechanical properties and wear resistance decreased with increasing amounts of MI-POSS, indicating that the MI-POSS agglomerates act as the mechanical weak point in the dental resins. The addition of small amounts of MA-POSS improved the mechanical and shrinkage properties. However, samples with a higher MA-POSS concentration showed lower flexural strength and flexural modulus, indicating that there is a limited range in which the reinforcement properties of MA-POSS can operate. This concentration dependence is attributed to phase separation at higher concentrations of POSS, which affects the structural integrity, and thus, the mechanical and shrinkage properties of the dental resin. Our results show that resin with 3% MA-POSS is a potential candidate for resin-based dental materials.

30 CFR 77.216-2 - Water, sediment, or slurry impoundments and impounding structures; minimum plan requirements...

Code of Federal Regulations, 2010 CFR

2010-07-01

... instrumentation. (9) Graphs showing area-capacity curves. (10) A statement of the runoff attributable to the probable maximum precipitation of 6-hour duration and the calculations used in determining such runoff. (11) A statement of the runoff attributable to the storm for which the structure is designed and the...

Structure of Energetic Particle Mediated Shocks Revisited

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

Mostafavi, P.; Zank, G. P.; Webb, G. M.

2017-05-20

The structure of collisionless shock waves is often modified by the presence of energetic particles that are not equilibrated with the thermal plasma (such as pickup ions [PUIs] and solar energetic particles [SEPs]). This is relevant to the inner and outer heliosphere and the Very Local Interstellar Medium (VLISM), where observations of shock waves (e.g., in the inner heliosphere) show that both the magnetic field and thermal gas pressure are less than the energetic particle component pressures. Voyager 2 observations revealed that the heliospheric termination shock (HTS) is very broad and mediated by energetic particles. PUIs and SEPs contribute bothmore » a collisionless heat flux and a higher-order viscosity. We show that the incorporation of both effects can completely determine the structure of collisionless shocks mediated by energetic ions. Since the reduced form of the PUI-mediated plasma model is structurally identical to the classical cosmic ray two-fluid model, we note that the presence of viscosity, at least formally, eliminates the need for a gas sub-shock in the classical two-fluid model, including in that regime where three are possible. By considering parameters upstream of the HTS, we show that the thermal gas remains relatively cold and the shock is mediated by PUIs. We determine the structure of the weak interstellar shock observed by Voyager 1 . We consider the inclusion of the thermal heat flux and viscosity to address the most general form of an energetic particle-thermal plasma two-fluid model.« less

Crystal structure of salt-tolerant glutaminase from Micrococcus luteus K-3 in the presence and absence of its product L-glutamate and its activator Tris.

PubMed

Yoshimune, Kazuaki; Shirakihara, Yasuo; Wakayama, Mamoru; Yumoto, Isao

2010-02-01

Glutaminase from Micrococcus luteus K-3 [Micrococcus glutaminase (Mglu); 456 amino acid residues (aa); 48 kDa] is a salt-tolerant enzyme. Our previous study determined the structure of its major 42-kDa fragment. Here, using new crystallization conditions, we determined the structures of the intact enzyme in the presence and absence of its product L-glutamate and its activator Tris, which activates the enzyme by sixfold. With the exception of a 'lid' part (26-29 aa) and a few other short stretches, the structures were all very similar over the entire polypeptide chain. However, the presence of the ligands significantly reduced the length of the disordered regions: 41 aa in the unliganded structure (N), 21 aa for L-glutamate (G), 8 aa for Tris (T) and 6 aa for both L-glutamate and Tris (TG). L-glutamate was identified in both the G and TG structures, whereas Tris was only identified in the TG structure. Comparison of the glutamate-binding site between Mglu and salt-labile glutaminase (YbgJ) from Bacillus subtilis showed significantly smaller structural changes of the protein part in Mglu. A comparison of the substrate-binding pocket of Mglu, which is highly specific for L-glutamine, with that of Erwinia carotovora asparaginase, which has substrates other than L-glutamine, shows that Mglu has a larger substrate-binding pocket that prevents the binding of L-asparagine with proper interactions.

Structure of the Apo Form of Bacillus stearothermophilus Phosphofructokinase

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

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

2012-02-08

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

Isolation and characterization of a bactericidal withanolide from Physalis virginiana.

PubMed

Gibson, Kathleen A; Reese, R Neil; Halaweish, Fathi T; Ren, Yulin

2012-01-01

Physalis virginiana (Virginia Groundcherry) is a member of the family Solenaceae. Several species of the Physalis genus have been used traditionally by American Indians as medicinal treatments. This study investigated the antibacterial activity of chemicals extracted from P. virginiana through antibacterial disc and cytotoxicity assays. Isolation and purification of an antimicrobial compound was achieved through flash chromatography and preparative HPLC. Finally, identification of chemical structure was determined from (1)H and (13)C NMR and MS. Disc assays showed that crude ethanol extracts were effective antibacterial agents against one gram-negative and seven gram-positive bacterial strains. Cytotoxicity assays indicated that it is less toxic than gentamicin controls. Isolation of the active component showed it to be a relatively polar compound. (1)H and (13)C NMR chemical shifts together with HRMS indicated a similar structure to withanolides previously identified from Physalis angulata. HRMS analysis showed a molecular mass of 472.2857 which corresponds to a molecular formula C(28)H(40)O(6). An antibacterial withanolide was isolated from P. virginiana using flash chromatography and HPLC separations. The chemical structure was determined by NMR and MS to be the withanolide physagulin V.

In-Situ Observation of Nano-Oxide Formation in Magnetic Thin Films

NASA Astrophysics Data System (ADS)

McCallum, Andrew; Russek, Stephen

2004-03-01

Exposure of a metal surface in a spin valve structure to oxygen creates a nano-oxide layer, or NOL, on that surface. Inclusion of NOLs into spin valve structures has been shown by many researchers to lower the resistance and increase the giant magnetoresistance effect. Four point in-situ conductance measurements were made during the deposition and oxidation of Co layers. These measurements show an initial decrease in conductance followed by an increase in conductance, due to a specularity increase of at least 0.10. RHEED measurements taken simultaneously with conductance measurements show the formation an amorphous oxide while the specularity increases. With further exposure of oxygen to the surface a CoO structure with a (111) texture forms. Magnetoconductance measurements during the oxidation of the free layer of bottom pinned spin valves show increases in the GMR of the spin valves. Estimates of the change in specularity and Co layer thickness were determined from the change in conductance and the change in magnetoconductance. Also determined from the magnetoconductance measurements was an increase in the coercivity of the free layer with oxidation. Adding Co onto the oxide had a strong effect on the coercivity and coupling between free and pinned layers.

Isolation and characterization of a bactericidal withanolide from Physalis virginiana

PubMed Central

Gibson, Kathleen A.; Reese, R. Neil; Halaweish, Fathi T.; Ren, Yulin

2012-01-01

Background: Physalis virginiana (Virginia Groundcherry) is a member of the family Solenaceae. Several species of the Physalis genus have been used traditionally by American Indians as medicinal treatments. Materials and Methods: This study investigated the antibacterial activity of chemicals extracted from P. virginiana through antibacterial disc and cytotoxicity assays. Isolation and purification of an antimicrobial compound was achieved through flash chromatography and preparative HPLC. Finally, identification of chemical structure was determined from 1H and 13C NMR and MS. Results: Disc assays showed that crude ethanol extracts were effective antibacterial agents against one gram-negative and seven gram-positive bacterial strains. Cytotoxicity assays indicated that it is less toxic than gentamicin controls. Isolation of the active component showed it to be a relatively polar compound. 1H and 13C NMR chemical shifts together with HRMS indicated a similar structure to withanolides previously identified from Physalis angulata. HRMS analysis showed a molecular mass of 472.2857 which corresponds to a molecular formula C28H40O6. Conclusion: An antibacterial withanolide was isolated from P. virginiana using flash chromatography and HPLC separations. The chemical structure was determined by NMR and MS to be the withanolide physagulin V. PMID:22438659

Accurate determination of interfacial protein secondary structure by combining interfacial-sensitive amide I and amide III spectral signals.

PubMed

Ye, Shuji; Li, Hongchun; Yang, Weilai; Luo, Yi

2014-01-29

Accurate determination of protein structures at the interface is essential to understand the nature of interfacial protein interactions, but it can only be done with a few, very limited experimental methods. Here, we demonstrate for the first time that sum frequency generation vibrational spectroscopy can unambiguously differentiate the interfacial protein secondary structures by combining surface-sensitive amide I and amide III spectral signals. This combination offers a powerful tool to directly distinguish random-coil (disordered) and α-helical structures in proteins. From a systematic study on the interactions between several antimicrobial peptides (including LKα14, mastoparan X, cecropin P1, melittin, and pardaxin) and lipid bilayers, it is found that the spectral profiles of the random-coil and α-helical structures are well separated in the amide III spectra, appearing below and above 1260 cm(-1), respectively. For the peptides with a straight backbone chain, the strength ratio for the peaks of the random-coil and α-helical structures shows a distinct linear relationship with the fraction of the disordered structure deduced from independent NMR experiments reported in the literature. It is revealed that increasing the fraction of negatively charged lipids can induce a conformational change of pardaxin from random-coil to α-helical structures. This experimental protocol can be employed for determining the interfacial protein secondary structures and dynamics in situ and in real time without extraneous labels.

Structure and phase formation behavior and dielectric and magnetic properties of lead iron tantalate-lead zirconate titanate multiferroic ceramics

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

Wongmaneerung, R., E-mail: re_nok@yahoo.com; Tipakontitikul, R.; Jantaratana, P.

2016-03-15

Highlights: • The multiferroic ceramics consisted of PFT and PZT. • Crystal structure changed from cubic to mixedcubic and tetragonal with increasing PZT content. • Dielectric showed the samples underwent a typical relaxor ferroelectric behavior. • Magnetic properties showed very interesting behavior with square saturated magnetic hysteresis loops. - Abstract: Multiferroic (1 − x)Pb(Fe{sub 0.5}Ta{sub 0.5})O{sub 3}–xPb(Zr{sub 0.53}Ti{sub 0.47})O{sub 3} (or PFT–PZT) ceramics were synthesized by solid-state reaction method. The crystal structure and phase formation of the ceramics were examined by X-ray diffraction (XRD). The local structure surrounding Fe and Ti absorbing atoms was investigated by synchrotron X-ray Absorption Near-Edgemore » Structure (XANES) measurement. Dielectric properties were studied as a function of frequency and temperature using a LCR meter. A vibrating sample magnetometer (VSM) was used to determine the magnetic hysteresis loops. XRD study indicated that the crystal structure of the sample changed from pure cubic to mixed cubic and tetragonal with increasing PZT content. XANES measurements showed that the local structure surrounding Fe and Ti ions was similar. Dielectric study showed that the samples underwent a typical relaxor ferroelectric behavior while the magnetic properties showed very interesting behavior with square saturated magnetic hysteresis loops.« less

Triosmium Clusters on a Support: Determination of Structure by X-Ray Absorption Spectroscopy and High-Resolution Microscopy

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

Shareghe, Mehraeen; Chi, Miaofang; Browning, Nigel D.

2011-01-01

The structures of small, robust metal clusters on a solid support were determined by a combination of spectroscopic and microscopic methods: extended X-ray absorption fine structure (EXAFS) spectroscopy, scanning transmission electron microscopy (STEM), and aberration-corrected STEM. The samples were synthesized from [Os{sub 3}(CO){sub 12}] on MgO powder to provide supported clusters intended to be triosmium. The results demonstrate that the supported clusters are robust in the absence of oxidants. Conventional high-angle annular dark-field (HAADF) STEM images demonstrate a high degree of uniformity of the clusters, with root-mean-square (rms) radii of 2.03 {+-} 0.06 {angstrom}. The EXAFS OsOs coordination number ofmore » 2.1 {+-} 0.4 confirms the presence of triosmium clusters on average and correspondingly determines an average rms cluster radius of 2.02 {+-} 0.04 {angstrom}. The high-resolution STEM images show the individual Os atoms in the clusters, confirming the triangular structures of their frames and determining OsOs distances of 2.80 {+-} 0.14 {angstrom}, matching the EXAFS value of 2.89 {+-} 0.06 {angstrom}. IR and EXAFS spectra demonstrate the presence of CO ligands on the clusters. This set of techniques is recommended as optimal for detailed and reliable structural characterization of supported clusters.« less

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

DOE PAGES

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe; ...

2014-06-16

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

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

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

Neutron and X-ray total scattering study of hydrogen disorder in fully hydrated hydrogrossular, Ca3Al2(O4H4)3

NASA Astrophysics Data System (ADS)

Keen, David A.; Keeble, Dean S.; Bennett, Thomas D.

2018-04-01

The structure of fully hydrated grossular, or katoite, contains an unusual arrangement of four O-H bonds within each O4 tetrahedra. Neutron and X-ray total scattering from a powdered deuterated sample have been measured to investigate the local arrangement of this O4D4 cluster. The O-D bond length determined directly from the pair distribution function is 0.954 Å, although the Rietveld-refined distance between average O and D positions was slightly smaller. Reverse Monte Carlo refinement of supercell models to the total scattering data show that other than the consequences of this correctly determined O-D bond length, there is little to suggest that the O4D4 structure is locally significantly different from that expected based on the average structure determined solely from Bragg diffraction.

Identification of Extracellular Segments by Mass Spectrometry Improves Topology Prediction of Transmembrane Proteins.

PubMed

Langó, Tamás; Róna, Gergely; Hunyadi-Gulyás, Éva; Turiák, Lilla; Varga, Julia; Dobson, László; Várady, György; Drahos, László; Vértessy, Beáta G; Medzihradszky, Katalin F; Szakács, Gergely; Tusnády, Gábor E

2017-02-13

Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions. Here we report a method for the high-throughput determination of extracellular segments of transmembrane proteins based on the identification of surface labeled and biotin captured peptide fragments by LC/MS/MS. We show that reliable identification of extracellular protein segments increases the accuracy and reliability of existing topology prediction algorithms. Using the experimental topology data as constraints, our improved prediction tool provides accurate and reliable topology models for hundreds of human transmembrane proteins.

Assembly kinetics determine the architecture of α-actinin crosslinked F-actin networks.

PubMed

Falzone, Tobias T; Lenz, Martin; Kovar, David R; Gardel, Margaret L

2012-05-29

The actin cytoskeleton is organized into diverse meshworks and bundles that support many aspects of cell physiology. Understanding the self-assembly of these actin-based structures is essential for developing predictive models of cytoskeletal organization. Here we show that the competing kinetics of bundle formation with the onset of dynamic arrest arising from filament entanglements and crosslinking determine the architecture of reconstituted actin networks formed with α-actinin crosslinks. Crosslink-mediated bundle formation only occurs in dilute solutions of highly mobile actin filaments. As actin polymerization proceeds, filament mobility and bundle formation are arrested concomitantly. By controlling the onset of dynamic arrest, perturbations to actin assembly kinetics dramatically alter the architecture of biochemically identical samples. Thus, the morphology of reconstituted F-actin networks is a kinetically determined structure similar to those formed by physical gels and glasses. These results establish mechanisms controlling the structure and mechanics in diverse semiflexible biopolymer networks.

The Proposal of a Evolutionary Strategy Generating the Data Structures Based on a Horizontal Tree for the Tests

NASA Astrophysics Data System (ADS)

Żukowicz, Marek; Markiewicz, Michał

2016-09-01

The aim of the article is to present a mathematical definition of the object model, that is known in computer science as TreeList and to show application of this model for design evolutionary algorithm, that purpose is to generate structures based on this object. The first chapter introduces the reader to the problem of presenting data using the TreeList object. The second chapter describes the problem of testing data structures based on TreeList. The third one shows a mathematical model of the object TreeList and the parameters, used in determining the utility of structures created through this model and in evolutionary strategy, that generates these structures for testing purposes. The last chapter provides a brief summary and plans for future research related to the algorithm presented in the article.

Application of the Spectral Element Method to Acoustic Radiation

NASA Technical Reports Server (NTRS)

Doyle, James F.; Rizzi, Stephen A. (Technical Monitor)

2000-01-01

This report summarizes research to develop a capability for analysis of interior noise in enclosed structures when acoustically excited by an external random source. Of particular interest was the application to the study of noise and vibration transmission in thin-walled structures as typified by aircraft fuselages. Three related topics are focused upon. The first concerns the development of a curved frame spectral element, the second shows how the spectral element method for wave propagation in folded plate structures is extended to problems involving curved segmented plates. These are of significance because by combining these curved spectral elements with previously presented flat spectral elements, the dynamic response of geometrically complex structures can be determined. The third topic shows how spectral elements, which incorporate the effect of fluid loading on the structure, are developed for analyzing acoustic radiation from dynamically loaded extended plates.

The Structure of Ethylbenzene, Styrene and Phenylacetylene Determined by Total Neutron Scattering

PubMed Central

Szala‐Bilnik, Joanna; Falkowska, Marta; Bowron, Daniel T.

2017-01-01

Abstract Organic solvents such as phenylacetylene, styrene and ethylbenzene are widely used in industrial processes, especially in the production of rubber or thermoplastics. Despite their important applications detailed knowledge about their structure is limited. In this paper the structures of these three aromatic solvents were investigated using neutron diffraction. The results show that many of their structural characteristics are similar, although the structure of phenylacetylene is more ordered and has a smaller solvation sphere than either ethylbenzene or styrene. Two regions within the first coordination sphere, in which the surrounding molecules show different preferable orientations with respect to the central molecule, were found for each liquid. Additionally, the localisation of the aliphatic chains reveals that they tend to favour closer interactions with each other than to the aromatic rings of the adjacent molecules. PMID:28672104

[Study on structure and phase transformation laws of natural FeS2 whisker by Raman spectroscopy].

PubMed

Huang, Fei; Kou, Da-Ming; Yao, Yu-Zeng; Ni, Pei; Ding, Jun-Ying

2009-08-01

FeS2 belongs to sulfide, including pyrite of isometric system and marcasite of orthorhombic system. The FeS2 discovered in Gengzhuang, Shanxi Province, was growing in the form of whisker. The study with scanning electron microscopy and electron probe show that the mineral components of FeS2 vary regularly. The structure of natural nano-micron FeS2 whisker was determined by micro-Raman spectroscopy. The results show that there exist two types of structure in FeS2 whiskers: pyrite and marcasite. Marcasite presents irregular shapes, such as coarse lotus root joints, crude columnar or beaded. Pyrite exists in the shape of straight line and smooth surface. In the early growing stage, Gengzhuang FeS2 whisker was mainly marcasite-type structure; in the middle stage it was coexistent structure of pyrite- and marcasite-type; in the late stage it was mainly pyrite-type. The growing stages of the whisker FeS2 show the phase transformation laws. Moreover, during the growing process marcasite was growing with pyrite coated on. Study on FeS2 whisker structure shows that there are correlations between phase transformation laws of the structure and forms, and between the forming time and the composition characteristics.

Purely Structural Protein Scoring Functions Using Support Vector Machine and Ensemble Learning.

PubMed

Mirzaei, Shokoufeh; Sidi, Tomer; Keasar, Chen; Crivelli, Silvia

2016-08-24

The function of a protein is determined by its structure, which creates a need for efficient methods of protein structure determination to advance scientific and medical research. Because current experimental structure determination methods carry a high price tag, computational predictions are highly desirable. Given a protein sequence, computational methods produce numerous 3D structures known as decoys. However, selection of the best quality decoys is challenging as the end users can handle only a few ones. Therefore, scoring functions are central to decoy selection. They combine measurable features into a single number indicator of decoy quality. Unfortunately, current scoring functions do not consistently select the best decoys. Machine learning techniques offer great potential to improve decoy scoring. This paper presents two machine-learning based scoring functions to predict the quality of proteins structures, i.e., the similarity between the predicted structure and the experimental one without knowing the latter. We use different metrics to compare these scoring functions against three state-of-the-art scores. This is a first attempt at comparing different scoring functions using the same non-redundant dataset for training and testing and the same features. The results show that adding informative features may be more significant than the method used.

Structure of the toxic core of α-synuclein from invisible crystals

DOE PAGES

Rodriguez, Jose A.; Ivanova, Magdalena I.; Sawaya, Michael R.; ...

2015-09-09

We report that the protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 Å resolution structure demonstrates thatmore » this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face β-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length α-synuclein. Finally, the NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils.« less

Modulus and yield stress of drawn LDPE

NASA Astrophysics Data System (ADS)

Thavarungkul, Nandh

Modulus and yield stress were investigated in drawn low density polyethylene (LDPE) film. Uniaxially drawn polymeric films usually show high values of modulus and yield stress, however, studies have normally only been conducted to identify the structural features that determine modulus. In this study small-angle x-ray scattering (SAXS), thermal shrinkage, birefringence, differential scanning calorimetry (DSC), and dynamic mechanical thermal analysis (DMTA) were used to examine, directly and indirectly, the structural features that determine both modulus and yield stress, which are often closely related in undrawn materials. Shish-kebab structures are proposed to account for the mechanical properties in drawn LDPE. The validity of this molecular/morphological model was tested using relationships between static mechanical data and structural and physical parameters. In addition, dynamic mechanical results are also in line with static data in supporting the model. In the machine direction (MD), "shish" and taut tie molecules (TTM) anchored in the crystalline phase account for E; whereas crystal lamellae with contributions from "shish" and TTM determine yield stress. In the transverse direction (TD), the crystalline phase plays an important roll in both modulus and yield stress. Modulus is determined by crystal lamellae functioning as platelet reinforcing elements in the amorphous matrix with an additional contributions from TTM and yield stress is determined by the crystal lamellae's resistance to deformation.

Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

PubMed Central

Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio; Collazo, Michael J.; Shi, Dan; Reyes, Francis E.; Gonen, Tamir; Eisenberg, David S.

2016-01-01

Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods. PMID:27647903

HRTEM and neutron diffraction study of Li{sub x}Mo{sub 5}O{sub 17}: From the ribbon (x=5) structure to the rock salt (x=12) structure

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

Lebedev, O.I.; Caignaert, V.; Raveau, B.

2011-04-15

Structure determination of the fully intercalated phase Li{sub 12}Mo{sub 5}O{sub 17} and of the deintercalated oxide Li{sub 5}Mo{sub 5}O{sub 17} has been carried out by electron microscopy and neutron powder diffraction. The reversible topotactic transformation between the ordered rock salt structure of the former and the ribbon structure of the latter (closely related to that of Li{sub 4}Mo{sub 5}O{sub 17}) is explained on the following basis: both structures can be described as strips built up as an assembly of infinite ribbons of MoO{sub 6} octahedra that are five octahedra thick, and that differ by slight displacements of the octahedral ribbons.more » We show that the electrochemical behavior of the Li{sub x}Mo{sub 5}O{sub 17} system is based on two sorts of Li{sup +} sites; those that are located within the strips between the ribbons, and those that are located at the border of the strips. The high rate of Li intercalation in this oxide and its reversibility are discussed in terms of its peculiar structure. -- Graphical abstract: Structure determination of the fully intercalated phase Li{sub 12}Mo{sub 5}O{sub 17} and of the deintercalated oxide Li{sub 5}Mo{sub 5}O{sub 17} has been carried out by electron microscopy and neutron powder diffraction. The reversible topotactic transformation between the ordered rock salt structure of the former and the ribbon structure of the latter is explained on the following basis: both structures can be described as strips built up as an assembly of infinite ribbons of MoO{sub 6} octahedra that are five octahedra thick, and that differ by slight displacements of the octahedral ribbons. We show that the electrochemical behavior of the Li{sub x}Mo{sub 5}O{sub 17} system is based on two sorts of Li{sup +} sites; those that are located within the strips between the ribbons, and those that are located at the border of the strips. The high rate of Li intercalation in this oxide and its reversibility are discussed in terms of its peculiar structure. Research highlights: {yields} Electron microscopy and neutron powder diffraction structure determination {yields} We have explained the reversible topotactic transformation between an ordered rock salt structure and a ribbon structure {yields} We show that the electrochemical behavior of the Li{sub x}Mo{sub 5}O{sub 17} system is based on two sorts of Li{sup +} sites {yields} The high rate of Li intercalation in this oxide and its reversibility are discussed in terms of its peculiar structure.« less

Interfacial electronic structure and full spectral Hamaker constants of Si{sub 3}N{sub 4} intergranular films from VUV and SR-VEEL spectroscopy

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

French, R.H.; Scheu, C.; Duscher, G.

1995-09-01

The interfacial electronic structure, presented as the interband transition strength J{sub cv}({omega}) of the interatomic bonds, can be determined by Kramers Kronig (KK) analysis of vacuum ultraviolet (VUV) reflectance or spatially resolved valence electron energy loss (SR-VEEL) spectra. For the wetted interfaces in Si{sub 3}N{sub 4}, equilibrium thin glass films are formed whose thickness is determined by a force balance between attractive and repulsive force terms KK analysis of J{sub cv}({omega}) to yield {var_epsilon}{sub 2}({xi}) for the phases present, permits the direct calculation of the configuration-dependent Hamaker constants for the attractive vdW forces from the interfacial electronic structure. Interband transitionmore » strengths and full spectral Hamaker constants for Si{sub 3}N{sub 4}samples containing a SiYAlON glass have been determined using SR-VEELS from grains and grain boundaries and compared with results from bulk VUV spectroscopy on separate samples of glass and nitride. The A{sub 121}Hamaker constant for Si{sub 3}N{sub 4} with glass of the bulk composition is 8 zJ (zJ = 10{sup {minus}21}J) from the more established optical method. The EELS method permits the determination of vdW forces based upon actual local compositions and structure, which may differ noticeably from bulk standards. Current results show that full spectral Hamaker constants determined from VUV and SR-VEEL measurements of uniform bulk samples agree, but care must be take in the single scattering and zero loss subtraction corrections, and more work is ongoing in this area. Still the results show that for the grain boundary films present in these polycrystalline Si{sub 3}N{sub 4} samples the glass composition is of lower index of refraction. This can arise from increased oxygen content in determined in situ from the SR-VEELS of a particular grain boundary film. 45 refs.« less

Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry.

PubMed

Shi, Xuesong; Walker, Peter; Harbury, Pehr B; Herschlag, Daniel

2017-05-05

The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures. We show that the XSI-based model of the TAR RNA ensemble closely resembles an independent model derived from NMR-RDC data. Further, we show how the TAR RNA ensemble changes shape at different salt concentrations. Finally, we demonstrate that a single hybrid model of the TAR RNA ensemble simultaneously fits both the XSI and NMR-RDC data set and show that XSI can be combined with NMR-RDC to further improve the quality of the determined ensemble. The results suggest that XSI-RNA will be a powerful approach for characterizing the solution conformational ensembles of RNAs and RNA-protein complexes under diverse solution conditions. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Three-Dimensional Molecular Modeling of a Diverse Range of SC Clan Serine Proteases

PubMed Central

Laskar, Aparna; Chatterjee, Aniruddha; Chatterjee, Somnath; Rodger, Euan J.

2012-01-01

Serine proteases are involved in a variety of biological processes and are classified into clans sharing structural homology. Although various three-dimensional structures of SC clan proteases have been experimentally determined, they are mostly bacterial and animal proteases, with some from archaea, plants, and fungi, and as yet no structures have been determined for protozoa. To bridge this gap, we have used molecular modeling techniques to investigate the structural properties of different SC clan serine proteases from a diverse range of taxa. Either SWISS-MODEL was used for homology-based structure prediction or the LOOPP server was used for threading-based structure prediction. The predicted models were refined using Insight II and SCRWL and validated against experimental structures. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. The structural geometry of the catalytic core shows clear deviations between taxa, but the relative positions of the catalytic triad residues were conserved. Evolutionary divergence was also exhibited by large variation in secondary structure features outside the core, differences in overall amino acid distribution, and unique surface electrostatic potential patterns between species. Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on SC clan serine proteases. PMID:23213528

Structural Determination of Functional Domains in Early B-cell Factor (EBF) Family of Transcription Factors Reveals Similarities to Rel DNA-binding Proteins and a Novel Dimerization Motif*

PubMed Central

Siponen, Marina I.; Wisniewska, Magdalena; Lehtiö, Lari; Johansson, Ida; Svensson, Linda; Raszewski, Grzegorz; Nilsson, Lennart; Sigvardsson, Mikael; Berglund, Helena

2010-01-01

The early B-cell factor (EBF) transcription factors are central regulators of development in several organs and tissues. This protein family shows low sequence similarity to other protein families, which is why structural information for the functional domains of these proteins is crucial to understand their biochemical features. We have used a modular approach to determine the crystal structures of the structured domains in the EBF family. The DNA binding domain reveals a striking resemblance to the DNA binding domains of the Rel homology superfamily of transcription factors but contains a unique zinc binding structure, termed zinc knuckle. Further the EBF proteins contain an IPT/TIG domain and an atypical helix-loop-helix domain with a novel type of dimerization motif. The data presented here provide insights into unique structural features of the EBF proteins and open possibilities for detailed molecular investigations of this important transcription factor family. PMID:20592035

Structural building principles of complex face-centered cubic intermetallics.

PubMed

Dshemuchadse, Julia; Jung, Daniel Y; Steurer, Walter

2011-08-01

Fundamental structural building principles are discussed for all 56 known intermetallic phases with approximately 400 or more atoms per unit cell and space-group symmetry F43m, Fd3m, Fd3, Fm3m or Fm3c. Despite fundamental differences in chemical composition, bonding and electronic band structure, their complex crystal structures show striking similarities indicating common building principles. We demonstrate that the structure-determining elements are flat and puckered atomic {110} layers stacked with periodicities 2p. The atoms on this set of layers, which intersect each other, form pentagon face-sharing endohedral fullerene-like clusters arranged in a face-centered cubic packing (f.c.c.). Due to their topological layer structure, all these crystal structures can be described as (p × p × p) = p(3)-fold superstructures of a common basic structure of the double-diamond type. The parameter p, with p = 3, 4, 7 or 11, is determined by the number of layers per repeat unit and the type of cluster packing, which in turn are controlled by chemical composition.

Quantitative Restoration of the Evolution of Mantle Structures Using Data Assimilation

NASA Astrophysics Data System (ADS)

Ismail-Zadeh, A.; Schubert, G.; Tsepelev, I.

2008-12-01

Rapid progress in imaging deep Earth structures and in studies of physical and chemical properties of mantle rocks facilitates research in assimilation of data related to mantle dynamics. We present a quantitative approach to assimilation of geophysical and geodetic data, which allows for incorporating observations and unknown initial conditions for mantle temperature and flow into a three-dimensional dynamic model in order to determine the initial conditions in the geological past. Once the conditions are determined the evolution of mantle structures can be restore backward in time. We apply data assimilation techniques to model the evolution of mantle plumes and lithospheric slabs. We show that the geometry of the mantle structures changes with time diminishing the degree of surface curvature of the structures, because the heat conduction smoothes the complex thermal surfaces of mantle bodies with time. Present seismic tomography images of mantle structures do not allow definition of the sharp shapes of these structures. Assimilation of mantle temperature and flow to the geological past instead provides a quantitative tool to restore thermal shapes of prominent structures in the past from their diffusive shapes at present.

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

Hill, Chris H.; Read, Randy J.; Deane, Janet E., E-mail: jed55@cam.ac.uk

A 1.8 Å resolution structure of the sphingolipid activator protein saposin A has been determined at pH 4.8, the physiologically relevant lysosomal pH for hydrolase enzyme activation and lipid-transfer activity. The saposins are essential cofactors for the normal lysosomal degradation of complex glycosphingolipids by acid hydrolase enzymes; defects in either saposin or hydrolase function lead to severe metabolic diseases. Saposin A (SapA) activates the enzyme β-galactocerebrosidase (GALC), which catalyzes the breakdown of β-d-galactocerebroside, the principal lipid component of myelin. SapA is known to bind lipids and detergents in a pH-dependent manner; this is accompanied by a striking transition from amore » ‘closed’ to an ‘open’ conformation. However, previous structures were determined at non-lysosomal pH. This work describes a 1.8 Å resolution X-ray crystal structure determined at the physiologically relevant lysosomal pH 4.8. In the absence of lipid or detergent at pH 4.8, SapA is observeed to adopt a conformation closely resembling the previously determined ‘closed’ conformation, showing that pH alone is not sufficient for the transition to the ‘open’ conformation. Structural alignments reveal small conformational changes, highlighting regions of flexibility.« less

Euphorbesulins A-P, Structurally Diverse Diterpenoids from Euphorbia esula.

PubMed

Zhou, Bin; Wu, Yan; Dalal, Seema; Cassera, Maria B; Yue, Jian-Min

2016-08-26

Aqueous ethanol extracts of powdered twigs of Euphorbia esula afforded 16 new diterpenoids, named euphorbesulins A-P. These euphorbesulins included presegetane (1-3), jatrophane (4-14), paraliane (15), and isopimarane (16) diterpenoids as well as six known analogues. Compounds 1-3 represent a rare type of presegetane diterpenoid. Their structures were determined by analysis of the spectroscopic data, and the absolute configuration of 1 was established by X-ray crystallography. Diterpenoid 7 showed low nanomolar antimalarial activity, while the remaining compounds showed only moderate or no antimalarial activity.

Structural and Biophysical Characterization of Cajanus cajan Protease Inhibitor

PubMed Central

Shamsi, Tooba Naz; Parveen, Romana; Ahamad, Shahzaib; Fatima, Sadaf

2017-01-01

Context: A large number of studies have proven that Protease inhibitors (PIs), specifically serine protease inhibitors, show immense divergence in regulation of proteolysis by targeting their specific proteases and hence, they play a key role in healthcare. Objective: We aimed to access in-vitro anticancer potential of PI from Cajanus cajan (CCPI). Also, crystallization of CCPI was targetted alongwith structure determination and its structure-function relationship. Materials and Methods: CCPI was purified from Cajanus cajan seeds by chromatographic techniques. The purity and molecular mass was determined by SDS-PAGE. Anticancer potential of CCPI was determined by MTT assay in normal HEK and cancerous A549 cells. The crystallization screening of CCPI was performed by commercially available screens. CCPI sequence was subject to BLASTp with homologous PIs. Progressive multiple alignment was performed using clustalw2 and was modelled using ab initio protocol of I-TASSER. Results: The results showed ~14kDa CCPI was purified in homogeneity. Also, CCPI showed low cytotoxic effects of in HEK i.e., 27% as compared with 51% cytotoxicity in A549 cells. CCPI crystallized at 16°C using 15% PEG 6000 in 0.1M potassium phosphate buffer (pH 6.0) in 2-3weeks as rod or needles visualized as clusters under the microscope. The molecular modelling revealed that it contains 3 beta sheets, 3 beta hairpins, 2 β-bulges, 6 strands, 3 helices, 1helix-helix interaction, 41 β-turns and 27 γ-turns. Discussion and Conclusion: The results indicate that CCPI may help to treat cancer in vivo aswell. Also, this is the first report on preliminary crystallization and structural studies of CCPI. PMID:28781485

A Logical OR Redundancy within the Asx-Pro-Asx-Gly Type 1 {Beta}-Turn Motif

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

Lee, Jihun; Dubey, Vikash Kumar; Longo, Lian M.

2008-04-19

Turn secondary structure is essential to the formation of globular protein architecture. Turn structures are, however, much more complex than either {alpha}-helix or {beta}-sheet, and the thermodynamics and folding kinetics are poorly understood. Type I {beta}-turns are the most common type of reverse turn, and they exhibit a statistical consensus sequence of Asx-Pro-Asx-Gly (where Asx is Asp or Asn). A comprehensive series of individual and combined Asx mutations has been constructed within three separate type I 3:5 G1 bulge {beta}-turns in human fibroblast growth factor-1, and their effects on structure, stability, and folding have been determined. The results show amore » fundamental logical OR relationship between the Asx residues in the motif, involving H-bond interactions with main-chain amides within the turn. These interactions can be modulated by additional interactions with residues adjacent to the turn at positions i + 4 and i + 6. The results show that the Asx residues in the turn motif make a substantial contribution to the overall stability of the protein, and the Asx logical OR relationship defines a redundant system that can compensate for deleterious point mutations. The results also show that the stability of the turn is unlikely to be the prime determinant of formation of turn structure in the folding transition state.« less

Oligomeric domain structure of human complement factor H by X-ray and neutron solution scattering

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

Perkins, S.J.; Nealis, A.S.; Sim, R.B.

1991-03-19

Factor H is a regulatory component of the complement system. It has a monomer M{sub r} of 150,000. Primary structure analysis shows that the polypeptide is divided into 20 homologous regions, each 60 amino acid residues long. These are independently folding domains and are termed short consensus repeats (SCRs) or complement control protein (CCP) repeats. High-flux synchrotron x-ray and neutron scatteriing studies were performed in order to define its solution structure in conditions close to physiological. The M{sub r} of factor H was determined as 250,000-320,000 to show that factor H is dimeric. The radius of gyration R{sub G} ofmore » native factor H by X-rays or by neutrons in 0% or 100% {sup 2}H{sub 2}O buffers is not measurable but is greater than 12.5 nm. Two cross-sectional radii of gyration R{sub XS-1} and R{sub XS-2} were determined as 3.0-3.1 and 1.8 nm, respectively. Analyses of the cross-sectional intensities show that factor H is composed of two distinct subunits. This model corresponds to an actual R{sub G} fo 21-23 nm. The separation between each SCR/CCP in factor H is close to 4 nm. In the solution structure of factor H, the SCR/CCP domains are in a highly extended conformation.« less

Correlation Function Analysis of Fiber Networks: Implications for Thermal Conductivity

NASA Technical Reports Server (NTRS)

Martinez-Garcia, Jorge; Braginsky, Leonid; Shklover, Valery; Lawson, John W.

2011-01-01

The heat transport in highly porous fiber structures is investigated. The fibers are supposed to be thin, but long, so that the number of the inter-fiber connections along each fiber is large. We show that the effective conductivity of such structures can be found from the correlation length of the two-point correlation function of the local conductivities. Estimation of the parameters, determining the conductivity, from the 2D images of the structures is analyzed.

Electronic structure of gadolinium complexes in ZnO in the GW approximation

NASA Astrophysics Data System (ADS)

Rosa, A. L.; Frauenheim, Th.

2018-04-01

The role of intrinsic defects has been investigated to determine binding energies and the electronic structure of Gd complexes in ZnO. We use density-functional theory and the GW method to show that the presence of vacancies and interstitials affect the electronic structure of Gd doped ZnO. However, the strong localization of the Gd-f and d states suggest that carrier mediated ferromagnetism in this material may be difficult to achieve.

Macromolecular structure of coals. 6. Mass spectroscopic analysis of coal-derived liquids

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

Hooker, D.T.; Lucht, L.M.; Peppas, N.A.

1986-02-01

The macromolecular structure of coal networks was analyzed by depolymerizing coal samples using the Sternberg reductive alkylation and the Miyake alkylation techniques. Electron impact mass spectra showed peaks of greater abundance of 125-132, 252-260, 383-391, and 511-520 m/z ratios. Based on analysis of the patterns of the spectra, the cluster size of the cross-linked structure of bituminous coals was determined as 126-130. Various chemical species were identified.

Parameter and Structure Inference for Nonlinear Dynamical Systems

NASA Technical Reports Server (NTRS)

Morris, Robin D.; Smelyanskiy, Vadim N.; Millonas, Mark

2006-01-01

A great many systems can be modeled in the non-linear dynamical systems framework, as x = f(x) + xi(t), where f() is the potential function for the system, and xi is the excitation noise. Modeling the potential using a set of basis functions, we derive the posterior for the basis coefficients. A more challenging problem is to determine the set of basis functions that are required to model a particular system. We show that using the Bayesian Information Criteria (BIC) to rank models, and the beam search technique, that we can accurately determine the structure of simple non-linear dynamical system models, and the structure of the coupling between non-linear dynamical systems where the individual systems are known. This last case has important ecological applications.

Analytical monitoring of soil bioengineering structures in the Tuscan Emilian Apennines of Italy

NASA Astrophysics Data System (ADS)

Selli, Lavinia; Guastini, Enrico

2014-05-01

Soil bioengineering has been an appropriate solution to deal with erosion problems and shallow landslides in the North Apennines, Italy. The objective of our research was a check about critical aspects of soil bioengineering works. We monitored the works that have been carried out in the Tuscan Emilian Apennines by testing the suitability of different plant species and analyzed in detail timber structures of wooden crib walls. Plant species were mainly Salix alba and Salix purpurea that gave good sprouting and survival rates. However, showed some issues in growing on dry and sunny Apennine lands, where other shrubs like Spanish Broom, blackthorn, cornel-tree and Eglantine would be more indicated. The localized analysis on wooden elements has been led gathering parts from the poles and obtaining samples in order to determine their density. The hypothetical initial density of the wood used in the structure has been estimated, then calculating the residual density. This analysis allows us to determine the general condition of the wood, highlighting the structures in worst condition (the one in Pianaccio show a residual density close to 70%, instead of 90% as found on other structures) and those whose degraded wood has undergone the greatest damage (Pianaccio here too, with 50%, followed by Campoferrario - 60% - and by Pian di Favale with 85%, a rather good value for the most degraded wood in the structure).

Graphical determination of wall temperatures for heat transfers through walls of arbitrary shape

NASA Technical Reports Server (NTRS)

Lutz, Otto

1950-01-01

A graphical method is given which permits determining of the temperature distribution during heat transfer in arbitrarily shaped walls. Three examples show the application of the method. The further development of heat engines depends to a great extent on the control of the thermal stresses in the walls. The thermal stresses stem from the nonuniform temperature distribution in heat transfer through walls which are, for structural reasons, of various thicknesses and sometimes complicated shape. Thus, it is important to know the temperature distribution in these structural parts. Following, a method is given which permits solution of this problem.

Spatial localization of the Ebola virus glycoprotein mucin-like domain determined by cryo-electron tomography.

PubMed

Tran, Erin E H; Simmons, James A; Bartesaghi, Alberto; Shoemaker, Charles J; Nelson, Elizabeth; White, Judith M; Subramaniam, Sriram

2014-09-01

The Ebola virus glycoprotein mucin-like domain (MLD) is implicated in Ebola virus cell entry and immune evasion. Using cryo-electron tomography of Ebola virus-like particles, we determined a three-dimensional structure for the full-length glycoprotein in a near-native state and compared it to that of a glycoprotein lacking the MLD. Our results, which show that the MLD is located at the apex and the sides of each glycoprotein monomer, provide a structural template for analysis of MLD function. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Structural studies of 4-aminoantipyrine derivatives

NASA Astrophysics Data System (ADS)

Cunha, Silvio; Oliveira, Shana M.; Rodrigues, Manoel T.; Bastos, Rodrigo M.; Ferrari, Jailton; de Oliveira, Cecília M. A.; Kato, Lucília; Napolitano, Hamilton B.; Vencato, Ivo; Lariucci, Carlito

2005-10-01

Reaction of 4-aminoantipyrine with acetylacetone, ethyl acetoacetate, benzoyl isothiocyanate, phenyl isothiocyanate, maleic anhydride and methoxymethylene Meldrum's acid afforded a series of new antipyrine derivatives. The antibacterial activity of the synthesized compounds against Micrococcus luteus ATCC 9341, Staphilococcus aureus ATCC 29737, and Escherichia coli ATCC 8739 was evaluated and the minimal inhibitory concentration determined. Modest activity was found only to the maleamic acid obtained from the reaction of 4-aminoantipyrine and maleic anhydride. 1H NMR investigation of this maleamic acid showed that it is slowly converted to the corresponding toxic maleimide. The structures of three derivatives were determined by X-ray diffraction analysis.

Crystal structure of [Eu(CyMe4-BTBP)2κ2O,O'-(NO3)](NO3)2·n-C8H17OH and its structure in 1-octanol solution.

PubMed

Lundberg, Daniel; Persson, Ingmar; Ekberg, Christian

2013-03-21

The structure of the [Eu(CyMe(4)-BTBP)(2)(NO(3))(n)]((3-n)+) complex in 1-octanol solution and solid state has been determined by EXAFS and X-ray crystallography. The crystal structure shows that 1-octanol binds only to the europium(III)-coordinated BTBP molecules through weak van der Waals forces, making it the first indication of the role of the extraction solvent.

Inside Titan Author Concept

NASA Image and Video Library

2012-06-28

This artist concept shows a possible scenario for the internal structure of Titan, as suggested by data from NASA Cassini spacecraft. Scientists have been trying to determine what is under Titan organic-rich atmosphere and icy crust.

Strain-engineering of Janus SiC monolayer functionalized with H and F atoms

NASA Astrophysics Data System (ADS)

Drissi, L. B.; Sadki, K.; Kourra, M.-H.; Bousmina, M.

2018-05-01

Based on ab initio density functional theory calculations, the structural, electronic, mechanical, acoustic, thermodynamic, and piezoelectric properties of (F,H) Janus SiC monolayers are studied. The new set of derivatives shows buckled structures and different band gap values. Under strain, the buckling changes and the structures pass from semiconducting to metallic. The elastic limits and the metastable regions are determined. The Young's modulus and Poisson ratio reveal stronger behavior for the modified conformers with respect to graphene. The values of the Debye temperature make the new materials suitable for thermal application. Moreover, all the conformers show in-plane and out-of-plane piezoelectric responses comparable with known two-dimensional materials. If engineered, such piezoelectric Janus structures may be promising materials for various nanoelectromechanical applications.

Influence of amorphous structure on polymorphism in vanadia

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

Stone, Kevin H.; Schelhas, Laura T.; Garten, Lauren M.

Normally we think of the glassy state as a single phase and therefore crystallization from chemically identical amorphous precursors should be identical. Here we show that the local structure of an amorphous precursor is distinct depending on the initial deposition conditions, resulting in significant differences in the final state material. Using grazing incidence total x-ray scattering, we have determined the local structure in amorphous thin films of vanadium oxide grown under different conditions using pulsed laser deposition (PLD). Here we show that the subsequent crystallization of films deposited using different initial PLD conditions result in the formation of different polymorphsmore » of VO 2. Ultimately this suggests the possibility of controlling the formation of metastable polymorphs by tuning the initial amorphous structure to different formation pathways.« less

Influence of amorphous structure on polymorphism in vanadia

DOE PAGES

Stone, Kevin H.; Schelhas, Laura T.; Garten, Lauren M.; ...

2016-07-13

Normally we think of the glassy state as a single phase and therefore crystallization from chemically identical amorphous precursors should be identical. Here we show that the local structure of an amorphous precursor is distinct depending on the initial deposition conditions, resulting in significant differences in the final state material. Using grazing incidence total x-ray scattering, we have determined the local structure in amorphous thin films of vanadium oxide grown under different conditions using pulsed laser deposition (PLD). Here we show that the subsequent crystallization of films deposited using different initial PLD conditions result in the formation of different polymorphsmore » of VO 2. Ultimately this suggests the possibility of controlling the formation of metastable polymorphs by tuning the initial amorphous structure to different formation pathways.« less

Disease spread in age structured populations with maternal age effects.

PubMed

Clark, Jessica; Garbutt, Jennie S; McNally, Luke; Little, Tom J

2017-04-01

Fundamental ecological processes, such as extrinsic mortality, determine population age structure. This influences disease spread when individuals of different ages differ in susceptibility or when maternal age determines offspring susceptibility. We show that Daphnia magna offspring born to young mothers are more susceptible than those born to older mothers, and consider this alongside previous observations that susceptibility declines with age in this system. We used a susceptible-infected compartmental model to investigate how age-specific susceptibility and maternal age effects on offspring susceptibility interact with demographic factors affecting disease spread. Our results show a scenario where an increase in extrinsic mortality drives an increase in transmission potential. Thus, we identify a realistic context in which age effects and maternal effects produce conditions favouring disease transmission. © 2017 The Authors Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space.

PubMed

Ahnert, S E; Fink, T M A

2016-07-01

Network motifs have been studied extensively over the past decade, and certain motifs, such as the feed-forward loop, play an important role in regulatory networks. Recent studies have used Boolean network motifs to explore the link between form and function in gene regulatory networks and have found that the structure of a motif does not strongly determine its function, if this is defined in terms of the gene expression patterns the motif can produce. Here, we offer a different, higher-level definition of the 'function' of a motif, in terms of two fundamental properties of its dynamical state space as a Boolean network. One is the basin entropy, which is a complexity measure of the dynamics of Boolean networks. The other is the diversity of cyclic attractor lengths that a given motif can produce. Using these two measures, we examine all 104 topologically distinct three-node motifs and show that the structural properties of a motif, such as the presence of feedback loops and feed-forward loops, predict fundamental characteristics of its dynamical state space, which in turn determine aspects of its functional versatility. We also show that these higher-level properties have a direct bearing on real regulatory networks, as both basin entropy and cycle length diversity show a close correspondence with the prevalence, in neural and genetic regulatory networks, of the 13 connected motifs without self-interactions that have been studied extensively in the literature. © 2016 The Authors.

Insights into Head-Tailed Viruses Infecting Extremely Halophilic Archaea

PubMed Central

Pietilä, Maija K.; Laurinmäki, Pasi; Russell, Daniel A.; Ko, Ching-Chung; Jacobs-Sera, Deborah; Butcher, Sarah J.

2013-01-01

Extremophilic archaea, both hyperthermophiles and halophiles, dominate in habitats where rather harsh conditions are encountered. Like all other organisms, archaeal cells are susceptible to viral infections, and to date, about 100 archaeal viruses have been described. Among them, there are extraordinary virion morphologies as well as the common head-tailed viruses. Although approximately half of the isolated archaeal viruses belong to the latter group, no three-dimensional virion structures of these head-tailed viruses are available. Thus, rigorous comparisons with bacteriophages are not yet warranted. In the present study, we determined the genome sequences of two of such viruses of halophiles and solved their capsid structures by cryo-electron microscopy and three-dimensional image reconstruction. We show that these viruses are inactivated, yet remain intact, at low salinity and that their infectivity is regained when high salinity is restored. This enabled us to determine their three-dimensional capsid structures at low salinity to a ∼10-Å resolution. The genetic and structural data showed that both viruses belong to the same T-number class, but one of them has enlarged its capsid to accommodate a larger genome than typically associated with a T=7 capsid by inserting an additional protein into the capsid lattice. PMID:23283946

Antigenic Determinants of Alpha-Like Proteins of Streptococcus agalactiae

PubMed Central

Maeland, Johan A.; Bevanger, Lars; Lyng, Randi Valsoe

2004-01-01

The majority of group B streptococcus (GBS) isolates express one or more of a family of surface-anchored proteins that vary by strain and that form ladder-like patterns on Western blotting due to large repeat units. These proteins, which are important as GBS serotype markers and as inducers of protective antibodies, include the alpha C (Cα) and R4 proteins and the recently described alpha-like protein 2 (Alp2), encoded by alp2, and Alp3, encoded by alp3. In this study, we examined antigenic determinants possessed by Alp2 and Alp3 by testing of antibodies raised in rabbits, mainly by using enzyme-linked immunosorbent assays (ELISA) and an ELISA absorption test. The results showed that Alp2 and Alp3 shared an antigenic determinant, which may be a unique immunological marker of the Alp variants of GBS proteins. Alp2, in addition, possessed an antigenic determinant which showed specificity for Alp2 and a third determinant which showed serological cross-reactivity with Cα. Alp3, in addition to the determinant common to Alp2 and Alp3, harbored an antigenic site which also was present in the R4 protein, whereas no Alp3-specific antigenic site was detected. These ELISA-based results were confirmed by Western blotting and a fluorescent-antibody test. The results are consistent with highly complex antigenic structures of the alpha-like proteins in a fashion which is in agreement with the recently described structural mosaicism of the alp2 and alp3 genes. The results are expected to influence GBS serotyping, immunoprotection studies, and GBS vaccine developments. PMID:15539502

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

PubMed

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

2013-04-01

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

Efficient Tuning of Optical Properties and Morphology of Mesoscopic CdS via a Facile Route

NASA Astrophysics Data System (ADS)

Aslam, Samia; Mustafa, Faiza; Jamil, Ayesha; Abbas, Ghazanfar; Raza, Rizwan; Ahmad, Muhammad Ashfaq

2018-03-01

A facile and simple synthetic route has been employed to synthesize rod-shaped optically efficient cadmium sulfide (CdS) mesoscopic structures using high concentrations of cetyl trimethyl ammonium bromide (CTAB) as the stabilizing agent. The mesoscopic structures were characterized using x-ray diffaractometer (XRD), scanning electron microscopy, UV-visible, photoluminescence (PL), and Fourier transform and infrared (FTIR) spectroscopy. It was found that, if the concentration of CTAB is significantly higher than its critical micelle concentration, the nucleation of CdS mesoscopic structures resulted in rod-like structures. The size of the mesoscopic structures initially increased and then decreased with band gaps 2.5-2.7 eV. XRD analysis showed that the samples had a pure cubic phase confirming the particle size. The values of Urbach energy for the absorption tail states were determined and found to be in agreement with the single crystal. PL spectra showed sharp green emission peaks in the 530-nm to 560-nm wavelength range. FTIR spectra showed the adsorption mode of CTAB onto the CdS mesoscopic structures. A possible mechanism of formation of rod-shaped CdS mesoscopic structures is also elucidated.

Mycobacterium tuberculosis acyl carrier protein synthase adopts two different pH-dependent structural conformations

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

Gokulan, Kuppan; Aggarwal, Anup; Shipman, Lance

2011-07-01

Bacterial acyl carrier protein synthase plays an essential role in the synthesis of fatty acids, nonribosomal peptides and polyketides. In Mycobacterium tuberculosis, AcpS or group I phosphopentatheine transferase exhibits two different structural conformations depending upon the pH. The crystal structures of acyl carrier protein synthase (AcpS) from Mycobacterium tuberculosis (Mtb) and Corynebacterium ammoniagenes determined at pH 5.3 and pH 6.5, respectively, are reported. Comparison of the Mtb apo-AcpS structure with the recently reported structure of the Mtb AcpS–ADP complex revealed that AcpS adopts two different conformations: the orthorhombic and trigonal space-group structures show structural differences in the α2 helix andmore » in the conformation of the α3–α4 connecting loop, which is in a closed conformation. The apo-AcpS structure shows electron density for the entire model and was obtained at lower pH values (4.4–6.0). In contrast, at a higher pH value (6.5) AcpS undergoes significant conformational changes, resulting in disordered regions that show no electron density in the AcpS model. The solved structures also reveal that C. ammoniagenes AcpS undergoes structural rearrangement in two regions, similar to the recently reported Mtb AcpS–ADP complex structure. In vitro reconstitution experiments show that AcpS has a higher post-translational modification activity between pH 4.4 and 6.0 than at pH values above 6.5, where the activity drops owing to the change in conformation. The results show that apo-AcpS and AcpS–ADP adopt different conformations depending upon the pH conditions of the crystallization solution.« less

Crystal structure of a β-aminopeptidase from an Australian Burkholderia sp.

PubMed

John-White, Marietta; Dumsday, Geoff J; Johanesen, Priscilla; Lyras, Dena; Drinkwater, Nyssa; McGowan, Sheena

2017-07-01

β-Aminopeptidases are a unique group of enzymes that have the unusual capability to hydrolyze N-terminal β-amino acids from synthetic β-peptides. β-Peptides can form secondary structures mimicking α-peptide-like structures that are resistant to degradation by most known proteases and peptidases. These characteristics of β-peptides give them great potential as peptidomimetics. Here, the X-ray crystal structure of BcA5-BapA, a β-aminopeptidase from a Gram-negative Burkholderia sp. that was isolated from activated sludge from a wastewater-treatment plant in Australia, is reported. The crystal structure of BcA5-BapA was determined to a resolution of 2.0 Å and showed a tetrameric assembly typical of the β-aminopeptidases. Each monomer consists of an α-subunit (residues 1-238) and a β-subunit (residues 239-367). Comparison of the structure of BcA5-BapA with those of other known β-aminopeptidases shows a highly conserved structure and suggests a similar proteolytic mechanism of action.

Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.

PubMed

Hurst, Travis; Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2018-05-10

The selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) method probes RNA local structural and dynamic information at single nucleotide resolution. To gain quantitative insights into the relationship between nucleotide flexibility, RNA 3D structure, and SHAPE reactivity, we develop a 3D Structure-SHAPE Relationship model (3DSSR) to rebuild SHAPE profiles from 3D structures. The model starts from RNA structures and combines nucleotide interaction strength and conformational propensity, ligand (SHAPE reagent) accessibility, and base-pairing pattern through a composite function to quantify the correlation between SHAPE reactivity and nucleotide conformational stability. The 3DSSR model shows the relationship between SHAPE reactivity and RNA structure and energetics. Comparisons between the 3DSSR-predicted SHAPE profile and the experimental SHAPE data show correlation, suggesting that the extracted analytical function may have captured the key factors that determine the SHAPE reactivity profile. Furthermore, the theory offers an effective method to sieve RNA 3D models and exclude models that are incompatible with experimental SHAPE data.

Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi)

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

Assefa, Netsanet Gizaw; Niiranen, Laila; University of Turku, FIN-20014 Turku

2014-08-01

A structural and biophysical study of the interactions between cod and human uracil-DNA N-glycosylase (UNG) and their inhibitor Ugi is presented. The stronger interaction between cod UNG and Ugi can be explained by a greater positive electrostatic surface potential. Uracil-DNA N-glycosylase from Atlantic cod (cUNG) shows cold-adapted features such as high catalytic efficiency, a low temperature optimum for activity and reduced thermal stability compared with its mesophilic homologue human UNG (hUNG). In order to understand the role of the enzyme–substrate interaction related to the cold-adapted properties, the structure of cUNG in complex with a bacteriophage encoded natural UNG inhibitor (Ugi)more » has been determined. The interaction has also been analyzed by isothermal titration calorimetry (ITC). The crystal structure of cUNG–Ugi was determined to a resolution of 1.9 Å with eight complexes in the asymmetric unit related through noncrystallographic symmetry. A comparison of the cUNG–Ugi complex with previously determined structures of UNG–Ugi shows that they are very similar, and confirmed the nucleotide-mimicking properties of Ugi. Biophysically, the interaction between cUNG and Ugi is very strong and shows a binding constant (K{sub b}) which is one order of magnitude larger than that for hUNG–Ugi. The binding of both cUNG and hUNG to Ugi was shown to be favoured by both enthalpic and entropic forces; however, the binding of cUNG to Ugi is mainly dominated by enthalpy, while the entropic term is dominant for hUNG. The observed differences in the binding properties may be explained by an overall greater positive electrostatic surface potential in the protein–Ugi interface of cUNG and the slightly more hydrophobic surface of hUNG.« less

Structural studies on molecular interactions between camel peptidoglycan recognition protein, CPGRP-S, and peptidoglycan moieties N-acetylglucosamine and N-acetylmuramic acid.

PubMed

Sharma, Pradeep; Yamini, Shavait; Dube, Divya; Singh, Amar; Sinha, Mau; Dey, Sharmistha; Mitra, Dipendra K; Kaur, Punit; Sharma, Sujata; Singh, Tej P

2012-06-22

Peptidoglycan (PGN) consists of repeating units of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc), which are cross-linked by short peptides. It is well known that PGN forms a major cell wall component of bacteria making it an important ligand for the recognition by peptidoglycan recognition proteins (PGRPs) of the host. The binding studies showed that PGN, GlcNAc, and MurNAc bind to camel PGRP-S (CPGRP-S) with affinities corresponding to dissociation constants of 1.3 × 10(-9), 2.6 × 10(-7), and 1.8 × 10(-7) M, respectively. The crystal structure determinations of the complexes of CPGRP-S with GlcNAc and MurNAc showed that the structures consist of four crystallographically independent molecules, A, B, C, and D, in the asymmetric unit that exists as A-B and C-D units of two neighboring linear polymers. The structure determinations showed that compounds GlcNAc and MurNAc bound to CPGRP-S at the same subsite in molecule C. Both GlcNAc and MurNAc form several hydrogen bonds and extensive hydrophobic interactions with protein atoms, indicating the specific nature of their bindings. Flow cytometric studies showed that PGN enhanced the secretions of TNF-α and IL-6 from human peripheral blood mononuclear cells. The introduction of CPGRP-S to the PGN-challenged cultured peripheral blood mononuclear cells reduced the expressions of proinflammatory cytokines, TNF-α and IL-6. This showed that CPGRP-S inhibited PGN-induced production of proinflammatory cytokines and down-regulated macrophage-mediated inflammation, indicating its potential applications as an antibacterial agent.

Graded Interface Models for more accurate Determination of van der Waals-London Dispersion Interactions across Grain Boundaries

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

van Benthem, Klaus; Tan, Guolong; French, Roger H

2006-01-01

Attractive van der Waals V London dispersion interactions between two half crystals arise from local physical property gradients within the interface layer separating the crystals. Hamaker coefficients and London dispersion energies were quantitatively determined for 5 and near- 13 grain boundaries in SrTiO3 by analysis of spatially resolved valence electron energy-loss spectroscopy (VEELS) data. From the experimental data, local complex dielectric functions were determined, from which optical properties can be locally analysed. Both local electronic structures and optical properties revealed gradients within the grain boundary cores of both investigated interfaces. The obtained results show that even in the presence ofmore » atomically structured grain boundary cores with widths of less than 1 nm, optical properties have to be represented with gradual changes across the grain boundary structures to quantitatively reproduce accurate van der Waals V London dispersion interactions. London dispersion energies of the order of 10% of the apparent interface energies of SrTiO3 were observed, demonstrating their significance in the grain boundary formation process. The application of different models to represent optical property gradients shows that long-range van der Waals V London dispersion interactions scale significantly with local, i.e atomic length scale property variations.« less

MHD Equilibrium with Reversed Current Density and Magnetic Islands Revisited: the Vacuum Vector Potential Calculus

NASA Astrophysics Data System (ADS)

L. Braga, F.

2013-10-01

The solution of Grad-Shafranov equation determines the stationary behavior of fusion plasma inside a tokamak. To solve the equation it is necessary to know the toroidal current density profile. Recent works show that it is possible to determine a magnetohydrodynamic (MHD) equilibrium with reversed current density (RCD) profiles that presents magnetic islands. In this work we show analytical MHD equilibrium with a RCD profile and analyze the structure of the vacuum vector potential associated with these equilibria using the virtual casing principle.

A new firefly luciferase with bimodal spectrum: identification of structural determinants of spectral pH-sensitivity in firefly luciferases.

PubMed

Viviani, Vadim R; Oehlmeyer, T L; Arnoldi, F G C; Brochetto-Braga, M R

2005-01-01

Fireflies emit flashes in the green-yellow region of the spectrum for the purpose of sexual attraction. The bioluminescence color is determined by the luciferases. It is well known that the in vitro bioluminescence color of firefly luciferases can be shifted toward the red by lower pH and higher temperature; for this reason they are classified as pH-sensitive luciferases. However, the mechanism and structural origin of pH sensitivity in fireflies remains unknown. Here we report the cloning of a new luciferase from the Brazilian twilight active firefly Macrolampis sp2, which displays an unusual bimodal spectrum. The recombinant luciferase displays a sensitive spectrum with the peak at 569 nm and a shoulder in the red region. Comparison of the bioluminescence spectra of Macrolampis, Photinus and Cratomorphus firefly luciferases shows that the distinct colors are determined by the ratio between green and red emitters under luciferase influence. Comparison of Macrolampis luciferase with the highly similar North American Photinus pyralis luciferase (91%) showed few substitutions potentially involved with the higher spectral sensitivity in Macrolampis luciferase. Site-directed mutagenesis showed that the natural substitution E354N determines the appearance of the shoulder in the red region of Macrolampis luciferase bioluminescence spectrum, helping to identify important interactions and residues involved in the pH-sensing mechanism in firefly luciferases.

Sequence Determinants of Compaction in Intrinsically Disordered Proteins

PubMed Central

Marsh, Joseph A.; Forman-Kay, Julie D.

2010-01-01

Abstract Intrinsically disordered proteins (IDPs), which lack folded structure and are disordered under nondenaturing conditions, have been shown to perform important functions in a large number of cellular processes. These proteins have interesting structural properties that deviate from the random-coil-like behavior exhibited by chemically denatured proteins. In particular, IDPs are often observed to exhibit significant compaction. In this study, we have analyzed the hydrodynamic radii of a number of IDPs to investigate the sequence determinants of this compaction. Net charge and proline content are observed to be strongly correlated with increased hydrodynamic radii, suggesting that these are the dominant contributors to compaction. Hydrophobicity and secondary structure, on the other hand, appear to have negligible effects on compaction, which implies that the determinants of structure in folded and intrinsically disordered proteins are profoundly different. Finally, we observe that polyhistidine tags seem to increase IDP compaction, which suggests that these tags have significant perturbing effects and thus should be removed before any structural characterizations of IDPs. Using the relationships observed in this analysis, we have developed a sequence-based predictor of hydrodynamic radius for IDPs that shows substantial improvement over a simple model based upon chain length alone. PMID:20483348

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement

DOE PAGES

Jackson, Ryan N.; McCoy, Airlie J.; Terwilliger, Thomas C.; ...

2015-07-30

Structures of multi-subunit macromolecular machines are primarily determined by either electron microscopy (EM) or X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for generating atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the "phase" information that is missing from an X-ray crystallography experiment, however integration of EM and X-ray diffraction data has been technically challenging.more » Here we show a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over non-crystallographic symmetry. As the resolution gap between EM and Xray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.« less

Crystal structure determination and analysis of 11S coconut allergen: Cocosin.

PubMed

Vajravijayan, S; Nandhagopal, N; Gunasekaran, K

2017-12-01

Allergy is an abnormal immune response against an innocuous target. Food allergy is an adverse reaction caused by common foods most well-known being those involving peanuts. Apart from mono sensitized food allergy, cross-reactivity with other food allergens is also commonly observed. To understand the phenomenon of cross-reactivity related to immune response, three dimensional structures of the allergens and their antigenic epitopes has to be analysed in detail. The X-ray crystal structure of Cocosin, a common 11S food allergen from coconut, has been determined at 2.2Å resolution using molecular replacement technique. The monomer of 52kDa is composed of two β-jelly roll domains, one with acidic and the other with basic character. The structure shows hexameric association with two trimers facing each other. Though the overall structure of Cocosin is similar to other 11S allergens, the occurrence of experimentally determined epitopes of the peanut allergen Ara h 3 at flexible as well as variable regions could be the reason for the clinically reported result of cross-reactivity that the peanut allergic patients are not sensitized with coconut allergen. Copyright © 2017 Elsevier Ltd. All rights reserved.

Crystal structure and confirmation of the alanine:glyoxylate aminotransferase activity of the YFL030w yeast protein.

PubMed

Meyer, Philippe; Liger, Dominique; Leulliot, Nicolas; Quevillon-Cheruel, Sophie; Zhou, Cong-Zhao; Borel, Franck; Ferrer, Jean-Luc; Poupon, Anne; Janin, Joël; van Tilbeurgh, Herman

2005-12-01

We have determined the three-dimensional crystal structure of the protein encoded by the open reading frame YFL030w from Saccharomyces cerevisiae to a resolution of 2.6 A using single wavelength anomalous diffraction. YFL030w is a 385 amino-acid protein with sequence similarity to the aminotransferase family. The structure of the protein reveals a homodimer adopting the fold-type I of pyridoxal 5'-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure. The protein shows close structural resemblance with the human alanine:glyoxylate aminotransferase (EC 2.6.1.44), an enzyme involved in the hereditary kidney stone disease primary hyperoxaluria type 1. In this paper we show that YFL030w codes for an alanine:glyoxylate aminotransferase, highly specific for its amino donor and acceptor substrates.

The Structure of Ethylbenzene, Styrene and Phenylacetylene Determined by Total Neutron Scattering.

PubMed

Szala-Bilnik, Joanna; Falkowska, Marta; Bowron, Daniel T; Hardacre, Christopher; Youngs, Tristan G A

2017-09-20

Organic solvents such as phenylacetylene, styrene and ethylbenzene are widely used in industrial processes, especially in the production of rubber or thermoplastics. Despite their important applications detailed knowledge about their structure is limited. In this paper the structures of these three aromatic solvents were investigated using neutron diffraction. The results show that many of their structural characteristics are similar, although the structure of phenylacetylene is more ordered and has a smaller solvation sphere than either ethylbenzene or styrene. Two regions within the first coordination sphere, in which the surrounding molecules show different preferable orientations with respect to the central molecule, were found for each liquid. Additionally, the localisation of the aliphatic chains reveals that they tend to favour closer interactions with each other than to the aromatic rings of the adjacent molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis of zinc sulfide nanoparticles and their incorporation into poly(hydroxybutyrate) matrix in the formation of a novel nanocomposite

NASA Astrophysics Data System (ADS)

Riaz, Shahina; Raza, Zulfiqar Ali; Majeed, Muhammad Irfan; Jan, Tariq

2018-05-01

In the present study, zinc sulfide (ZnS) nanoparticles (NPs) were successfully synthesized through a modified chemical precipitation protocol and then mediated into poly(hydroxybutyrate) (PHB) matrix to get ZnS/PHB nanocomposite. Mean diameter and zeta potential of ZnS NPs, as determined using dynamic light scattering technique (DLS), were observed to be 53 nm and ‑89 mV, respectively. The structural investigations performed using x-ray diffraction (XRD) technique depicted the phase purity of ZnS NPs exhibiting cubic crystal structure. Fourier transform infrared (FTIR) spectroscopic analysis was conducted to identify the presence or absence of bonding vibrational modes on the surface of synthesized single phase ZnS NPs. The FTIR analysis confirmed the metal to sulphur bond formation by showing the characteristic band at 1123 cm‑1. The UV–vis absorption spectra of ZnS NPs confirmed the synthesis of particles in nanoscale regime showing a λ max of 302 nm. These NPs were then successfully incorporated into PHB matrix to synthesize ZnS/PHB nanocomposite. The synthesis of nanocomposite was confirmed by EDX analysis. The chemical bonding and structural properties of ZnS/PHB nanocomposite were determined by FTIR and XRD analysis, respectively. The FTIR analysis confirmed the synthesis of ZnS/PHB nanocomposite. Moreover, XRD analysis showed that structure of nanocomposite was completely controlled by ZnS NPs as pure PHB exhibited orthorhombic crystal structure while the nanocomposite demonstrated cubic crystal structure of ZnS. Thermal properties of nanocomposite were studied through thermogravimetric analysis revealing that the incorporation of ZnS NPs into PHB matrix lead to enhance heat resistance properties of PHB.

Integrating NOE and RDC using sum-of-squares relaxation for protein structure determination.

PubMed

Khoo, Y; Singer, A; Cowburn, D

2017-07-01

We revisit the problem of protein structure determination from geometrical restraints from NMR, using convex optimization. It is well-known that the NP-hard distance geometry problem of determining atomic positions from pairwise distance restraints can be relaxed into a convex semidefinite program (SDP). However, often the NOE distance restraints are too imprecise and sparse for accurate structure determination. Residual dipolar coupling (RDC) measurements provide additional geometric information on the angles between atom-pair directions and axes of the principal-axis-frame. The optimization problem involving RDC is highly non-convex and requires a good initialization even within the simulated annealing framework. In this paper, we model the protein backbone as an articulated structure composed of rigid units. Determining the rotation of each rigid unit gives the full protein structure. We propose solving the non-convex optimization problems using the sum-of-squares (SOS) hierarchy, a hierarchy of convex relaxations with increasing complexity and approximation power. Unlike classical global optimization approaches, SOS optimization returns a certificate of optimality if the global optimum is found. Based on the SOS method, we proposed two algorithms-RDC-SOS and RDC-NOE-SOS, that have polynomial time complexity in the number of amino-acid residues and run efficiently on a standard desktop. In many instances, the proposed methods exactly recover the solution to the original non-convex optimization problem. To the best of our knowledge this is the first time SOS relaxation is introduced to solve non-convex optimization problems in structural biology. We further introduce a statistical tool, the Cramér-Rao bound (CRB), to provide an information theoretic bound on the highest resolution one can hope to achieve when determining protein structure from noisy measurements using any unbiased estimator. Our simulation results show that when the RDC measurements are corrupted by Gaussian noise of realistic variance, both SOS based algorithms attain the CRB. We successfully apply our method in a divide-and-conquer fashion to determine the structure of ubiquitin from experimental NOE and RDC measurements obtained in two alignment media, achieving more accurate and faster reconstructions compared to the current state of the art.

Distinct dimensions defining the Adult ADHD Self-Report Scale: Implications for assessing inattentive and hyperactive/impulsive symptoms.

PubMed

Stanton, Kasey; Forbes, Miriam K; Zimmerman, Mark

2018-06-07

There has been growing interest in studying attention-deficit/hyperactivity disorder (ADHD) in adulthood as a result of research indicating that ADHD often persists into adulthood and frequently is comorbid with other psychiatric disorders. Adult ADHD symptoms are most commonly assessed via self-report, but prior research examining the structure of self-reported adult ADHD symptoms has yielded discrepant results. Explicating the factor structure of ADHD symptom measures is essential to determine if such self-report measures assess symptom dimensions showing distinctive relations with other psychopathology and psychosocial functioning. Consequently, we examined the structure of adult ADHD symptoms in a large sample of adult outpatients (N = 1,094). Symptoms were assessed via the Adult ADHD Self-Report Scale (ASRS; Kessler et al., 2005), which has become the most widely used self-report ADHD measure. Additionally, we extended prior research by examining the relations for emergent ADHD dimensions with other psychopathology and psychosocial impairment. Results indicated that the ASRS's items define a bifactor structure with specific dimensions of inattentiveness, motor hyperactivity/impulsivity, and verbal hyperactivity/impulsivity. Our results indicate that specific ADHD factors show distinctive relations in some ways. For example, verbal hyperactivity/impulsivity showed negative relations with major depressive disorder, whereas inattentiveness showed positive relations with major depression. These results highlight the need for future research determining the extent to which making distinctions among various ADHD symptom types (i.e., distinguishing motor and verbal hyperactivity/impulsivity) is empirically warranted and clinically useful. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Monitoring Data-Structure Evolution in Distributed Message-Passing Programs

NASA Technical Reports Server (NTRS)

Sarukkai, Sekhar R.; Beers, Andrew; Woodrow, Thomas S. (Technical Monitor)

1996-01-01

Monitoring the evolution of data structures in parallel and distributed programs, is critical for debugging its semantics and performance. However, the current state-of-art in tracking and presenting data-structure information on parallel and distributed environments is cumbersome and does not scale. In this paper we present a methodology that automatically tracks memory bindings (not the actual contents) of static and dynamic data-structures of message-passing C programs, using PVM. With the help of a number of examples we show that in addition to determining the impact of memory allocation overheads on program performance, graphical views can help in debugging the semantics of program execution. Scalable animations of virtual address bindings of source-level data-structures are used for debugging the semantics of parallel programs across all processors. In conjunction with light-weight core-files, this technique can be used to complement traditional debuggers on single processors. Detailed information (such as data-structure contents), on specific nodes, can be determined using traditional debuggers after the data structure evolution leading to the semantic error is observed graphically.

Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design.

PubMed

Krol, Jacek; Sobczak, Krzysztof; Wilczynska, Urszula; Drath, Maria; Jasinska, Anna; Kaczynska, Danuta; Krzyzosiak, Wlodzimierz J

2004-10-01

We have established the structures of 10 human microRNA (miRNA) precursors using biochemical methods. Eight of these structures turned out to be different from those that were computer-predicted. The differences localized in the terminal loop region and at the opposite side of the precursor hairpin stem. We have analyzed the features of these structures from the perspectives of miRNA biogenesis and active strand selection. We demonstrated the different thermodynamic stability profiles for pre-miRNA hairpins harboring miRNAs at their 5'- and 3'-sides and discussed their functional implications. Our results showed that miRNA prediction based on predicted precursor structures may give ambiguous results, and the success rate is significantly higher for the experimentally determined structures. On the other hand, the differences between the predicted and experimentally determined structures did not affect the stability of termini produced through "conceptual dicing." This result confirms the value of thermodynamic analysis based on mfold as a predictor of strand section by RNAi-induced silencing complex (RISC).

Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach.

PubMed

Zhang, Kaiming; Keane, Sarah C; Su, Zhaoming; Irobalieva, Rossitza N; Chen, Muyuan; Van, Verna; Sciandra, Carly A; Marchant, Jan; Heng, Xiao; Schmid, Michael F; Case, David A; Ludtke, Steven J; Summers, Michael F; Chiu, Wah

2018-03-06

Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, respectively. We combined these techniques to study a 30 kDa HIV-1 dimer initiation site RNA ([DIS] 2 ; 47 nt/strand). A 9 Å cryo-EM map clearly shows major groove features of the double helix and a right-handed superhelical twist. Simulated cryo-EM maps generated from time-averaged molecular dynamics trajectories (10 ns) exhibited levels of detail similar to those in the experimental maps, suggesting internal structural flexibility limits the cryo-EM resolution. Simultaneous inclusion of the cryo-EM map and 2 H-edited NMR-derived distance restraints during structure refinement generates a structure consistent with both datasets and supporting a flipped-out base within a conserved purine-rich bulge. Our findings demonstrate the power of combining global and local structural information from these techniques for structure determination of modest-sized RNAs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Structure and application of antifreeze proteins from Antarctic bacteria.

PubMed

Muñoz, Patricio A; Márquez, Sebastián L; González-Nilo, Fernando D; Márquez-Miranda, Valeria; Blamey, Jenny M

2017-08-07

Antifreeze proteins (AFPs) production is a survival strategy of psychrophiles in ice. These proteins have potential in frozen food industry avoiding the damage in the structure of animal or vegetal foods. Moreover, there is not much information regarding the interaction of Antarctic bacterial AFPs with ice, and new determinations are needed to understand the behaviour of these proteins at the water/ice interface. Different Antarctic places were screened for antifreeze activity and microorganisms were selected for the presence of thermal hysteresis in their crude extracts. Isolates GU1.7.1, GU3.1.1, and AFP5.1 showed higher thermal hysteresis and were characterized using a polyphasic approach. Studies using cucumber and zucchini samples showed cellular protection when samples were treated with partially purified AFPs or a commercial AFP as was determined using toluidine blue O and neutral red staining. Additionally, genome analysis of these isolates revealed the presence of genes that encode for putative AFPs. Deduced amino acids sequences from GU3.1.1 (gu3A and gu3B) and AFP5.1 (afp5A) showed high similarity to reported AFPs which crystal structures are solved, allowing then generating homology models. Modelled proteins showed a triangular prism form similar to β-helix AFPs with a linear distribution of threonine residues at one side of the prism that could correspond to the putative ice binding side. The statistically best models were used to build a protein-water system. Molecular dynamics simulations were then performed to compare the antifreezing behaviour of these AFPs at the ice/water interface. Docking and molecular dynamics simulations revealed that gu3B could have the most efficient antifreezing behavior, but gu3A could have a higher affinity for ice. AFPs from Antarctic microorganisms GU1.7.1, GU3.1.1 and AFP5.1 protect cellular structures of frozen food showing a potential for frozen food industry. Modeled proteins possess a β-helix structure, and molecular docking analysis revealed the AFP gu3B could be the most efficient AFPs in order to avoid the formation of ice crystals, even when gu3A has a higher affinity for ice. By determining the interaction of AFPs at the ice/water interface, it will be possible to understand the process of adaptation of psychrophilic bacteria to Antarctic ice.

Attitude Control of Flexible Structures.

DTIC Science & Technology

1990-09-01

arm has been determined experimentally and compared with analytical * predictions obtained by using the GIFTS finite element analysis program. The...frequencies of the flexible arm have been determined experimentally and compared with analytical predictiens obtained by using the GIFTS finite element...exception of the first mode. Table V shows the difference between the frequencies obtained from the GIFTS program and the experimental values. TABLE

Autonomy Support, Need Satisfaction, and Motivation for Support among Adults with Intellectual Disability: Testing a Self-Determination Theory Model

ERIC Educational Resources Information Center

Frielink, Noud; Schuengel, Carlo; Embregts, Petri J. C. M.

2018-01-01

The tenets of self-determination theory as applied to support were tested with structural equation modelling for 186 people with ID with a mild to borderline level of functioning. The results showed that (a) perceived autonomy support was positively associated with autonomous motivation and with satisfaction of need for autonomy, relatedness, and…

Tilt-Pair Analysis of Images from a Range of Different Specimens in Single-Particle Electron Cryomicroscopy

PubMed Central

Henderson, Richard; Chen, Shaoxia; Chen, James Z.; Grigorieff, Nikolaus; Passmore, Lori A.; Ciccarelli, Luciano; Rubinstein, John L.; Crowther, R. Anthony; Stewart, Phoebe L.; Rosenthal, Peter B.

2011-01-01

The comparison of a pair of electron microscope images recorded at different specimen tilt angles provides a powerful approach for evaluating the quality of images, image-processing procedures, or three-dimensional structures. Here, we analyze tilt-pair images recorded from a range of specimens with different symmetries and molecular masses and show how the analysis can produce valuable information not easily obtained otherwise. We show that the accuracy of orientation determination of individual single particles depends on molecular mass, as expected theoretically since the information in each particle image increases with molecular mass. The angular uncertainty is less than 1° for particles of high molecular mass (∼ 50 MDa), several degrees for particles in the range 1–5 MDa, and tens of degrees for particles below 1 MDa. Orientational uncertainty may be the major contributor to the effective temperature factor (B-factor) describing contrast loss and therefore the maximum resolution of a structure determination. We also made two unexpected observations. Single particles that are known to be flexible showed a wider spread in orientation accuracy, and the orientations of the largest particles examined changed by several degrees during typical low-dose exposures. Smaller particles presumably also reorient during the exposure; hence, specimen movement is a second major factor that limits resolution. Tilt pairs thus enable assessment of orientation accuracy, map quality, specimen motion, and conformational heterogeneity. A convincing tilt-pair parameter plot, where 60% of the particles show a single cluster around the expected tilt axis and tilt angle, provides confidence in a structure determined using electron cryomicroscopy. PMID:21939668

Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods

PubMed Central

Mandal, Kalyaneswar; Pentelute, Brad L; Tereshko, Valentina; Thammavongsa, Vilasak; Schneewind, Olaf; Kossiakoff, Anthony A; Kent, Stephen B H

2009-01-01

We describe the use of racemic crystallography to determine the X-ray structure of the natural product plectasin, a potent antimicrobial protein recently isolated from fungus. The protein enantiomers l-plectasin and d-plectasin were prepared by total chemical synthesis; interestingly, l-plectasin showed the expected antimicrobial activity, while d-plectasin was devoid of such activity. The mirror image proteins were then used for racemic crystallization. Synchrotron X-ray diffraction data were collected to atomic resolution from a racemic plectasin crystal; the racemate crystallized in the achiral centrosymmetric space group with one l-plectasin molecule and one d-plectasin molecule forming the unit cell. Dimer-like intermolecular interactions between the protein enantiomers were observed, which may account for the observed extremely low solvent content (13%–15%) and more highly ordered nature of the racemic crystals. The structure of the plectasin molecule was well defined for all 40 amino acids and was generally similar to the previously determined NMR structure, suggesting minimal impact of the crystal packing on the plectasin conformation. PMID:19472324

Attenuation Tomography Based on Strong Motion Data: Case Study of Central Honshu Region, Japan

NASA Astrophysics Data System (ADS)

Kumar, Parveen; Joshi, A.; Verma, O. P.

2013-12-01

Three-dimensional frequency dependent S-wave quality factor (Qβ(f)) value for the central Honshu region of Japan has been determined in this paper using an algorithm based on inversion of strong motion data. The method of inversion for determination of three-dimensional attenuation coefficients is proposed by H ashida and S himazaki (J Phys Earth. 32, 299-316, 1984) and has been used and modified by J oshi (Curr Sci. 90, 581-585, 2006; Nat Hazards. 43, 129-146, 2007) and J oshi et al. (J. Seismol. 14, 247-272, 2010). Twenty-one earthquakes digitally recorded on strong motion stations of Kik-net network have been used in this work. The magnitude of these earthquake ranges from 3.1 to 4.2 and depth ranging from 5 to 20 km, respectively. The borehole data having high signal to noise ratio and minimum site effect is used in the present work. The attenuation structure is determined by dividing the entire area into twenty-five three-dimensional blocks of uniform thickness having different frequency-dependent shear wave quality factor. Shear wave quality factor values have been determined at frequencies of 2.5, 7.0 and 10 Hz from record in a rectangular grid defined by 35.4°N to 36.4°N and 137.2°E to 138.2°E. The obtained attenuation structure is compared with the available geological features in the region and comparison shows that the obtained structure is capable of resolving important tectonic features present in the area. The proposed attenuation structure is compared with the probabilistic seismic hazard map of the region and shows that it bears some remarkable similarity in the patterns seen in seismic hazard map.

Analysis of the effects of firing Orbiter primary reaction control system jets with an attached truss structure

NASA Technical Reports Server (NTRS)

Kaszubowski, M.; Raney, J. P.

1986-01-01

A study was conducted to determine the dynamic effects of firing the orbiter primary reaction control jets during assembly of protoflight space station structure. Maximum longeron compressive load was calculated as a function of jet pulse time length, number of jet pulses, and total torque imposed by the reaction control jets. The study shows that it is possible to fire selected jets to achieve a pitch maneuver without causing failure of the attached structure.

Automatic building of a web-like structure based on thermoplastic adhesive.

PubMed

Leach, Derek; Wang, Liyu; Reusser, Dorothea; Iida, Fumiya

2014-09-01

Animals build structures to extend their control over certain aspects of the environment; e.g., orb-weaver spiders build webs to capture prey, etc. Inspired by this behaviour of animals, we attempt to develop robotics technology that allows a robot to automatically builds structures to help it accomplish certain tasks. In this paper we show automatic building of a web-like structure with a robot arm based on thermoplastic adhesive (TPA) material. The material properties of TPA, such as elasticity, adhesiveness, and low melting temperature, make it possible for a robot to form threads across an open space by an extrusion-drawing process and then combine several of these threads into a web-like structure. The problems addressed here are discovering which parameters determine the thickness of a thread and determining how web-like structures may be used for certain tasks. We first present a model for the extrusion and the drawing of TPA threads which also includes the temperature-dependent material properties. The model verification result shows that the increasing relative surface area of the TPA thread as it is drawn thinner increases the heat loss of the thread, and that by controlling how quickly the thread is drawn, a range of diameters can be achieved from 0.2-0.75 mm. We then present a method based on a generalized nonlinear finite element truss model. The model was validated and could predict the deformation of various web-like structures when payloads are added. At the end, we demonstrate automatic building of a web-like structure for payload bearing.

Ab initio structure determination and quantitative disorder analysis on nanoparticles by electron diffraction tomography.

PubMed

Krysiak, Yaşar; Barton, Bastian; Marler, Bernd; Neder, Reinhard B; Kolb, Ute

2018-03-01

Nanoscaled porous materials such as zeolites have attracted substantial attention in industry due to their catalytic activity, and their performance in sorption and separation processes. In order to understand the properties of such materials, current research focuses increasingly on the determination of structural features beyond the averaged crystal structure. Small particle sizes, various types of disorder and intergrown structures render the description of structures at atomic level by standard crystallographic methods difficult. This paper reports the characterization of a strongly disordered zeolite structure, using a combination of electron exit-wave reconstruction, automated diffraction tomography (ADT), crystal disorder modelling and electron diffraction simulations. Zeolite beta was chosen for a proof-of-principle study of the techniques, because it consists of two different intergrown polymorphs that are built from identical layer types but with different stacking sequences. Imaging of the projected inner Coulomb potential of zeolite beta crystals shows the intergrowth of the polymorphs BEA and BEB. The structures of BEA as well as BEB could be extracted from one single ADT data set using direct methods. A ratio for BEA/BEB = 48:52 was determined by comparison of the reconstructed reciprocal space based on ADT data with simulated electron diffraction data for virtual nanocrystals, built with different ratios of BEA/BEB. In this way, it is demonstrated that this smart interplay of the above-mentioned techniques allows the elaboration of the real structures of functional materials in detail - even if they possess a severely disordered structure.

Structure-to-property relationships in fuel cell catalyst supports: Correlation of surface chemistry and morphology with oxidation resistance of carbon blacks

NASA Astrophysics Data System (ADS)

Artyushkova, Kateryna; Pylypenko, Svitlana; Dowlapalli, Madhu; Atanassov, Plamen

2012-09-01

Linking durability of carbon blacks, expressed as their oxidation resistance, used in PEMFCs as catalyst supports, with their chemistry and morphology is an important task towards designing carbon blacks with desired properties. Structure-to-property relationship between surface chemistry determined by X-ray photoelectron spectroscopy (XPS), morphological structure determined by digital image processing of scanning electron microscopy (SEM) images, physical properties, and electrochemical corrosion behavior determined in an air-breathing gas-diffusion electrode is studied for several un-altered and several modified carbon blacks. We are showing that surface chemistry, graphitic content and certain physical characteristics such as Brunauer-Emmett-Teller (BET) surface area and pore volume, determined by nitrogen adsorptions are not sufficient to explain high corrosion instability of types of carbon blacks. Inclusion of morphological characteristics, such as roughness, texture and shape parameters provide for more inclusive description and therefore more complete structure-to-property correlations of corrosion behavior of carbon blacks. This paper presents the first direct statistically-derived structure-to-property relationship, developed by multivariate analysis (MVA) that links chemical and physical structural properties of the carbon blacks to their critical properties as supports for PEMFC catalysts. We have found that balance between electrocatalytic activity and high resistance towards oxidation and corrosion is achieved by balance between amount of graphitic content and surface oxide coverage, smaller overall roughness and, finally, larger amount of big elongated and loose, and, hypothetically, more hydrophobic pores.

Novel interpretation of the mean structure of feroxyhyte

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

Sestu, Matteo, E-mail: msestu@unica.it; Carta, Daniela; Casula, Maria F.

2015-05-15

The structure of the iron oxyhydroxide called feroxyhyte (δ-FeOOH), which shows an elusive X-ray powder diffraction pattern, has been represented so far using models describing a mean structure based on the crystalline network of the iron(III) oxide hematite (α-Fe{sub 2}O{sub 3}). In this paper, a novel description of the mean structure of feroxyhyte is presented, which is based on the structure of the thermodynamically stable iron oxyhydroxide goethite. Starting from different local arrangements present in the goethite network, a mean structural model is determined which shows an X-ray powder diffraction pattern almost coincident with previous studies. This outcome enables tomore » integrate the structure of feroxyhyte among those of other well characterized iron oxyhydroxides. - Graphical abstract: The structure of the iron oxy-hydroxide feroxyhyte can be described by local arrangements present in the goethite network. - Highlights: • The structure of feroxyhyte (δ-FeOOH) proposed in literature is discussed. • The structure of goethite (α-FeOOH) is analyzed. • A structural relationship between feroxyhyte and goethite is found. • New interpretation of the mean structure of δ-FeOOH is given.« less

Modeling helical proteins using residual dipolar couplings, sparse long-range distance constraints and a simple residue-based force field

PubMed Central

Eggimann, Becky L.; Vostrikov, Vitaly V.; Veglia, Gianluigi; Siepmann, J. Ilja

2013-01-01

We present a fast and simple protocol to obtain moderate-resolution backbone structures of helical proteins. This approach utilizes a combination of sparse backbone NMR data (residual dipolar couplings and paramagnetic relaxation enhancements) or EPR data with a residue-based force field and Monte Carlo/simulated annealing protocol to explore the folding energy landscape of helical proteins. By using only backbone NMR data, which are relatively easy to collect and analyze, and strategically placed spin relaxation probes, we show that it is possible to obtain protein structures with correct helical topology and backbone RMS deviations well below 4 Å. This approach offers promising alternatives for the structural determination of proteins in which nuclear Overha-user effect data are difficult or impossible to assign and produces initial models that will speed up the high-resolution structure determination by NMR spectroscopy. PMID:24639619

The importance of bulk density determination in gravity data processing for structure interpretation

NASA Astrophysics Data System (ADS)

Wildan, D.; Akbar, A. M.; Novranza, K. M. S.; Sobirin, R.; Permadi, A. N.; Supriyanto

2017-07-01

Gravity method use rock density variation for determining subsurface lithology and geological structure. In the "green area" where measurement of rock density has not been done, an attemp to find density is usually performed by calculating using Parasnis method, or by using using the average of rock density in the earth's crust (2,67 gr/cm3) or by using theoritical value of dominant rock density in the survey area (2,90 gr/cm3). Those three values of densities are applied to gravity data analysis in the hilly "X" area. And we have compared all together in order to observed which value has represented the structure better. The result showed that the higher value of rock density, the more obvious structure in the Bouguer anomaly profile. It is due to the contrast of maximum and minimum value of Bouguer anomaly that will affect the exageration in distance vs Bouguer anomaly graphic.

Experimental and calculated structural parameters of 5-trihalomethyl-4,5-dihydro-1 H-pyrazole derivatives, novel analgesic agents

NASA Astrophysics Data System (ADS)

Machado, Pablo; Campos, Patrick T.; Lima, Glauber R.; Rosa, Fernanda A.; Flores, Alex F. C.; Bonacorso, Helio G.; Zanatta, Nilo; Martins, Marcos A. P.

2009-01-01

The crystal structures of four novel analgesic agents, methyl 5-hydroxy-3- or 4-methyl-5-trichloro[trifluoro]methyl-4,5-dihydro-1 H-pyrazole-1-carboxylate, have been determined by X-ray diffractometry. The data demonstrated that the molecular packing was stabilized mainly by O sbnd H⋯O hydrogen bonds of the 5-hydroxy and 1-carboxymethyl groups. The 4,5-dihydro-1 H-pyrazole rings were obtained as almost planar structures showing RMS deviation at a range of 0.0052-0.0805 Å. Additionally, computational investigation using semi-empirical AM1 and PM3 methods were performed to find a correlation between experimental and calculated geometrical parameters. The data obtained suggest that the structural data furnished by the AM1 method is in better agreement with those experimentally determined for the above compounds.

Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases

PubMed Central

Mariani, Simona; Dell'Orco, Daniele; Felline, Angelo; Raimondi, Francesco; Fanelli, Francesca

2013-01-01

A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEγ binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions. PMID:24009494

Chiral discrimination in diastereomeric salts of chlorine-substituted mandelic acid and phenylethylamine.

PubMed

He, Quan; Gomaa, Hassan; Rohani, Sohrab; Zhu, Jesse; Jennings, Michael

2010-08-01

The crystal structures of diastereomeric salts of chloromandelic acid and phenylethylamine were determined and are presented herein. The structure comparison between less soluble salts and more soluble salts shows that weak interactions such as CH/pi interactions and van der Waals gain importance and contribute to chiral recognition when the hydrogen bonding patterns are very similar. Copyright 2010 Wiley-Liss, Inc.

Size effect of ZnO nanorods on physicochemical properties of plasticized starch composites.

PubMed

Guz, L; Famá, L; Candal, R; Goyanes, S

2017-02-10

This work demonstrates that the size of ZnO nanorods (ZnONR) with similar aspect ratio determines several physicochemical and microbiological properties of thermoplastic starch composites (TPS/ZnONR) at a given concentration of ZnONRs. A combination of sol-gel and hydrothermal methods was developed to synthesize ZnONR with different sizes but similar aspect ratios. Starch composites containing 1wt.% of ZnONR were prepared by casting. Composites with smaller size nanorods (ZnONR-S) showed more efficiency in shielding UVA radiation and had a higher solubility and water vapor permeability than those with larger nanorods (ZnONR-L). Mechanical properties, biodegradability and antibacterial activity were also influenced by the size of the ZnONR. X-ray diffraction analysis showed that composites with ZnONR-S maintained the typical B-V type starch structure, intensifying the V-type starch structure peaks, while composite with ZnONR-L induced the formation of an amorphous structure, preventing starch retrogradation during storage. Properties affected by nanorods size are fundamental in determining composite applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular disassembly of rice and lotus starches during thermal processing and its effect on starch digestibility.

PubMed

Wang, Shujun; Sun, Yue; Wang, Jinrong; Wang, Shuo; Copeland, Les

2016-02-01

The molecular disassembly of starch during thermal processing is a major determinant for the susceptibility of starch to enzymatic digestion. In the present study, the effects of thermal processing on the disassembly of the granular structure and the in vitro enzymatic digestibility of rice and lotus starches were investigated. After heating at 50 °C, rice and lotus starches did not show significant changes in granular morphology, long-range crystallinity and short-range molecular order. As the temperature increased to 60 °C, rice starch underwent a partial gelatinization followed by an incomplete disruption of granular morphology, crystallites and molecular order. In contrast, lotus starch was almost completely gelatinized at 60 °C. At 70 °C or higher, both starches were fully gelatinized with complete disruption of the micro and macro structures. Our results show that gelatinization greatly increased the in vitro enzymatic digestibility of both starches, but that the degree of disassembly of the starch structure during thermal processing was not a major determinant of the digestibility of gelatinized starch.

Study of a Simulation Tool to Determine Achievable Control Dynamics and Control Power Requirements with Perfect Tracking

NASA Technical Reports Server (NTRS)

Ostroff, Aaron J.

1998-01-01

This paper contains a study of two methods for use in a generic nonlinear simulation tool that could be used to determine achievable control dynamics and control power requirements while performing perfect tracking maneuvers over the entire flight envelope. The two methods are NDI (nonlinear dynamic inversion) and the SOFFT(Stochastic Optimal Feedforward and Feedback Technology) feedforward control structure. Equivalent discrete and continuous SOFFT feedforward controllers have been developed. These equivalent forms clearly show that the closed-loop plant model loop is a plant inversion and is the same as the NDI formulation. The main difference is that the NDI formulation has a closed-loop controller structure whereas SOFFT uses an open-loop command model. Continuous, discrete, and hybrid controller structures have been developed and integrated into the formulation. Linear simulation results show that seven different configurations all give essentially the same response, with the NDI hybrid being slightly different. The SOFFT controller gave better tracking performance compared to the NDI controller when a nonlinear saturation element was added. Future plans include evaluation using a nonlinear simulation.

Temperature structure of the Uranian upper atmosphere

NASA Technical Reports Server (NTRS)

Elliot, J. L.; Dunham, E.

1979-01-01

The temperature structure of the upper atmosphere of Uranus at two locations on the planet was determined from observations of the occultation of the star SAO158687 by Uranus on 10 March 1977, carried out at the Kuiper Airborne Observatory. The temperature-pressure relationships obtained from the immersion and emersion data for 7280 A channel show peak-to-peak variations of 45 K for immersion and 35 K for emersion. The mean temperature for both immersion and emersion profiles is about 100 K, which shows that Uranus has a temperature inversion between 0.001 mbar and the 100 mbar level probed by IR measurements. Both profiles show wavelike temperature variations, which may be due to dynamical or photochemical processes.

Structure-dependent water transport across nanopores of carbon nanotubes: toward selective gating upon temperature regulation.

PubMed

Zhao, Kuiwen; Wu, Huiying

2015-04-28

Determining water structure in nanopores and its influence on water transport behaviour is of great importance for understanding and regulating the transport across nanopores. Here we report an ultrafast-slow flow transition phenomenon for water transport across nanopores of carbon nanotubes owing to the change in water structure in nanopores induced by temperature. By performing extensive molecular dynamics simulations, we show the dependence of water transport behaviours on water structures. Our results indicate that owing to the change in water structure in nanopores, water flux across nanopores with certain pore sizes decreases sharply (nearly 3 orders of magnitude) with the decreasing temperature. This phenomenon is very sensitive to the pore size. The threshold temperatures for the occurrence of the ultrafast-slow flow transition for water transport are also determined for various pore sizes. These findings suggest a novel protocol for selective gating of water and proton conduction across nanopores and temperature-controlled drug release.

Chemical Approaches for Structure and Function of RNA in Postgenomic Era

PubMed Central

Ro-Choi, Tae Suk; Choi, Yong Chun

2012-01-01

In the study of cellular RNA chemistry, a major thrust of research focused upon sequence determinations for decades. Structures of snRNAs (4.5S RNA I (Alu), U1, U2, U3, U4, U5, and U6) were determined at Baylor College of Medicine, Houston, Tex, in an earlier time of pregenomic era. They show novel modifications including base methylation, sugar methylation, 5′-cap structures (types 0–III) and sequence heterogeneity. This work offered an exciting problem of posttranscriptional modification and underwent numerous significant advances through technological revolutions during pregenomic, genomic, and postgenomic eras. Presently, snRNA research is making progresses involved in enzymology of snRNA modifications, molecular evolution, mechanism of spliceosome assembly, chemical mechanism of intron removal, high-order structure of snRNA in spliceosome, and pathology of splicing. These works are destined to reach final pathway of work “Function and Structure of Spliceosome” in addition to exciting new exploitation of other noncoding RNAs in all aspects of regulatory functions. PMID:22347623

Oxygen vacancy-driven evolution of structural and electrical properties in SrFeO 3₋δ thin films and a method of stabilization

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

Enriquez, Erik M.; Chen, Aiping; Harrell, Zachary John

Epitaxial SrFeO 3-δ (SFO) thin films have been grown on various substrates by pulsed laser deposition. The structural and electrical properties of SFO thin films are monitored with time in different atmospheres at room temperature, showing time-dependent crystal structure and electrical conductivity. The increased out-of-plane lattice parameter and resistivity over time are associated with the increased oxygen vacancies density in SFO thin films. The epitaxial strain plays an important role in determining the initial resistivity, and the sample environment determines the trend of resistivity change over time. An amorphous Al 2O 3 passivation layer has been found to be effectivemore » in stabilizing the structure and electrical properties of SFO thin films. Lastly, this work explores time dependent structure and properties variation in oxide films and provides a way to stabilize thin film materials that are sensitive to oxygen vacancies.« less

Crystal Structure of the Catalytic Domain of a Serine Threonine Protein Phosphatase

NASA Technical Reports Server (NTRS)

Swinglel, Mark; Honkanel, Richard; Ciszak, Ewa

2003-01-01

Reversible phosphorylation of serine and threonine residues is a well-recognized mechanism in eukaryotic cells for the regulation of cell-cycle progression, cell growth and metabolism. Human serine/threonine phosphatases can be placed into two major families, PPP and PPM. To date the structure on one PPP family member (PPl) has been determined. Here we present the structure of a 323-residue catalytic domain of a second phosphatase belonging to the PPP family of enzyme. catalytic domain of the enzyme has been determined to 1.60Angstrom resolution and refined to R=17.5 and Rfree = 20.8%. The catalytic domain possesses a unique fold consisting of a largely monolithic structure, divisible into closely-associated helical and sheet regions. The catalytic site contains two manganese ions that are involved in substrate binding and catalysis. The enzyme crystallizes as a dimer that completely buries catalytic surfaces of both monomers, Also, the structure shows evidence of some flexibility around the active site cleft that may be related to substrate specificity of this enzyme.

Oxygen vacancy-driven evolution of structural and electrical properties in SrFeO 3₋δ thin films and a method of stabilization

DOE PAGES

Enriquez, Erik M.; Chen, Aiping; Harrell, Zachary John; ...

2016-10-03

Epitaxial SrFeO 3-δ (SFO) thin films have been grown on various substrates by pulsed laser deposition. The structural and electrical properties of SFO thin films are monitored with time in different atmospheres at room temperature, showing time-dependent crystal structure and electrical conductivity. The increased out-of-plane lattice parameter and resistivity over time are associated with the increased oxygen vacancies density in SFO thin films. The epitaxial strain plays an important role in determining the initial resistivity, and the sample environment determines the trend of resistivity change over time. An amorphous Al 2O 3 passivation layer has been found to be effectivemore » in stabilizing the structure and electrical properties of SFO thin films. Lastly, this work explores time dependent structure and properties variation in oxide films and provides a way to stabilize thin film materials that are sensitive to oxygen vacancies.« less

Crystal-chemical characteristics of nontronites from bottom sediments of Pacific ocean

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

Palchik, N. A., E-mail: nadezhda@igm.nsc.ru; Moroz, T. N.; Grigorieva, T. N.

A crystal-chemical analysis of the nontronite samples formed in deep-water sediments of the underwater Juan-de-Fuca ridge in the Pacific ocean has been performed using powder X-ray diffraction, IR spectroscopy, and Mössbauer spectroscopy. A comparison with the previously investigated nontronites from different regions of the Sea of Okhotsk showed that the structural features of these formations are due to the difference in the physicochemical parameters of their crystallization. The values of the basal interplanar spacing d{sub 001} (within 11–13 Å) in the samples analyzed are determined by the degree of hydration and cation filling of the interlayer space, while the differencesmore » in the IR spectra are due to isomorphic substitutions in the structure. The character of cation distribution and the nature and concentration of stacking faults in nontronite structures are determined. The differences in the composition, structure, and properties of nontronites of different origin are confirmed by theoretical calculations of their structural parameters.« less

Structure-guided statistical textural distinctiveness for salient region detection in natural images.

PubMed

Scharfenberger, Christian; Wong, Alexander; Clausi, David A

2015-01-01

We propose a simple yet effective structure-guided statistical textural distinctiveness approach to salient region detection. Our method uses a multilayer approach to analyze the structural and textural characteristics of natural images as important features for salient region detection from a scale point of view. To represent the structural characteristics, we abstract the image using structured image elements and extract rotational-invariant neighborhood-based textural representations to characterize each element by an individual texture pattern. We then learn a set of representative texture atoms for sparse texture modeling and construct a statistical textural distinctiveness matrix to determine the distinctiveness between all representative texture atom pairs in each layer. Finally, we determine saliency maps for each layer based on the occurrence probability of the texture atoms and their respective statistical textural distinctiveness and fuse them to compute a final saliency map. Experimental results using four public data sets and a variety of performance evaluation metrics show that our approach provides promising results when compared with existing salient region detection approaches.

Killing-Yano equations with torsion, worldline actions and G-structures

NASA Astrophysics Data System (ADS)

Papadopoulos, G.

2012-06-01

We determine the geometry of the target spaces of supersymmetric non-relativistic particles with torsion and magnetic couplings, and with symmetries generated by the fundamental forms of G-structures for G = U(n), SU(n), Sp(n), Sp(n) · Sp(1), G2 and Spin(7). We find that the Killing-Yano equation, which arises as a condition for the invariance of the worldline action, does not always determine the torsion coupling uniquely in terms of the metric and fundamental forms. We show that there are several connections with skew-symmetric torsion for G = U(n), SU(n) and G2 that solve the invariance conditions. We describe all these compatible connections for each of the G-structures and explain the geometric nature of the couplings.

Dual-Doppler lidar observation of horizontal convective rolls and near-surface streaks

NASA Astrophysics Data System (ADS)

Iwai, Hironori; Ishii, Shoken; Tsunematsu, Nobumitsu; Mizutani, Kohei; Murayama, Yasuhiro; Itabe, Toshikazu; Yamada, Izumi; Matayoshi, Naoki; Matsushima, Dai; Weiming, Sha; Yamazaki, Takeshi; Iwasaki, Toshiki

2008-07-01

Dual-Doppler lidar and heliborne sensors were used to investigate the three-dimensional (3D) structure of the wind field over Sendai Airport in June 2007. The 3D structures of several-hundred-meter-scale horizontal convective rolls (HCRs) in the sea-breeze layer were observed by the dual-Doppler lidar. The scale of the HCRs determined by the heliborne sensors roughly agreed with that determined by the dual-Doppler lidar. Analysis of the dual-Doppler lidar data showed that the region of upward flow in the HCRs originated in near-surface low-speed streaks. This structure is consistent with the results of large-eddy simulations of the atmospheric boundary layer. The aspect ratios of the HCRs were close to those predicted by linear theories.

Microscopic observation of carrier-transport dynamics in quantum-structure solar cells using a time-of-flight technique

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

Toprasertpong, Kasidit; Fujii, Hiromasa; Sugiyama, Masakazu

2015-07-27

In this study, we propose a carrier time-of-flight technique to evaluate the carrier transport time across a quantum structure in an active region of solar cells. By observing the time-resolved photoluminescence signal with a quantum-well probe inserted under the quantum structure at forward bias, the carrier transport time can be efficiently determined at room temperature. The averaged drift velocity shows linear dependence on the internal field, allowing us to estimate the quantum structure as a quasi-bulk material with low effective mobility containing the information of carrier dynamics. We show that this direct and real-time observation is more sensitive to carriermore » transport than other conventional techniques, providing better insights into microscopic carrier transport dynamics to overcome a device design difficulty.« less

Analysis of structure of hyperfine poly(3-hydroxybutyrate) fibers (PHB) for controlled drug delivery

NASA Astrophysics Data System (ADS)

Olkhov, A. A.; Kosenko, R. Yu; Markin, V. S.; Zykova, A. K.; Pantyukhov, P. V.; Karpova, S. G.; Iordanskii, A. L.

2017-12-01

Hyperfine fibers based on biodegradable poly (3-hydroxybutyrate) with encapsulated drug substance (dipyridamol) were obtained by using electrospinning method. Addition of dipyridamol has a significant effect on geometrical shape and structure of microfibers as well as total porosity of fibrous material. Observation of fibers using scanning electron microscopy (SEM) method showed that without or at lower dipyridamol content (<3%) fibers consisted of interleaved ellipsoid and cylindrical fragments. At higher dipyridamol content (3-5%) anomalous ellipsoid structures did not practically form, and fiber’s shape became cylindrical. The totality of morphological and structural characteristics determined the rate of dipyridamol diffusive transports. The simplified model of drug desorption from fibrous matrix was presented. In current work it was showed that the rate-limiting stage of transport was the diffusion of dipyridamol in the bulk of cylindrical fibers.

Fourier Analysis and Structure Determination: Part I: Fourier Transforms.

ERIC Educational Resources Information Center

Chesick, John P.

1989-01-01

Provides a brief introduction with some definitions and properties of Fourier transforms. Shows relations, ways of understanding the mathematics, and applications. Notes proofs are not included but references are given. First of three part series. (MVL)

Ion-Beam-Induced Atomic Mixing in Ge, Si, and SiGe, Studied by Means of Isotope Multilayer Structures

PubMed Central

Radek, Manuel; Liedke, Bartosz; Schmidt, Bernd; Voelskow, Matthias; Bischoff, Lothar; Lundsgaard Hansen, John; Nylandsted Larsen, Arne; Bougeard, Dominique; Böttger, Roman; Prucnal, Slawomir; Posselt, Matthias; Bracht, Hartmut

2017-01-01

Crystalline and preamorphized isotope multilayers are utilized to investigate the dependence of ion beam mixing in silicon (Si), germanium (Ge), and silicon germanium (SiGe) on the atomic structure of the sample, temperature, ion flux, and electrical doping by the implanted ions. The magnitude of mixing is determined by secondary ion mass spectrometry. Rutherford backscattering spectrometry in channeling geometry, Raman spectroscopy, and transmission electron microscopy provide information about the structural state after ion irradiation. Different temperature regimes with characteristic mixing properties are identified. A disparity in atomic mixing of Si and Ge becomes evident while SiGe shows an intermediate behavior. Overall, atomic mixing increases with temperature, and it is stronger in the amorphous than in the crystalline state. Ion-beam-induced mixing in Ge shows no dependence on doping by the implanted ions. In contrast, a doping effect is found in Si at higher temperature. Molecular dynamics simulations clearly show that ion beam mixing in Ge is mainly determined by the thermal spike mechanism. In the case of Si thermal spike, mixing prevails at low temperature whereas ion beam-induced enhanced self-diffusion dominates the atomic mixing at high temperature. The latter process is attributed to highly mobile Si di-interstitials formed under irradiation and during damage annealing. PMID:28773172

Ion-Beam-Induced Atomic Mixing in Ge, Si, and SiGe, Studied by Means of Isotope Multilayer Structures.

PubMed

Radek, Manuel; Liedke, Bartosz; Schmidt, Bernd; Voelskow, Matthias; Bischoff, Lothar; Hansen, John Lundsgaard; Larsen, Arne Nylandsted; Bougeard, Dominique; Böttger, Roman; Prucnal, Slawomir; Posselt, Matthias; Bracht, Hartmut

2017-07-17

Crystalline and preamorphized isotope multilayers are utilized to investigate the dependence of ion beam mixing in silicon (Si), germanium (Ge), and silicon germanium (SiGe) on the atomic structure of the sample, temperature, ion flux, and electrical doping by the implanted ions. The magnitude of mixing is determined by secondary ion mass spectrometry. Rutherford backscattering spectrometry in channeling geometry, Raman spectroscopy, and transmission electron microscopy provide information about the structural state after ion irradiation. Different temperature regimes with characteristic mixing properties are identified. A disparity in atomic mixing of Si and Ge becomes evident while SiGe shows an intermediate behavior. Overall, atomic mixing increases with temperature, and it is stronger in the amorphous than in the crystalline state. Ion-beam-induced mixing in Ge shows no dependence on doping by the implanted ions. In contrast, a doping effect is found in Si at higher temperature. Molecular dynamics simulations clearly show that ion beam mixing in Ge is mainly determined by the thermal spike mechanism. In the case of Si thermal spike, mixing prevails at low temperature whereas ion beam-induced enhanced self-diffusion dominates the atomic mixing at high temperature. The latter process is attributed to highly mobile Si di-interstitials formed under irradiation and during damage annealing.

The effects of surfactant on the structure of ZnCr2O4 dendrimer like nanostructures used in degradation of Eriochrome Black T

NASA Astrophysics Data System (ADS)

Sabet, Mohammad; Jahangiri, Hasan

2018-01-01

In this experimental work, we synthesized ZnCr2O4 nano dendrimer-like structures via a simple hydrothermal method. Different parameters such as the reaction time and temperature and the surfactant kind were changed to obtain different particle sizes and morphologies. Scanning electron microscopy was utilized to obtain the products morphologies. The results showed the product is mainly composed of dendrimer-like structures. Also, it was found the mentioned parameters had significant effects on the product sizes and morphologies. Furthermore, it was found key parameters that determine the morphology of the product is surfactant type and each surfactant creates a unique morphology. The crystallinity and crystallite size were studied by x-ray diffraction pattern. Also, the composition of the product was determined by energy dispersive x-ray analysis. Diffuse reflectance spectroscopy (DRS) was used to the investigation of the optical properties of the product. The results obtained from DRS spectra showed the product has about 3.3 eV band gap. The photocatalytic activity of the product showed that ZnCr2O4 has a significant photocatalytic activity and it can decompose Eriochrome Black T about 91% under ultra violet radiation.

Structural study of some divalent aluminoborate glasses using ultrasonic and positron annihilation techniques

NASA Astrophysics Data System (ADS)

Saddeek, Yasser B.; Mohamed, Hamdy F. M.; Azooz, Moenis A.

2004-07-01

Positron annihilation lifetime (PAL), ultrasonic techniques, and differential thermal analysis (DTA) were performed to study the structure of some aluminoborate glasses. The basic compositions of these glasses are 50 B2O3 + 10 Al2O3 + 40 RO (wt%), where RO is the divalent oxide (MgO, CaO, SrO, and CdO). The ultrasonic data show that the rigidity increases from MgO to CaO then decrease at SrO and again increases at CdO. The glass transition temperature (determined from DTA) decreases from MgO to SrO then increases at CdO. The trend of the thermal properties was attributed to thermal stability. The experimental data are correlated with the internal glass structure and its connectivity. The PAL data show that an inversely correlation between the relative fractional of the open hole volume and the density of the samples. Also, there is a good correlation between the ortho-positronium (o-Ps) lifetime (open hole volume size) and the bulk modulus of the samples (determined from ultrasonic technique). The open volume hole size distribution for the samples shows that the open volume holes expand in size for CaO, SrO, MgO, and CdO, respectively with their distribution function moving to higher volume size.

Map showing structure contours on the top of the upper Jurassic Morrison Formation, Powder River basin, Wyoming and Montana

USGS Publications Warehouse

Crysdale, B.L.

1991-01-01

This map is one in a series of U.S. Geological Survey Miscellaneous Field Studies (MF) maps showing computer-generated structure contours, isopachs, and cross sections of selected formations in the Powder River basin, Wyoming and Montana. The map and cross sections were constructed from information stored in a U.S. Geological Survey Evolution of Sedimentary Basins data base. This data base contains picks of geologic formation and (or) unit tops and bases determined from electric resistivity and gamma-ray logs of 8,592 wells penetrating Tertiary and older rocks in the Powder River basin. Well completion cards (scout tickets) were reviewed and compared with copies of all logs, and formation or unit contacts determined by N. M. Denson, D.L. Macke, R. R. Schumann and others. This isopach map is based on information from 2,429 of these wells that penetrate the Minnelusa Formation and equivalents.

The State of the Summer: a Review of Child Summer Weight Gain and Efforts to Prevent It.

PubMed

Tanskey, Lindsay A; Goldberg, Jeanne; Chui, Kenneth; Must, Aviva; Sacheck, Jennifer

2018-06-01

Accumulating evidence shows that children in the USA gain weight more rapidly during the summer, when school is not in session. This narrative review spanning 2007 to 2017 summarizes efforts to characterize the problem, identify key determinants, and intervene to prevent excess summer weight gain. Summer weight gain remains a concern for elementary-age youth. Few studies have examined its determinants, but unfavorable summertime shifts in diet, physical activity, sedentary time, screen media use, and sleep have been reported. Increased structure is thought to protect against summer weight gain. Interventions to support physical activity and nutrition during the summer show promise, though large-scale impact on weight outcomes remains to be seen. Supporting health behaviors during the summer remains a priority for obesity prevention researchers, practitioners, and policymakers. Strategies to expand access to structured programs and reach beyond such programs to improve behaviors at home are of particular importance.

Determination of macro-scale soil properties from pore-scale structures: model derivation.

PubMed

Daly, K R; Roose, T

2018-01-01

In this paper, we use homogenization to derive a set of macro-scale poro-elastic equations for soils composed of rigid solid particles, air-filled pore space and a poro-elastic mixed phase. We consider the derivation in the limit of large deformation and show that by solving representative problems on the micro-scale we can parametrize the macro-scale equations. To validate the homogenization procedure, we compare the predictions of the homogenized equations with those of the full equations for a range of different geometries and material properties. We show that the results differ by [Formula: see text] for all cases considered. The success of the homogenization scheme means that it can be used to determine the macro-scale poro-elastic properties of soils from the underlying structure. Hence, it will prove a valuable tool in both characterization and optimization.

Biochemical and antimicrobial activity of phloretin and its glycosilated derivatives present in apple and kumquat.

PubMed

Barreca, Davide; Bellocco, Ersilia; Laganà, Giuseppina; Ginestra, Giovanna; Bisignano, Carlo

2014-10-01

Phloretin and its glycosylated derivatives (phlorizin and phloretin 3',5'-di-C-glucoside) are dihydrochalcones that have many interesting biological properties. The results obtained showed that the dihydrochalcones are able to inhibit growth of Gram positive bacteria, in particular Staphylococcus aureus ATCC 6538, Listeria monocytogenes ATCC 13932 and methicillin-resistant S. aureus clinical strains. Moreover, phloretin is active also against the Gram negative bacteria Salmonella typhimurium ATCC 13311. The determination of the enzymatic activity of key metabolic enzymes allowed us to shed some light on the biochemical mechanism of aglycon cell growth inhibition, showing as it remarkably influences the energetic metabolism of S. aureus. In addition, structure/activity determinations highlighted that the presence of a glycosyl moiety bound to the chalcone structure dramatically decreases the antimicrobial activity of phloretin. Copyright © 2014 Elsevier Ltd. All rights reserved.

Dynamic Behavior of Engineered Lattice Materials

PubMed Central

Hawreliak, J. A.; Lind, J.; Maddox, B.; Barham, M.; Messner, M.; Barton, N.; Jensen, B. J.; Kumar, M.

2016-01-01

Additive manufacturing (AM) is enabling the fabrication of materials with engineered lattice structures at the micron scale. These mesoscopic structures fall between the length scale associated with the organization of atoms and the scale at which macroscopic structures are constructed. Dynamic compression experiments were performed to study the emergence of behavior owing to the lattice periodicity in AM materials on length scales that approach a single unit cell. For the lattice structures, both bend and stretch dominated, elastic deflection of the structure was observed ahead of the compaction of the lattice, while no elastic deformation was observed to precede the compaction in a stochastic, random structure. The material showed lattice characteristics in the elastic response of the material, while the compaction was consistent with a model for compression of porous media. The experimental observations made on arrays of 4 × 4 × 6 lattice unit cells show excellent agreement with elastic wave velocity calculations for an infinite periodic lattice, as determined by Bloch wave analysis, and finite element simulations. PMID:27321697

Orthorhombic Zr2Co11 phase revisited

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

Li, X. -Z.; Zhang, W. Y.; Sellmyer, D. J.

2014-10-01

The structure of the orthorhombic Zr2Co11 phase was revisited in the present work. Selected-area electron diffraction (SAED) and high-resolution electron microscopy (HREM) techniques were used to investigate the structure. They show the orthorhombic Zr2Co11 phase has a 1-D incommensurate modulated structure. The structure can be approximately described as a B-centered orthorhombic lattice. The lattice parameters of the orthorhombic Zr2Co11 phase have been determined by a tilt series of SAED patterns. A hexagonal network with a modulation wave has been observed in the HREM image and the hexagonal motif is considered as the basic structural unit.

Effect of edge pruning on structural controllability and observability of complex networks

PubMed Central

Mengiste, Simachew Abebe; Aertsen, Ad; Kumar, Arvind

2015-01-01

Controllability and observability of complex systems are vital concepts in many fields of science. The network structure of the system plays a crucial role in determining its controllability and observability. Because most naturally occurring complex systems show dynamic changes in their network connectivity, it is important to understand how perturbations in the connectivity affect the controllability of the system. To this end, we studied the control structure of different types of artificial, social and biological neuronal networks (BNN) as their connections were progressively pruned using four different pruning strategies. We show that the BNNs are more similar to scale-free networks than to small-world networks, when comparing the robustness of their control structure to structural perturbations. We introduce a new graph descriptor, ‘the cardinality curve’, to quantify the robustness of the control structure of a network to progressive edge pruning. Knowing the susceptibility of control structures to different pruning methods could help design strategies to destroy the control structures of dangerous networks such as epidemic networks. On the other hand, it could help make useful networks more resistant to edge attacks. PMID:26674854

Crystal structure studies of NADP{sup +} dependent isocitrate dehydrogenase from Thermus thermophilus exhibiting a novel terminal domain

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

Kumar, S.M.; Pampa, K.J.; Manjula, M.

2014-06-20

Highlights: • We determined the structure of isocitrate dehydrogenase with citrate and cofactor. • The structure reveals a unique novel terminal domain involved in dimerization. • Clasp domain shows significant difference, and catalytic residues are conserved. • Oligomerization of the enzyme is quantized with subunit-subunit interactions. • Novel domain of this enzyme is classified as subfamily of the type IV. - Abstract: NADP{sup +} dependent isocitrate dehydrogenase (IDH) is an enzyme catalyzing oxidative decarboxylation of isocitrate into oxalosuccinate (intermediate) and finally the product α-ketoglutarate. The crystal structure of Thermus thermophilus isocitrate dehydrogenase (TtIDH) ternary complex with citrate and cofactor NADP{supmore » +} was determined using X-ray diffraction method to a resolution of 1.80 Å. The overall fold of this protein was resolved into large domain, small domain and a clasp domain. The monomeric structure reveals a novel terminal domain involved in dimerization, very unique and novel domain when compared to other IDH’s. And, small domain and clasp domain showing significant differences when compared to other IDH’s of the same sub-family. The structure of TtIDH reveals the absence of helix at the clasp domain, which is mainly involved in oligomerization in other IDH’s. Also, helices/beta sheets are absent in the small domain, when compared to other IDH’s of the same sub family. The overall TtIDH structure exhibits closed conformation with catalytic triad residues, Tyr144-Asp248-Lys191 are conserved. Oligomerization of the protein is quantized using interface area and subunit–subunit interactions between protomers. Overall, the TtIDH structure with novel terminal domain may be categorized as a first structure of subfamily of type IV.« less

CHROMOSOMAL DIFFERENTIATIONS OF THE LAMPBRUSH TYPE FORMED BY THE Y CHROMOSOME IN DROSOPHILA HYDEI AND DROSOPHILA NEOHYDEI

PubMed Central

Hess, Oswald; Meyer, Günther F.

1963-01-01

The nuclei of growing spermatocytes in Drosophila hydei and D. neohydei are characterized by the appearance of phase-specific, paired, loop-shaped structures thought to be similar to the loops in lampbrush chromosomes of amphibian oocytes. In X/O-males of D. hydei spermatogenesis is completely blocked before the first maturation division. No spermatozoa are formed in such testes. In the nuclei of X/O-spermatocytes, paired loop formations are absent. This shows the dependence of these chromosomal functional structures upon the Y chromosome. The basis of this dependence could be shown through an investigation of males with two Y chromosomes. All loop pairs are present in duplicate in XYY males. This proves that the intranuclear formations are structural modifications of the Y chromosome itself. These functional structures are species-specific and characteristically different in Drosophila hydei and D. neohydei. Reciprocal species crosses and a backcross showed that the spermatocyte nuclei of all hybrid males possess the functional structures corresponding to the species which donated the Y chromosome. This shows that the morphological character of the functional structures is also determined by the Y chromosome. PMID:13954225

Boron/aluminum graphite/resin advanced fiber composite hybrids

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Lark, R. F.; Sullivan, T. L.

1975-01-01

Fabrication feasibility and potential of an adhesively bonded metal and resin matrix fiber-composite hybrid are determined as an advanced material for aerospace and other structural applications. The results show that using this hybrid concept makes possible a composite design which, when compared with nonhybrid composites, has greater transverse strength, transverse stiffness, and impact resistance with only a small penalty on density and longitudinal properties. The results also show that laminate theory is suitable for predicting the structural response of such hybrids. The sequence of fracture modes indicates that these types of hybrids can be readily designed to meet fail-safe requirements.

SVD-aided pseudo principal-component analysis: A new method to speed up and improve determination of the optimum kinetic model from time-resolved data

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

Oang, Key Young; Yang, Cheolhee; Muniyappan, Srinivasan

Determination of the optimum kinetic model is an essential prerequisite for characterizing dynamics and mechanism of a reaction. Here, we propose a simple method, termed as singular value decomposition-aided pseudo principal-component analysis (SAPPA), to facilitate determination of the optimum kinetic model from time-resolved data by bypassing any need to examine candidate kinetic models. We demonstrate the wide applicability of SAPPA by examining three different sets of experimental time-resolved data and show that SAPPA can efficiently determine the optimum kinetic model. In addition, the results of SAPPA for both time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) data of themore » same protein reveal that global structural changes of protein, which is probed by TRXSS, may occur more slowly than local structural changes around the chromophore, which is probed by TA spectroscopy.« less

Ultraviolet Imaging Telescope ultraviolet images - Large-scale structure, H II regions, and extinction in M81

NASA Technical Reports Server (NTRS)

Hill, Jesse K.; Bohlin, Ralph C.; Cheng, Kwang-Ping; Hintzen, Paul M. N.; Landsman, Wayne B.; Neff, Susan G.; O'Connell, Robert W.; Roberts, Morton S.; Smith, Andrew M.; Smith, Eric P.

1992-01-01

The study employs UV images of M81 obtained by the Ultraviolet Imaging Telescope (UIT) during the December 1990 Astro-1 spacelab mission to determine 2490- and 1520-A fluxes from 46 H II regions and global surface brightness profiles. Comparison photometry in the V band is obtained from a ground-based CCD image. UV radial profiles show bulge and exponential disk components, with a local decrease in disk surface brightness inside the inner Lindblad Resonance about 4 arcmin from the nucleus. The V profile shows typical bulge plus exponential disk structure, with no local maximum in the disk. There is little change of UV color across the disk, although there is a strong gradient in the bulge. Observed m152-V colors of the H II regions are consistent with model spectra for young clusters, after dereddening using Av determined from m249-V and the Galactic extinction curve. The value of Av, so determined, is 0.4 mag greater on the average than Av derived from radio continuum and H-alpha fluxes.

ARPES investigations of parent compounds of 122 Fe-based superconductors and their 3d transition metal cousins

NASA Astrophysics Data System (ADS)

Richard, Pierre; Zhang, W.-L.; Wu, S.-F.; van Roekeghem, A.; Zhang, P.; Miao, H.; Qian, T.; Nie, S.-M.; Chen, G.-F.; Ding, H.; Xu, N.; Biermann, S.; Capan, C.; Fisk, Z.; Saparov, B. I.; Sefat, A. S.

2015-03-01

It is widely believed that the key ingredients for high-temperature superconductivity are already present in the non-superconducting parent compounds. With its ability to probe the single-particle electronic structure directly in the momentum space, ARPES is a very powerful tool to determine which parameters of the electronic structure are possibly relevant for promoting superconductivity. Here we report ARPES studies on the parent compounds of the 122 family of Fe-based superconductors and their 3 d transition metal pnictide cousins. In particular, we show that the Fe-compound exhibits the largest electronic correlations, possibly a determining factor for unconventional superconductivity.

Detecting determinism from point processes.

PubMed

Andrzejak, Ralph G; Mormann, Florian; Kreuz, Thomas

2014-12-01

The detection of a nonrandom structure from experimental data can be crucial for the classification, understanding, and interpretation of the generating process. We here introduce a rank-based nonlinear predictability score to detect determinism from point process data. Thanks to its modular nature, this approach can be adapted to whatever signature in the data one considers indicative of deterministic structure. After validating our approach using point process signals from deterministic and stochastic model dynamics, we show an application to neuronal spike trains recorded in the brain of an epilepsy patient. While we illustrate our approach in the context of temporal point processes, it can be readily applied to spatial point processes as well.

Identification and classification of cathinone unknowns by statistical analysis processing of direct analysis in real time-high resolution mass spectrometry-derived "neutral loss" spectra.

PubMed

Fowble, Kristen L; Shepard, Jason R E; Musah, Rabi A

2018-03-01

An approach to the rapid determination of the structures of novel synthetic cathinone designer drugs, also known as bath salts, is reported. While cathinones fragment so extensively by electron impact mass spectrometry that their mass spectra often cannot be used to identify the structure, collision-induced dissociation (CID) direct analysis in real time-high resolution mass spectrometry (DART-HRMS) experiments furnished spectra that provided diagnostic fragmentation patterns for the analyzed cathinones. From this data, neutral loss spectra, which reflect the presence of specific chemical moieties, could be acquired. These spectra showed striking similarities between cathinones sharing structural features such as pyrrolidine rings and methylenedioxy moieties. Principle component analysis (PCA) of the neutral loss spectra of nine synthetic cathinones of various types including ethcathinones, those containing a methylenedioxy moiety appended to the benzene ring, and pyrrolidine-containing structures, illustrated that cathinones falling within the same class clustered together and could be distinguished from those of other classes. Furthermore, hierarchical clustering analysis of the neutral loss data of a model set derived from 44 synthetic cathinones, furnished a dendrogram in which structurally similar cathinones clustered together. The ability of this model system to facilitate structure determination was tested using 4-fluoroethcathinone, 3,4-methylenedioxy-α-pyrrolidinohexanophenone (MDPHP), and ethylone, which fall into the ethcathinone, pyrrolidine-containing, and methylenedioxy-containing subclasses respectively. The results showed that their neutral loss spectra correctly fell within the ethcathinone, pyrrolidine-containing and methylenedioxy-containing cathinone clades of the dendrogram, and that the neutral loss information could be used to infer the structures of these compounds. The analysis and data processing steps are rapid and samples can be analyzed in their native form without any sample processing steps. The robustness of the dendrogram dataset can be readily increased by continued addition of newly discovered structures. The approach can be broadly applied to structure determination of unknowns, and would be particularly useful for analyses where sample amounts are limited. Copyright © 2017 Elsevier B.V. All rights reserved.

High-throughput crystallization screening.

PubMed

Skarina, Tatiana; Xu, Xiaohui; Evdokimova, Elena; Savchenko, Alexei

2014-01-01

Protein structure determination by X-ray crystallography is dependent on obtaining a single protein crystal suitable for diffraction data collection. Due to this requirement, protein crystallization represents a key step in protein structure determination. The conditions for protein crystallization have to be determined empirically for each protein, making this step also a bottleneck in the structure determination process. Typical protein crystallization practice involves parallel setup and monitoring of a considerable number of individual protein crystallization experiments (also called crystallization trials). In these trials the aliquots of purified protein are mixed with a range of solutions composed of a precipitating agent, buffer, and sometimes an additive that have been previously successful in prompting protein crystallization. The individual chemical conditions in which a particular protein shows signs of crystallization are used as a starting point for further crystallization experiments. The goal is optimizing the formation of individual protein crystals of sufficient size and quality to make them suitable for diffraction data collection. Thus the composition of the primary crystallization screen is critical for successful crystallization.Systematic analysis of crystallization experiments carried out on several hundred proteins as part of large-scale structural genomics efforts allowed the optimization of the protein crystallization protocol and identification of a minimal set of 96 crystallization solutions (the "TRAP" screen) that, in our experience, led to crystallization of the maximum number of proteins.

Production, Purification and Preliminary X-ray Crystallographic Studies of Adeno-Associated Virus Serotype 9

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

Mitchell, M.; Nam, H; Carter, A

2009-01-01

Adeno-associated virus (AAV) serotype 9, which is under development for gene-delivery applications, shows significantly enhanced capsid-associated transduction efficiency in muscle compared with other AAV serotypes. With the aim of characterizing the structural determinants of this property, the purification, crystallization and preliminary X-ray crystallographic analyses of the AAV9 viral capsid are reported. The crystals diffracted X-rays to 2.8 A resolution using synchrotron radiation and belonged to the trigonal space group P32, with unit-cell parameters a = b = 251.0, c = 640.0 A. There are three complete viral capsids in the crystal unit cell. The orientation and position of the asymmetricmore » unit capsid have been determined by molecular-replacement methods and structure determination is in progress.« less

Polyamides based on the renewable monomer, 1,13-tridecane diamine I: synthesis and characterization of nylon 13,T

DOE PAGES

He, Jie; Samanta, Satyabrata; Selvakumar, Sermadurai; ...

2013-06-01

Nylon 13,T was successfully synthesized and chemical composition, thermal properties, crystal structure, and moisture absorption characterized. Melting temperature and glass transition temperature were determined to be 263 °C and 90 °C, respectively, while the equilibrium melting temperature was determined to be 289 °C. Characterization of the crystallization kinetics showed that nylon 13,T exhibits very fast crystallization compared to the industrially important nylons, nylon 6 and nylon 6,6. In addition, the moisture absorption of nylon 13,T was dramatically lower than nylon 6 and nylon 6,6 which is consistent with the much lower amide content of nylon 13,T. The crystal structure wasmore » determined to be pseudohexagonal.« less

Structural Identifiability of Dynamic Systems Biology Models

PubMed Central

Villaverde, Alejandro F.

2016-01-01

A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas. PMID:27792726

Three-dimensional Structure of Saccharomyces Invertase

PubMed Central

Sainz-Polo, M. Angela; Ramírez-Escudero, Mercedes; Lafraya, Alvaro; González, Beatriz; Marín-Navarro, Julia; Polaina, Julio; Sanz-Aparicio, Julia

2013-01-01

Invertase is an enzyme that is widely distributed among plants and microorganisms and that catalyzes the hydrolysis of the disaccharide sucrose into glucose and fructose. Despite the important physiological role of Saccharomyces invertase (SInv) and the historical relevance of this enzyme as a model in early biochemical studies, its structure had not yet been solved. We report here the crystal structure of recombinant SInv at 3.3 Å resolution showing that the enzyme folds into the catalytic β-propeller and β-sandwich domains characteristic of GH32 enzymes. However, SInv displays an unusual quaternary structure. Monomers associate in two different kinds of dimers, which are in turn assembled into an octamer, best described as a tetramer of dimers. Dimerization plays a determinant role in substrate specificity because this assembly sets steric constraints that limit the access to the active site of oligosaccharides of more than four units. Comparative analysis of GH32 enzymes showed that formation of the SInv octamer occurs through a β-sheet extension that seems unique to this enzyme. Interaction between dimers is determined by a short amino acid sequence at the beginning of the β-sandwich domain. Our results highlight the role of the non-catalytic domain in fine-tuning substrate specificity and thus supplement our knowledge of the activity of this important family of enzymes. In turn, this gives a deeper insight into the structural features that rule modularity and protein-carbohydrate recognition. PMID:23430743

Application of far-infrared spectroscopy to the structural identification of protein materials.

PubMed

Han, Yanchen; Ling, Shengjie; Qi, Zeming; Shao, Zhengzhong; Chen, Xin

2018-05-03

Although far-infrared (IR) spectroscopy has been shown to be a powerful tool to determine peptide structure and to detect structural transitions in peptides, it has been overlooked in the characterization of proteins. Herein, we used far-IR spectroscopy to monitor the structure of four abundant non-bioactive proteins, namely, soybean protein isolate (SPI), pea protein isolate (PPI) and two types of silk fibroins (SFs), domestic Bombyx mori and wild Antheraea pernyi. The two globular proteins SPI and PPI result in broad and weak far-IR bands (between 50 and 700 cm-1), in agreement with those of some other bioactive globular proteins previously studied (lysozyme, myoglobin, hemoglobin, etc.) that generally only have random amino acid sequences. Interestingly, the two SFs, which are characterized by a structure composed of highly repetitive motifs, show several sharp far-IR characteristic absorption peaks. Moreover, some of these characteristic peaks (such as the peaks at 260 and 428 cm-1 in B. mori, and the peaks at 245 and 448 cm-1 in A. pernyi) are sensitive to conformational changes; hence, they can be directly used to monitor conformational transitions in SFs. Furthermore, since SF absorption bands clearly differ from those of globular proteins and different SFs even show distinct adsorption bands, far-IR spectroscopy can be applied to distinguish and determine the specific SF component within protein blends.

Outsourcing versus in-house maintenance of medical devices: a longitudinal, empirical study.

PubMed

Miguel-Cruz, Antonio; Rios-Rincón, Adriana; Haugan, Gregory L

2014-03-01

To determine what factors have a significant influence on the performance of medical device maintenance outsourcing, and to determine how the performance of external governance structures differs depending on whether a hospital is private or public. This was a longitudinal study of 590 maintenance transactions at 20 hospitals in Bogotá, Colombia, involving 764 medical devices and 72 maintenance service providers. Maintenance performance data (i.e., turn-around time in hours; TAT) for the service providers (either in-house or outsourced) were primarily collected over a 20-month period, from December 2009-August 2011, by means of a monitoring procedure; then, a hazards model was run. The availability of specific repair parts, in-stock, in the city in which the medical devices were located, had a positive impact on the performance of both internal and external governance structures. Online service also had a positive impact on both, with a stronger positive impact on the performance of internal governance than on that of external governance. For transactions governed by external structures, better performance was seen in private hospitals than in public ones. In public health institutions, internal governance showed better performance than external governance. Both internal and external governance structures showed better performance in private healthcare institutions than in public ones. In public health institutions, internal governance shows better performance than external governance; this suggests that healthcare managers should reconsider the trend to eliminate in-house maintenance service staff in public healthcare institutions.

Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska.

PubMed

Kim, Hye Min; Jung, Ji Young; Yergeau, Etienne; Hwang, Chung Yeon; Hinzman, Larry; Nam, Sungjin; Hong, Soon Gyu; Kim, Ok-Sun; Chun, Jongsik; Lee, Yoo Kyung

2014-08-01

The subarctic region is highly responsive and vulnerable to climate change. Understanding the structure of subarctic soil microbial communities is essential for predicting the response of the subarctic soil environment to climate change. To determine the composition of the bacterial community and its relationship with soil properties, we investigated the bacterial community structure and properties of surface soil from the moist acidic tussock tundra in Council, Alaska. We collected 70 soil samples with 25-m intervals between sampling points from 0-10 cm to 10-20 cm depths. The bacterial community was analyzed by pyrosequencing of 16S rRNA genes, and the following soil properties were analyzed: soil moisture content (MC), pH, total carbon (TC), total nitrogen (TN), and inorganic nitrogen (NH4+ and NO3-). The community compositions of the two different depths showed that Alphaproteobacteria decreased with soil depth. Among the soil properties measured, soil pH was the most significant factor correlating with bacterial community in both upper and lower-layer soils. Bacterial community similarity based on jackknifed unweighted unifrac distance showed greater similarity across horizontal layers than through the vertical depth. This study showed that soil depth and pH were the most important soil properties determining bacterial community structure of the subarctic tundra soil in Council, Alaska. © 2014 The Authors. FEMS Microbiology Ecology published by John Wiley & Sons Ltd on behalf of the Federation of European Microbiological Societies.

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

PubMed Central

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

2015-01-01

Adeno-associated virus (AAV) is the only eukaryotic virus with the property of establishing latency by integrating site-specifically into the human genome. The integration site known as AAVS1 is located in chromosome 19 and contains multiple GCTC repeats that are recognized by the AAV non-structural Rep proteins. These proteins are multifunctional, with an N-terminal origin-binding domain (OBD) and a helicase domain joined together by a short linker. As a first step to understand the process of site-specific integration, we proceeded to characterize the recognition and assembly of Rep68 onto the AAVS1 site. We first determined the x-ray structure of AAV-2 Rep68 OBD in complex with the AAVS1 DNA site. Specificity is achieved through the interaction of a glycine-rich loop that binds the major groove and an α-helix that interacts with a downstream minor groove on the same face of the DNA. Although the structure shows a complex with three OBD molecules bound to the AAVS1 site, we show by using analytical centrifugation and electron microscopy that the full-length Rep68 forms a heptameric complex. Moreover, we determined that a minimum of two direct repeats is required to form a stable complex and to melt DNA. Finally, we show that although the individual domains bind DNA poorly, complex assembly requires oligomerization and cooperation between its OBD, helicase, and the linker domains. PMID:26370092

FP-LAPW investigation of Al3(Sc1‑xTix) alloys properties in L12 and D022 structures

NASA Astrophysics Data System (ADS)

Khenioui, Youcef; Boulechfar, Rahima; Maazi, Noureddine; Ghemid, Sebti

2018-06-01

The ab-initio calculations based on the density functional theory (DFT) have been performed to study the structural, mechanical, electronic, thermal and thermodynamic properties of Al3Sc and Al3Ti binary compounds and their ternary mixture Al3(Sc1‑xTix) in L12 and D022 structures. The total energy calculations show that the L12 structure is the more stable one. The Al3Sc0.25Ti0.75 undergoes a martensitic transformation and the formation enthalpies and the lattice parameters decrease with increasing concentration x. The elastic constants are determined and the results show that all compounds are mechanically stable and the cubic cells are more easily deformed by shearing than by unidirectional compression. The elastic modulus indicates that the addition of Ti atoms to Al3Sc improves its ductility. The densities of states (DOSs) calculations show the strong spd hybridization which leads to the formation of a pseudo-gap near the Fermi level in ternary alloys. The densities of states at the Fermi level N(EF) confirm the phase stability. The quasi-harmonic Debye model is used to predict the thermal properties such as heat capacity, Debye temperature, Grüneisen parameter and thermal expansion coefficient of the considered alloys. The determination of Gibbs free mixing energy at different concentrations has been used to calculate the T-x diagram.

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

Linaburg, Matthew R.; McClure, Eric T.; Majher, Jackson D.

The structures of the lead halide perovskites CsPbCl3 and CsPbBr3 have been determined from X-ray powder diffraction data to be orthorhombic with Pnma space group symmetry. Their structures are distorted from the cubic structure of their hybrid analogs, CH3NH3PbX3 (X = Cl, Br), by tilts of the octahedra (Glazer tilt system a–b+a–). Substitution of the smaller Rb+ for Cs+ increases the octahedral tilting distortion and eventually destabilizes the perovskite structure altogether. To understand this behavior, bond valence parameters appropriate for use in chloride and bromide perovskites have been determined for Cs+, Rb+, and Pb2+. As the tolerance factor decreases, themore » band gap increases, by 0.15 eV in Cs1–xRbxPbCl3 and 0.20 eV in Cs1–xRbxPbBr3, upon going from x = 0 to x = 0.6. The band gap shows a linear dependence on tolerance factor, particularly for the Cs1–xRbxPbBr3 system. Comparison with the cubic perovskites CH3NH3PbCl3 and CH3NH3PbBr3 shows that the band gaps of the methylammonium perovskites are anomalously large for APbX3 perovskites with a cubic structure. This comparison suggests that the local symmetry of CH3NH3PbCl3 and CH3NH3PbBr3 deviate significantly from the cubic symmetry of the average structure.« less

Determination of uranyl incorporation into biogenic manganese oxides using X-ray absorption spectroscopy and scattering

USGS Publications Warehouse

Webb, S.M.; Fuller, C.C.; Tebo, B.M.; Bargar, J.R.

2006-01-01

Biogenic manganese oxides are common and an important source of reactive mineral surfaces in the environment that may be potentially enhanced in bioremediation cases to improve natural attenuation. Experiments were performed in which the uranyl ion, UO22+ (U(VI)), at various concentrations was present during manganese oxide biogenesis. At all concentrations, there was strong uptake of U onto the oxides. Synchrotron-based extended X-ray absorption fine structure (EXAFS) spectroscopy and X-ray diffraction (XRD) studies were carried out to determine the molecular-scale mechanism by which uranyl is incorporated into the oxide and how this incorporation affects the resulting manganese oxide structure and mineralogy. The EXAFS experiments show that at low concentrations (2 mol % U, >4 ??M U(VI) in solution), the presence of U(VI) affects the stability and structure of the Mn oxide to form poorly ordered Mn oxide tunnel structures, similar to todorokite. EXAFS modeling shows that uranyl is present in these oxides predominantly in the tunnels of the Mn oxide structure in a tridentate complex. Observations by XRD corroborate these results. Structural incorporation may lead to more stable U(VI) sequestration that may be suitable for remediation uses. These observations, combined with the very high uptake capacity of the Mn oxides, imply that Mn-oxidizing bacteria may significantly influence dissolved U(VI) concentrations in impacted waters via sorption and incorporation into Mn oxide biominerals. ?? 2006 American Chemical Society.

Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: close structural resemblance to E. coli pantothenate kinase.

PubMed

Li de La Sierra-Gallay, Ines; Collinet, Bruno; Graille, Marc; Quevillon-Cheruel, Sophie; Liger, Dominique; Minard, Philippe; Blondeau, Karine; Henckes, Gilles; Aufrère, Robert; Leulliot, Nicolas; Zhou, Cong-Zhao; Sorel, Isabelle; Ferrer, Jean-Luc; Poupon, Anne; Janin, Joël; van Tilbeurgh, Herman

2004-03-01

The protein product of the YGR205w gene of Saccharomyces cerevisiae was targeted as part of our yeast structural genomics project. YGR205w codes for a small (290 amino acids) protein with unknown structure and function. The only recognizable sequence feature is the presence of a Walker A motif (P loop) indicating a possible nucleotide binding/converting function. We determined the three-dimensional crystal structure of Se-methionine substituted protein using multiple anomalous diffraction. The structure revealed a well known mononucleotide fold and strong resemblance to the structure of small metabolite phosphorylating enzymes such as pantothenate and phosphoribulo kinase. Biochemical experiments show that YGR205w binds specifically ATP and, less tightly, ADP. The structure also revealed the presence of two bound sulphate ions, occupying opposite niches in a canyon that corresponds to the active site of the protein. One sulphate is bound to the P-loop in a position that corresponds to the position of beta-phosphate in mononucleotide protein ATP complex, suggesting the protein is indeed a kinase. The nature of the phosphate accepting substrate remains to be determined. Copyright 2004 Wiley-Liss, Inc.

Determination of the X-ray structure of the snake venom protein omwaprin by total chemical synthesis and racemic protein crystallography.

PubMed

Banigan, James R; Mandal, Kalyaneswar; Sawaya, Michael R; Thammavongsa, Vilasak; Hendrickx, Antoni P A; Schneewind, Olaf; Yeates, Todd O; Kent, Stephen B H

2010-10-01

The 50-residue snake venom protein L-omwaprin and its enantiomer D-omwaprin were prepared by total chemical synthesis. Radial diffusion assays were performed against Bacillus megaterium and Bacillus anthracis; both L- and D-omwaprin showed antibacterial activity against B. megaterium. The native protein enantiomer, made of L-amino acids, failed to crystallize readily. However, when a racemic mixture containing equal amounts of L- and D-omwaprin was used, diffraction quality crystals were obtained. The racemic protein sample crystallized in the centrosymmetric space group P2(1)/c and its structure was determined at atomic resolution (1.33 A) by a combination of Patterson and direct methods based on the strong scattering from the sulfur atoms in the eight cysteine residues per protein. Racemic crystallography once again proved to be a valuable method for obtaining crystals of recalcitrant proteins and for determining high-resolution X-ray structures by direct methods.

NMR determination of an incommensurate helical antiferromagnetic structure in EuCo 2 As 2

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

Ding, Q. -P.; Higa, N.; Sangeetha, N. S.

In this paper, we report 153Eu, 75As, and 59Co nuclear magnetic resonance (NMR) results on EuCo 2As 2 single crystal. Observations of 153Eu and 75As NMR spectra in zero magnetic field at 4.3 K below an antiferromagnetic (AFM) ordering temperature T N = 45 K and its external magnetic field dependence clearly evidence an incommensurate helical AFM structure in EuCo 2As 2. Furthermore, based on 59Co NMR data in both the paramagnetic and the incommensurate AFM states, we have determined the model-independent value of the AFM propagation vector k = (0,0,0.73 ± 0.07)2π/c, where c is the c lattice parameter.more » Finally, the incommensurate helical AFM state was characterized by only NMR data with model-independent analyses, showing NMR to be a unique tool for determination of the spin structure in incommensurate helical AFMs.« less

NMR determination of an incommensurate helical antiferromagnetic structure in EuCo 2 As 2

DOE PAGES

Ding, Q. -P.; Higa, N.; Sangeetha, N. S.; ...

2017-05-05

In this paper, we report 153Eu, 75As, and 59Co nuclear magnetic resonance (NMR) results on EuCo 2As 2 single crystal. Observations of 153Eu and 75As NMR spectra in zero magnetic field at 4.3 K below an antiferromagnetic (AFM) ordering temperature T N = 45 K and its external magnetic field dependence clearly evidence an incommensurate helical AFM structure in EuCo 2As 2. Furthermore, based on 59Co NMR data in both the paramagnetic and the incommensurate AFM states, we have determined the model-independent value of the AFM propagation vector k = (0,0,0.73 ± 0.07)2π/c, where c is the c lattice parameter.more » Finally, the incommensurate helical AFM state was characterized by only NMR data with model-independent analyses, showing NMR to be a unique tool for determination of the spin structure in incommensurate helical AFMs.« less

Structure dependent antioxidant capacity of phlorotannins from Icelandic Fucus vesiculosus by UHPLC-DAD-ECD-QTOFMS.

PubMed

Hermund, Ditte B; Plaza, Merichel; Turner, Charlotta; Jónsdóttir, Rosa; Kristinsson, Hordur G; Jacobsen, Charlotte; Nielsen, Kristian Fog

2018-02-01

Brown algae are rich in polyphenolic compounds, phlorotannins, which have been found to possess high in vitro antioxidant capacity, especially DPPH radical scavenging activity, due to the high number of hydroxyl groups. Whereas, the overall antioxidant capacity of brown algae extracts has been widely studied, the antioxidant capacity of individual phlorotannins has been rarely explored. The aim of this study was to determine the structure dependant antioxidant capacity of phlorotannins from Icelandic brown algae, Fucus vesiculosus. The antioxidant capacity of individual phlorotannins was determined by an on-line method using liquid chromatography and an electrochemical detector followed by quadrupole Time of Flight mass spectrometry (UHPLC-DAD-ECD-QTOFMS). Tentative structural elucidation of 13 phlorotannin isomers from EAF was obtained by LC-DAD-QTOFMS, ranging from 374 to 870Da. On-line determination of antioxidant capacity of the individual phlorotannins generally showed that low molecular phlorotannins exhibited higher antioxidant capacity and that the capacity decreased with polymerisation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Conformational Aspects of the O-acetylation of C-tetra(phenyl)calixpyrogallol[4]arene.

PubMed

Casas-Hinestroza, José Luis; Maldonado, Mauricio

2018-05-20

Reaction between pyrogallol and benzaldehyde results in a conformational mixture of C- tetra(phenyl)pyrogallol[4]arene (crown and chair). The conformer mixture was separated using crystallization procedures and the structures were determined using FTIR, ¹H-NMR, and 13 C-NMR. O -acetylation of C- tetra(phenyl)pyrogallol[4]arene (chair) with acetic anhydride, in pyridine results in the formation of dodecaacetyl-tetra(phenyl)pyrogallol[4]arene. The structure was determined using ¹H-NMR and 13 C-NMR finding that the product maintains the conformation of the starting conformer. On the other hand, the O -acetylation reaction of C- tetra(phenyl)pirogallol[4]arene (crown) under same conditions proceeded efficiently, and its structure was determined using ¹H-NMR and 13 C-NMR. Dynamic ¹H-NMR of acetylated pyrogallolarene was studied by means of variable temperature in DMSO- d ₆ solution, and it revealed that two conformers are formed in the solution. Boat conformations for acetylated pyrogallolarene showed a slow interconversion at room temperature.

Assembly Kinetics Determine the Architecture of α-actinin Crosslinked F-actin Networks

PubMed Central

Falzone, Tobias T.; Lenz, Martin; Kovar, David R.; Gardel, Margaret L.

2013-01-01

The actin cytoskeleton is organized into diverse meshworks and bundles that support many aspects of cell physiology. Understanding the self-assembly of these actin-based structures is essential for developing predictive models of cytoskeletal organization. Here we show that the competing kinetics of bundle formation with the onset of dynamic arrest arising from filament entanglements and cross-linking determine the architecture of reconstituted actin networks formed with α-actinin cross-links. Cross-link mediated bundle formation only occurs in dilute solutions of highly mobile actin filaments. As actin polymerization proceeds, filament mobility and bundle formation are arrested concomitantly. By controlling the onset of dynamic arrest, perturbations to actin assembly kinetics dramatically alter the architecture of biochemically identical samples. Thus, the morphology of reconstituted F-actin networks is a kinetically determined structure similar to those formed by physical gels and glasses. These results establish mechanisms controlling the structure and mechanics in diverse semi-flexible biopolymer networks. PMID:22643888

Quantum imaging with incoherently scattered light from a free-electron laser

NASA Astrophysics Data System (ADS)

Schneider, Raimund; Mehringer, Thomas; Mercurio, Giuseppe; Wenthaus, Lukas; Classen, Anton; Brenner, Günter; Gorobtsov, Oleg; Benz, Adrian; Bhatti, Daniel; Bocklage, Lars; Fischer, Birgit; Lazarev, Sergey; Obukhov, Yuri; Schlage, Kai; Skopintsev, Petr; Wagner, Jochen; Waldmann, Felix; Willing, Svenja; Zaluzhnyy, Ivan; Wurth, Wilfried; Vartanyants, Ivan A.; Röhlsberger, Ralf; von Zanthier, Joachim

2018-02-01

The advent of accelerator-driven free-electron lasers (FEL) has opened new avenues for high-resolution structure determination via diffraction methods that go far beyond conventional X-ray crystallography methods. These techniques rely on coherent scattering processes that require the maintenance of first-order coherence of the radiation field throughout the imaging procedure. Here we show that higher-order degrees of coherence, displayed in the intensity correlations of incoherently scattered X-rays from an FEL, can be used to image two-dimensional objects with a spatial resolution close to or even below the Abbe limit. This constitutes a new approach towards structure determination based on incoherent processes, including fluorescence emission or wavefront distortions, generally considered detrimental for imaging applications. Our method is an extension of the landmark intensity correlation measurements of Hanbury Brown and Twiss to higher than second order, paving the way towards determination of structure and dynamics of matter in regimes where coherent imaging methods have intrinsic limitations.

Development and testing of improved polyimide actuator rod seals at higher temperatures for use in advanced aircraft hydraulic systems

NASA Technical Reports Server (NTRS)

Robinson, E. D.; Waterman, A. W.; Nelson, W. G.

1972-01-01

Polyimide second stage rod seals were evaluated to determine their suitability for application in advanced aircraft systems. The configurations of the seals are described. The conditions of the life cycle tests are provided. It was determined that external rod seal leakage was within prescribed limits and that the seals showed no signs of structural degradation.

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

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

Biedermannová, Lada, E-mail: lada.biedermannova@ibt.cas.cz; Schneider, Bohdan

2015-10-27

The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. Themore » results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.« less

Visual Depth from Motion Parallax and Eye Pursuit

PubMed Central

Stroyan, Keith; Nawrot, Mark

2012-01-01

A translating observer viewing a rigid environment experiences “motion parallax,” the relative movement upon the observer’s retina of variously positioned objects in the scene. This retinal movement of images provides a cue to the relative depth of objects in the environment, however retinal motion alone cannot mathematically determine relative depth of the objects. Visual perception of depth from lateral observer translation uses both retinal image motion and eye movement. In (Nawrot & Stroyan, 2009, Vision Res. 49, p.1969) we showed mathematically that the ratio of the rate of retinal motion over the rate of smooth eye pursuit mathematically determines depth relative to the fixation point in central vision. We also reported on psychophysical experiments indicating that this ratio is the important quantity for perception. Here we analyze the motion/pursuit cue for the more general, and more complicated, case when objects are distributed across the horizontal viewing plane beyond central vision. We show how the mathematical motion/pursuit cue varies with different points across the plane and with time as an observer translates. If the time varying retinal motion and smooth eye pursuit are the only signals used for this visual process, it is important to know what is mathematically possible to derive about depth and structure. Our analysis shows that the motion/pursuit ratio determines an excellent description of depth and structure in these broader stimulus conditions, provides a detailed quantitative hypothesis of these visual processes for the perception of depth and structure from motion parallax, and provides a computational foundation to analyze the dynamic geometry of future experiments. PMID:21695531

Single master regulatory gene coordinates the evolution and development of butterfly color and iridescence

PubMed Central

Zhang, Linlin

2017-01-01

The optix gene has been implicated in butterfly wing pattern adaptation by genetic association, mapping, and expression studies. The actual developmental function of this gene has remained unclear, however. Here we used CRISPR/Cas9 genome editing to show that optix plays a fundamental role in nymphalid butterfly wing pattern development, where it is required for determination of all chromatic coloration. optix knockouts in four species show complete replacement of color pigments with melanins, with corresponding changes in pigment-related gene expression, resulting in black and gray butterflies. We also show that optix simultaneously acts as a switch gene for blue structural iridescence in some butterflies, demonstrating simple regulatory coordination of structural and pigmentary coloration. Remarkably, these optix knockouts phenocopy the recurring “black and blue” wing pattern archetype that has arisen on many independent occasions in butterflies. Here we demonstrate a simple genetic basis for structural coloration, and show that optix plays a deeply conserved role in butterfly wing pattern development. PMID:28923944

Single master regulatory gene coordinates the evolution and development of butterfly color and iridescence.

PubMed

Zhang, Linlin; Mazo-Vargas, Anyi; Reed, Robert D

2017-10-03

The optix gene has been implicated in butterfly wing pattern adaptation by genetic association, mapping, and expression studies. The actual developmental function of this gene has remained unclear, however. Here we used CRISPR/Cas9 genome editing to show that optix plays a fundamental role in nymphalid butterfly wing pattern development, where it is required for determination of all chromatic coloration. optix knockouts in four species show complete replacement of color pigments with melanins, with corresponding changes in pigment-related gene expression, resulting in black and gray butterflies. We also show that optix simultaneously acts as a switch gene for blue structural iridescence in some butterflies, demonstrating simple regulatory coordination of structural and pigmentary coloration. Remarkably, these optix knockouts phenocopy the recurring "black and blue" wing pattern archetype that has arisen on many independent occasions in butterflies. Here we demonstrate a simple genetic basis for structural coloration, and show that optix plays a deeply conserved role in butterfly wing pattern development.

Theoretical study of the gas-phase structures of sodiated and cesiated leucine and isoleucine: zwitterionic structure disfavored in kinetic method experiments.

PubMed

Rozman, Marko

2005-10-01

The most stable charge-solvated (CS) and zwitterionic (ZW) structures of sodiated and cesiated leucine and isoleucine were studied by density functional theory methods. According to the Boltzmann distribution in gas phase, both forms of LeuNa+ and IleNa+ exist, but in LeuCs+ and IleCs+, the ZW forms are dominant. Results for the sodiated compounds are consistent with the relationship found between decrease in relative stability of CS versus ZW form and aliphatic amino acid side chain length. The observed degeneracy in energy for IleNa+ conformers is at odds with kinetic method results. Additional calculations showed that kinetic method structural determinations for IleNa+ do not reflect relative order of populations in the lowest energy conformers. Since complexation of cationized amino acids into ion-bound dimers disfavors ZW structure by approximately 8 kJ mol(-1), it is suggested that for energy close conformers of sodium-cationized amino acids, the kinetic method may not be reliable for structural determinations. Copyright (c) 2005 John Wiley & Sons, Ltd.

Crystal structure of simple metals at high pressures

NASA Astrophysics Data System (ADS)

Degtyareva, Olga

2010-09-01

The effects of pressure on the crystal structure of simple (or sp-) elements are analysed in terms of changes in coordination number, packing density, and interatomic distances, and general rules are established. In the polyvalent elements from groups 14-17, the covalently bonded structures tend to transform to metallic phases with a gradual increase in coordination number and packing density, a behaviour normally expected under pressure. Group 1 and 2 metallic elements, however, show a reverse trend towards structures with low packing density due to intricate changes in their electronic structure. Complex crystal structures such as host-guest and incommensurately modulated structures found in these elements are given special attention in this review in an attempt to determine their role in the observed phase-transition sequences.

Acyl carrier protein structural classification and normal mode analysis

PubMed Central

Cantu, David C; Forrester, Michael J; Charov, Katherine; Reilly, Peter J

2012-01-01

All acyl carrier protein primary and tertiary structures were gathered into the ThYme database. They are classified into 16 families by amino acid sequence similarity, with members of the different families having sequences with statistically highly significant differences. These classifications are supported by tertiary structure superposition analysis. Tertiary structures from a number of families are very similar, suggesting that these families may come from a single distant ancestor. Normal vibrational mode analysis was conducted on experimentally determined freestanding structures, showing greater fluctuations at chain termini and loops than in most helices. Their modes overlap more so within families than between different families. The tertiary structures of three acyl carrier protein families that lacked any known structures were predicted as well. PMID:22374859

Multicellular structures developing during maize microspore culture express endosperm and embryo-specific genes and show different embryogenic potentialities.

PubMed

Massonneau, Agnes; Coronado, Maria-José; Audran, Arthur; Bagniewska, Agnieszka; Mòl, Rafal; Testillano, Pilar S; Goralski, Grzegorz; Dumas, Christian; Risueño, Maria-Carmen; Matthys-Rochon, Elisabeth

2005-07-01

During maize pollen embryogenesis, a range of multicellular structures are formed. Using different approaches, the "nature" of these structures has been determined in terms of their embryogenic potential. In situ molecular identification techniques for gene transcripts and products, and a novel cell tracking system indicated the presence of embryogenic (embryo-like structures, ELS) and non-embryogenic (callus-like structures, CLS) structures that occurred for short periods within the cultures. Some multicellular structures with a compact appearance generated embryos. RT-PCR and fluorescence in situ hybridization (FISH) with confocal microscopy techniques using specific gene markers of the endosperm (ZmESR2, ZmAE3) and embryo (LTP2 and ZmOCL1, ZmOCL3) revealed "embryo" and "endosperm" potentialities in these various multicellular structures present in the cultures. The results presented here showed distinct and specific patterns of gene expression. Altogether, the results demonstrate the presence of different molecules on both embryonic and non-embryonic structures. Their possible roles are discussed in the context of a parallel between embryo/endosperm interactions in planta and embryonic and non-embryonic structure interrelations under in vitro conditions.

Structural determination of Bi-doped magnetite multifunctional nanoparticles for contrast imaging.

PubMed

Laguna-Marco, M A; Piquer, C; Roca, A G; Boada, R; Andrés-Vergés, M; Veintemillas-Verdaguer, S; Serna, C J; Iadecola, A; Chaboy, J

2014-09-14

To determine with precision how Bi atoms are distributed in Bi-doped iron oxide nanoparticles their structural characterization has been carried out by X-ray absorption spectroscopy (XAS) recorded at the K edge of Fe and at the L3 edge of Bi. The inorganic nanoparticles are nominally hybrid structures integrating an iron oxide core and a bismuth oxide shell. Fe K-edge XAS indicates the formation of a structurally ordered, non-stoichiometric magnetite (Fe3-δO4) phase for all the nanoparticles. The XAS spectra show that, in the samples synthesized by precipitation in aqueous media and laser pyrolysis, the Bi atoms neither enter into the iron oxide spinel lattice nor form any other mixed Bi-Fe oxides. No modification of the local structure around the Fe atoms induced by the Bi atoms is observed at the Fe K edge. In addition, contrary to expectations, our results indicate that the Bi atoms do not form a well-defined Bi oxide structure. The XAS study at the Bi L3 edge indicates that the environment around Bi atoms is highly disordered and only a first oxygen coordination shell is observed. Indefinite [BiO6-x(OH)x] units (isolated or aggregated forming tiny amorphous clusters) bonded through hydroxyl bridges to the nanoparticle, rather than a well defined Bi2O3 shell, surround the nanoparticle. On the other hand, the XAS study indicates that, in the samples synthesized by thermal decomposition, the Bi atoms are embedded in a longer range ordered structure showing the first and second neighbors.

Role of κ→λ light-chain constant-domain switch in the structure and functionality of A17 reactibody

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

Ponomarenko, Natalia; Chatziefthimiou, Spyros D.; Kurkova, Inna

2014-03-01

Catalytic antibody variants with κ and λ light-chain constant domains show differences in their crystal structures which lead to subtle changes in catalytic efficiency and thermodynamic parameters as well as in their affinity for peptide substrates. The engineering of catalytic function in antibodies requires precise information on their structure. Here, results are presented that show how the antibody domain structure affects its functionality. The previously designed organophosphate-metabolizing reactibody A17 has been re-engineered by replacing its constant κ light chain by the λ chain (A17λ), and the X-ray structure of A17λ has been determined at 1.95 Å resolution. It was foundmore » that compared with A17κ the active centre of A17λ is displaced, stabilized and made more rigid owing to interdomain interactions involving the CDR loops from the V{sub L} and V{sub H} domains. These V{sub L}/V{sub H} domains also have lower mobility, as deduced from the atomic displacement parameters of the crystal structure. The antibody elbow angle is decreased to 126° compared with 138° in A17κ. These structural differences account for the subtle changes in catalytic efficiency and thermodynamic parameters determined with two organophosphate ligands, as well as in the affinity for peptide substrates selected from a combinatorial cyclic peptide library, between the A17κ and A17λ variants. The data presented will be of interest and relevance to researchers dealing with the design of antibodies with tailor-made functions.« less

Congruence between morphological and molecular markers inferred from the analysis of the intra-morphotype genetic diversity and the spatial structure of Oxalis tuberosa Mol.

PubMed

Pissard, Audrey; Arbizu, Carlos; Ghislain, Marc; Faux, Anne-Michèle; Paulet, Sébastien; Bertin, Pierre

2008-01-01

Oxalis tuberosa is an important crop cultivated in the highest Andean zones. A germplasm collection is maintained ex situ by CIP, which has developed a morphological markers system to classify the accessions into morphotypes, i.e. groups of morphologically identical accessions. However, their genetic uniformity is currently unknown. The ISSR technique was used in two experiments to determine the relationships between both morphological and molecular markers systems. The intra-morphotype genetic diversity, the spatial structures of the diversity and the congruence between both markers systems were determined. In the first experience, 44 accessions representing five morphotypes, clearly distinct from each other, were analyzed. At the molecular level, the accessions exactly clustered according to their morphotypes. However, a genetic variability was observed inside each morphotype. In the second experiment, 34 accessions gradually differing from each other on morphological base were analyzed. The morphological clustering showed no geographical structure. On the opposite, the molecular analysis showed that the genetic structure was slightly related to the collection site. The correlation between both markers systems was weak but significant. The lack of perfect congruence between morphological and molecular data suggests that the morphological system may be useful for the morphotypes management but is not appropriate to study the genetic structure of the oca. The spatial structure of the genetic diversity can be related to the evolution of the species and the discordance between the morphological and molecular structures may result from similar selection pressures at different places leading to similar forms with a different genetic background.

Performance-based plastic design of earthquake resistant reinforced concrete moment frames

NASA Astrophysics Data System (ADS)

Liao, Wen-Cheng

Performance-Based Plastic Design (PBPD) method has been recently developed to achieve enhanced performance of earthquake resistant structures. The design concept uses pre-selected target drift and yield mechanism as performance criteria. The design base shear for selected hazard level is determined by equating the work needed to push the structure monotonically up to the target drift to the corresponding energy demand of an equivalent SDOF oscillator. This study presents development of the PBPD approach as applied to reinforced concrete special moment frame (RC SMF) structures. RC structures present special challenge because of their complex and degrading ("pinched") hysteretic behavior. In order to account for the degrading hysteretic behavior the 1-EMA 440 C2 factor approach was used in the process of determining the design base shear. Four baseline RC SMF (4, 8, 12 and 20-story) as used in the FEMA P695 were selected for this study. Those frames were redesigned by the PBPD approach. The baseline frames and the PBPD frames were subjected to extensive inelastic pushover and time-history analyses. The PBPD frames showed much improved response meeting all desired performance objectives, including the intended yield mechanisms and the target drifts. On the contrary, the baseline frames experienced large story drifts due to flexural yielding of the columns. The work-energy equation to determine design base shear can also be used to estimate seismic demands, called the energy spectrum method. In this approach the skeleton force-displacement (capacity) curve of the structure is converted into energy-displacement plot (Ec) which is superimposed over the corresponding energy demand plot ( Ed) for the specified hazard level to determine the expected peak displacement demands. In summary, this study shows that the PBPD approach can be successfully applied to RC moment frame structures as well, and that the responses of the example moment frames were much improved over those of the corresponding baseline frames. In addition, the drift demands of all study frames as computed by the energy spectrum method were in excellent agreement with those obtained from detailed inelastic dynamic analyses.

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

PubMed Central

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

2013-01-01

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

Toward Protein Structure In Situ: Comparison of Two Bifunctional Rhodamine Adducts of Troponin C

PubMed Central

Julien, Olivier; Sun, Yin-Biao; Knowles, Andrea C.; Brandmeier, Birgit D.; Dale, Robert E.; Trentham, David R.; Corrie, John E. T.; Sykes, Brian D.; Irving, Malcolm

2007-01-01

As part of a program to develop methods for determining protein structure in situ, sTnC was labeled with a bifunctional rhodamine (BR or BSR), cross-linking residues 56 and 63 of its C-helix. NMR spectroscopy of the N-terminal domain of BSR-labeled sTnC in complex with Ca2+ and the troponin I switch peptide (residues 115–131) showed that BSR labeling does not significantly affect the secondary structure of the protein or its dynamics in solution. BR-labeling was previously shown to have no effect on the solution structure of this complex. Isometric force generation in isolated demembranated fibers from rabbit psoas muscle into which BR- or BSR-labeled sTnC had been exchanged showed reduced Ca2+-sensitivity, and this effect was larger with the BSR label. The orientation of rhodamine dipoles with respect to the fiber axis was determined by polarized fluorescence. The mean orientations of the BR and BSR dipoles were almost identical in relaxed muscle, suggesting that both probes accurately report the orientation of the C-helix to which they are attached. The BSR dipole had smaller orientational dispersion, consistent with less flexible linkers between the rhodamine dipole and cysteine-reactive groups. PMID:17483167

Enhanced Structural Interpretation Using Multitrace Seismic Attribute For Oligo-Miocene Target at Madura Strait Offshore

NASA Astrophysics Data System (ADS)

Pratama Wahyu Hidayat, Putra; Hary Murti, Antonius; Sudarmaji; Shirly, Agung; Tiofan, Bani; Damayanti, Shinta

2018-03-01

Geometry is an important parameter for the field of hydrocarbon exploration and exploitation, it has significant effect to the amount of resources or reserves, rock spreading, and risk analysis. The existence of geological structure or fault becomes one factor affecting geometry. This study is conducted as an effort to enhance seismic image quality in faults dominated area namely offshore Madura Strait. For the past 10 years, Oligo-Miocene carbonate rock has been slightly explored on Madura Strait area, the main reason because migration and trap geometry still became risks to be concern. This study tries to determine the boundary of each fault zone as subsurface image generated by converting seismic data into variance attribute. Variance attribute is a multitrace seismic attribute as the derivative result from amplitude seismic data. The result of this study shows variance section of Madura Strait area having zero (0) value for seismic continuity and one (1) value for discontinuity of seismic data. Variance section shows the boundary of RMKS fault zone with Kendeng zone distinctly. Geological structure and subsurface geometry for Oligo-Miocene carbonate rock could be identified perfectly using this method. Generally structure interpretation to identify the boundary of fault zones could be good determined by variance attribute.

Antifungal Indole and Pyrrolidine-2,4-Dione Derivative Peptidomimetic Lead Design Based on In Silico Study of Bioactive Peptide Families

PubMed Central

Moradi, Shoeib; Azerang, Parisa; Khalaj, Vahid; Sardari, Soroush

2013-01-01

Background The rise of opportunistic fungal infections highlights the need for development of new antimicrobial agents. Antimicrobial Peptides (AMPs) and Antifungal Peptides (AFPs) are among the agents with minimal resistance being developed against them, therefore they can be used as structural templates for design of new antimicrobial agents. Methods In the present study four antifungal peptidomimetic structures named C1 to C4 were designed based on plant defensin of Pisum sativum. Minimum inhibitory concentrations (MICs) for these structures were determined against Aspergillus niger N402, Candida albicans ATCC 10231, and Saccharomyces cerevisiae PTCC 5052. Results C1 and C2 showed more potent antifungal activity against these fungal strains compared to C3 and C4. The structure C2 demonstrated a potent antifungal activity among them and could be used as a template for future study on antifungal peptidomemetics design. Sequences alignments led to identifying antifungal decapeptide (KTCENLADTY) named KTC-Y, which its MIC was determined on fungal protoplast showing 25 (µg/ml) against Aspergillus fumigatus Af293. Conclusion The present approach to reach the antifungal molecules seems to be a powerful approach in design of bioactive agents based on AMP mimetic identification. PMID:23626876

Effect of gravity on the stability and structure of lean hydrogen-air flames

NASA Technical Reports Server (NTRS)

Patnaik, G.; Kailasanath, K.

1991-01-01

Detailed, time-dependent, 2D numerical simulations with full hydrogen-oxygen chemistry are used to investigate the effects of gravity on the stability and structure of laminar flames in lean, premixed hydrogen-air mixtures. The calculations show that the effects of gravity becomes more important as the lean flammability limit is approached. In a 12 percent hydrogen-air mixture, gravity plays only a secondary role in determining the multidimensional structure of the flame with the stability and structure of the flame controlled primarily by the thermo-diffusive instability mechanism. However, in leaner hydrogen-air mixtures gravity becomes more important. Upward-propagating flames are highly curved and evolve into a bubble rising upwards in the tube. Downward-propagating flames are flat or even oscillate between structures with concave and convex curvatures. The zero-gravity flame shows only cellular structures. Cellular structures which are present in zero gravity can be suppressed by the effect of buoyancy for mixtures leaner than 11 percent hydrogen. These observations are explained on the basis of an interaction between the processes leading to buoyancy-induced Rayleigh-Taylor instability and the thermo-diffusive instability.

Crystal structure of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17

PubMed Central

Godoy, Andre S.; de Lima, Mariana Z. T.; Camilo, Cesar M.; Polikarpov, Igor

2016-01-01

Given the current interest in second-generation biofuels, carbohydrate-active enzymes have become the most important tool to overcome the structural recalcitrance of the plant cell wall. While some glycoside hydrolase families have been exhaustively described, others remain poorly characterized, especially with regard to structural information. The family 43 glycoside hydrolases are a diverse group of inverting enzymes; the available structure information on these enzymes is mainly from xylosidases and arabinofuranosidase. Currently, only one structure of an exo-β-1,3-galactanase is available. Here, the production, crystallization and structure determination of a putative exo-β-1,3-galactanase from Bifidobacterium bifidum S17 (BbGal43A) are described. BbGal43A was successfully produced and showed activity towards synthetic galactosides. BbGal43A was subsequently crystallized and data were collected to 1.4 Å resolution. The structure shows a single-domain molecule, differing from known homologues, and crystal contact analysis predicts the formation of a dimer in solution. Further biochemical studies are necessary to elucidate the differences between BbGal43A and its characterized homologues. PMID:27050262

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

PubMed Central

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

2000-01-01

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

Protein Structure Determination using Metagenome sequence data

PubMed Central

Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A.; Kim, David E.; Kamisetty, Hetunandan; Kyrpides, Nikos C.; Baker, David

2017-01-01

Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families, and that metagenome sequence data more than triples the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact based structure matching and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the PDB. This approach provides the representative models for large protein families originally envisioned as the goal of the protein structure initiative at a fraction of the cost. PMID:28104891

Quality of dry-cured ham compared with quality of dry-cured shoulder.

PubMed

Reina, Raquel; Sánchez del Pulgar, José; Tovar, Jorge; López-Buesa, Pascual; García, Carmen

2013-08-01

The physicochemical and sensory properties of 30 dry-cured hams and 30 dry-cured shoulders were analyzed to determine the relationships between them. The variables used to characterize both products were: compositional parameters, instrumental texture, amino acid and fatty acid composition, and sensory profile. Despite being products from the same animal and composed mainly of fat, lean, and bone, their morphological differences determine the conditions of the processing time, which produced differences between products in most of the parameters evaluated. Dry-cured shoulders showed lower moisture content and greater instrumental hardness due to their morphology and muscular structure. Besides, these samples showed lower amino acid content according to the shorter ripening time. For the same reason, the dry-cured hams showed higher moisture content, lower instrumental hardness, and higher amino acid content. However, the differences in the muscular structure did not affect the sensory characteristics, which were more related with some compositional parameters, such as chloride, moisture, and amino acid content and with the length of the curing process. © 2013 Extremadura University.

Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.

PubMed

Kuzmanic, Antonija; Zagrovic, Bojan

2010-03-03

Root mean-square deviation (RMSD) after roto-translational least-squares fitting is a measure of global structural similarity of macromolecules used commonly. On the other hand, experimental x-ray B-factors are used frequently to study local structural heterogeneity and dynamics in macromolecules by providing direct information about root mean-square fluctuations (RMSF) that can also be calculated from molecular dynamics simulations. We provide a mathematical derivation showing that, given a set of conservative assumptions, a root mean-square ensemble-average of an all-against-all distribution of pairwise RMSD for a single molecular species, (1/2), is directly related to average B-factors () and (1/2). We show this relationship and explore its limits of validity on a heterogeneous ensemble of structures taken from molecular dynamics simulations of villin headpiece generated using distributed-computing techniques and the Folding@Home cluster. Our results provide a basis for quantifying global structural diversity of macromolecules in crystals directly from x-ray experiments, and we show this on a large set of structures taken from the Protein Data Bank. In particular, we show that the ensemble-average pairwise backbone RMSD for a microscopic ensemble underlying a typical protein x-ray structure is approximately 1.1 A, under the assumption that the principal contribution to experimental B-factors is conformational variability. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.