Accurate Determination of the Frequency Response Function of Submerged and Confined Structures by Using PZT-Patches†.

PubMed

Presas, Alexandre; Valentin, David; Egusquiza, Eduard; Valero, Carme; Egusquiza, Mònica; Bossio, Matias

2017-03-22

To accurately determine the dynamic response of a structure is of relevant interest in many engineering applications. Particularly, it is of paramount importance to determine the Frequency Response Function (FRF) for structures subjected to dynamic loads in order to avoid resonance and fatigue problems that can drastically reduce their useful life. One challenging case is the experimental determination of the FRF of submerged and confined structures, such as hydraulic turbines, which are greatly affected by dynamic problems as reported in many cases in the past. The utilization of classical and calibrated exciters such as instrumented hammers or shakers to determine the FRF in such structures can be very complex due to the confinement of the structure and because their use can disturb the boundary conditions affecting the experimental results. For such cases, Piezoelectric Patches (PZTs), which are very light, thin and small, could be a very good option. Nevertheless, the main drawback of these exciters is that the calibration as dynamic force transducers (relationship voltage/force) has not been successfully obtained in the past. Therefore, in this paper, a method to accurately determine the FRF of submerged and confined structures by using PZTs is developed and validated. The method consists of experimentally determining some characteristic parameters that define the FRF, with an uncalibrated PZT exciting the structure. These parameters, which have been experimentally determined, are then introduced in a validated numerical model of the tested structure. In this way, the FRF of the structure can be estimated with good accuracy. With respect to previous studies, where only the natural frequencies and mode shapes were considered, this paper discuss and experimentally proves the best excitation characteristic to obtain also the damping ratios and proposes a procedure to fully determine the FRF. The method proposed here has been validated for the structure vibrating in air comparing the FRF experimentally obtained with a calibrated exciter (impact Hammer) and the FRF obtained with the described method. Finally, the same methodology has been applied for the structure submerged and close to a rigid wall, where it is extremely important to not modify the boundary conditions for an accurate determination of the FRF. As experimentally shown in this paper, in such cases, the use of PZTs combined with the proposed methodology gives much more accurate estimations of the FRF than other calibrated exciters typically used for the same purpose. Therefore, the validated methodology proposed in this paper can be used to obtain the FRF of a generic submerged and confined structure, without a previous calibration of the PZT.

Protein Models Docking Benchmark 2

PubMed Central

Anishchenko, Ivan; Kundrotas, Petras J.; Tuzikov, Alexander V.; Vakser, Ilya A.

2015-01-01

Structural characterization of protein-protein interactions is essential for our ability to understand life processes. However, only a fraction of known proteins have experimentally determined structures. Such structures provide templates for modeling of a large part of the proteome, where individual proteins can be docked by template-free or template-based techniques. Still, the sensitivity of the docking methods to the inherent inaccuracies of protein models, as opposed to the experimentally determined high-resolution structures, remains largely untested, primarily due to the absence of appropriate benchmark set(s). Structures in such a set should have pre-defined inaccuracy levels and, at the same time, resemble actual protein models in terms of structural motifs/packing. The set should also be large enough to ensure statistical reliability of the benchmarking results. We present a major update of the previously developed benchmark set of protein models. For each interactor, six models were generated with the model-to-native Cα RMSD in the 1 to 6 Å range. The models in the set were generated by a new approach, which corresponds to the actual modeling of new protein structures in the “real case scenario,” as opposed to the previous set, where a significant number of structures were model-like only. In addition, the larger number of complexes (165 vs. 63 in the previous set) increases the statistical reliability of the benchmarking. We estimated the highest accuracy of the predicted complexes (according to CAPRI criteria), which can be attained using the benchmark structures. The set is available at http://dockground.bioinformatics.ku.edu. PMID:25712716

Comparative atmosphere structure experiment

NASA Technical Reports Server (NTRS)

Sommer, S.

1974-01-01

Atmospheric structure of outer planets as determined by pressure, temperature, and accelerometers is reviewed and results obtained from the PAET earth entry are given. In order to describe atmospheric structure, entry is divided into two regimes, high and low speed. Acceleration is then measured: from these measurements density is determined as a function of time. The equations of motion are integrated to determine velocity, flight path angle, and altitude as a function of time. Density is then determined as a function of altitude from the previous determinations of density and altitude as a function of time. Hydrostatic equilibrium was assumed to determine pressure as a function of altitude. Finally the equation of space applied to determine temperature as a function of altitude, if the mean molecular weight is known. The mean molecular weight is obtained independently from either the low speed experiment or from the composition experiments.

Determination of Elevator and Rudder Hinge Forces on the Learjet Model 55 Aircraft

NASA Technical Reports Server (NTRS)

Boroughs, R. R.; Padmanabhan, V.

1983-01-01

The empennage structure on the Learjet 55 aircraft was quite similar to the empennage structure on earlier Learjet models. However, due to an important structural change in the vertical fin along with the new loads environment on the 50 series aircraft, a structural test was required on the vertical fin, but the horizontal tail was substantiated by a comparative analysis with previous tests. NASTRAN analysis was used to investigate empennage deflections, stress levels, and control surface hinge forces. The hinge force calculations were made with the control surfaces in the deflected as well as undeflected configurations. A skin panel buckling analysis was also performed, and the non-linear effects of buckling were simulated in the NASTRAN model to more accurately define internal loads and stress levels. Comparisons were then made between the Model 55 and the Model 35/36 stresses and internal forces to determine which components were qualified by previous tests. Some of the methods and techniques used in this analysis are described.

Structure and physics of solar faculae

NASA Astrophysics Data System (ADS)

Pecker, J.-C.; Dumont, S.; Mouradian, Z.

1992-04-01

The optical depths of layers in the chromosphere-corona transition (CCT) zone, which is responsible for resolved structures in CII, CIII, OIV, and OVI lines, were determined using a new method that takes into account the effect of roughness (or local departures from sphericity) of the emitting layers in the CCT zone. The method allows determination of the angle alpha typical of the roughness (in case of availability of resolved data) and the two optical depths tau-1 and tau-2. It is shown that, even in unresolved cases, the new method gives a more realistic determination of the optical depths than previously determined.

NMR crystallography of zeolites: How far can we go without diffraction data?

PubMed

Brouwer, Darren H; Van Huizen, Jared

2018-05-10

Nuclear magnetic resonance (NMR) crystallography-an approach to structure determination that seeks to integrate solid-state NMR spectroscopy, diffraction, and computation methods-has emerged as an effective strategy to determine structures of difficult-to-characterize materials, including zeolites and related network materials. This paper explores how far it is possible to go in determining the structure of a zeolite framework from a minimal amount of input information derived only from solid-state NMR spectroscopy. It is shown that the framework structure of the fluoride-containing and tetramethylammonium-templated octadecasil clathrasil material can be solved from the 1D 29 Si NMR spectrum and a single 2D 29 Si NMR correlation spectrum alone, without the space group and unit cell parameters normally obtained from diffraction data. The resulting NMR-solved structure is in excellent agreement with the structures determined previously by diffraction methods. It is anticipated that NMR crystallography strategies like this will be useful for structure determination of other materials, which cannot be solved from diffraction methods alone. Copyright © 2018 John Wiley & Sons, Ltd.

The Molecular Structure of cis-FONO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.; Rice, Julia E.; Langhoff, Stephen R. (Technical Monitor)

1994-01-01

The molecular structure of cis-FONO has been determined with the CCSD(T) correlation method using an spdf quality basis set. In agreement with previous coupled-cluster calculations but in disagreement with density functional theory, cis-FONO is found to exhibit normal bond distances. The quadratic and cubic force fields of cis-FONO have also been determined in order to evaluate the effect of vibrational averaging on the molecular geometry. Vibrational averaging is found to increase bond distances, as expected, but it does not affect the qualitative nature of the bonding. The CCSD(T)/spdf harmonic frequencies of cis-FONO support our previous assertion that a band observed at 1200 /cm is a combination band (upsilon(sub 3) + upsilon(sub 4)), and not a fundamental.

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

Wu, Hong; Zeng, Hong; Lam, Robert

Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson–Crick base pairs in the genome. Pathogenic mutations in theMLH1gene are associated with a predisposition to Lynch and Turcot's syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. Lastly, the structure shares a high degree of similarity with previously determined prokaryoticMLH1homologs; however, this structure affords a more accurate platform for the classification ofMLH1variants.

Determination of the crystalline structure of scale solids from the 16H evaporator gravity drain line to tank 38H

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

Oji, L. N.

2015-10-01

August 2015, scale solids from the 16H Evaporator Gravity Drain Line (GDL) to the Tank 38H were delivered to SRNL for analysis. The desired analytical goal was to identify and confirm the crystalline structure of the scale material and determine if the form of the aluminosilicate mineral was consistent with previous analysis of the scale material from the GDL.

Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus.

PubMed

Organtini, Lindsey J; Lee, Hyunwook; Iketani, Sho; Huang, Kai; Ashley, Robert E; Makhov, Alexander M; Conway, James F; Parrish, Colin R; Hafenstein, Susan

2016-11-01

Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM. Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced conformational changes in regions of the virus capsid that control receptor binding. The antibody footprint is markedly different from the previous one identified by using a 12 Å structure. This work emphasizes the need for a high-resolution structure to guide mutational analysis and cautions against relying on older low-resolution structures even though they were interpreted with the best methodology available at the time. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus

PubMed Central

Organtini, Lindsey J.; Lee, Hyunwook; Iketani, Sho; Huang, Kai; Ashley, Robert E.; Makhov, Alexander M.; Conway, James F.

2016-01-01

ABSTRACT Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM. IMPORTANCE Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced conformational changes in regions of the virus capsid that control receptor binding. The antibody footprint is markedly different from the previous one identified by using a 12 Å structure. This work emphasizes the need for a high-resolution structure to guide mutational analysis and cautions against relying on older low-resolution structures even though they were interpreted with the best methodology available at the time. PMID:27535057

Full-scale tank car rollover tests - survivability of top fittings and top fittings protective structures : final report.

DOT National Transportation Integrated Search

2016-05-01

Full-scale rollover crash tests were performed on three non-pressure tank carbodies to validate previous analytical work and : determine the effectiveness of two different types of protective structures in protecting the top fittings. The tests were ...

Lysability of fibrin clots is a potential new determinant of stroke risk in atrial fibrillation.

PubMed

Skov, Jane; Sidelmann, Johannes J; Bladbjerg, Else-Marie; Jespersen, Jørgen; Gram, Jørgen

2014-09-01

Atrial fibrillation increases the risk of ischemic stroke, but the risk depends on other factors as well. Present risk stratification schemes use age and co-morbidities, but not biochemical markers. We investigated the hypothesis that the formation, structure and lysability of fibrin clots are potential determinants of stroke risk in patients with atrial fibrillation. A total of 179 patients with atrial fibrillation in stable anticoagulant treatment were included. Thirty-two had a previous ischemic stroke. We measured thrombin generation, plasma concentrations of fibrinogen and C-reactive protein and analysed fibrin structure and lysability by turbidity. Fibrinolytic capacity was measured using the euglobulin fraction of plasma expressed in terms of t-PA equivalents (IU/ml). The patients with previous stroke had a slightly higher burden of co-morbidities compared with the remaining patients as indicated by the CHA2DS2-VASc score, but no significant differences were found regarding age, fibrinogen concentration, C-reactive protein, thrombin generation or fibrinolytic capacity. Furthermore, the patients with previous stroke had a higher mass/length ratio of fibrin fibers (5.5 vs. 5.1 x10(12) Da/cm, p=0.044) and an increased lysability (79.3 vs. 55.3%, p<0.01). The higher lysability of fibrin clots in atrial fibrillation patients with previous stroke is most likely a result of a difference in fibrin fiber properties. An increased lysability may increase the risk of embolization of clots formed in the atria, and therefore fibrin clot structure seems to be a determinant of stroke risk in atrial fibrillation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Semiexperimental equilibrium structures for building blocks of organic and biological molecules: the B2PLYP route.

PubMed

Penocchio, Emanuele; Piccardo, Matteo; Barone, Vincenzo

2015-10-13

The B2PLYP double hybrid functional, coupled with the correlation-consistent triple-ζ cc-pVTZ (VTZ) basis set, has been validated in the framework of the semiexperimental (SE) approach for deriving accurate equilibrium structures of molecules containing up to 15 atoms. A systematic comparison between new B2PLYP/VTZ results and several equilibrium SE structures previously determined at other levels, in particular B3LYP/SNSD and CCSD(T) with various basis sets, has put in evidence the accuracy and the remarkable stability of such model chemistry for both equilibrium structures and vibrational corrections. New SE equilibrium structures for phenylacetylene, pyruvic acid, peroxyformic acid, and phenyl radical are discussed and compared with literature data. Particular attention has been devoted to the discussion of systems for which lack of sufficient experimental data prevents a complete SE determination. In order to obtain an accurate equilibrium SE structure for these situations, the so-called templating molecule approach is discussed and generalized with respect to our previous work. Important applications are those involving biological building blocks, like uracil and thiouracil. In addition, for more general situations the linear regression approach has been proposed and validated.

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.

Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome

DOE PAGES

Wu, Hong; Zeng, Hong; Lam, Robert; ...

2015-08-01

Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson–Crick base pairs in the genome. Pathogenic mutations in theMLH1gene are associated with a predisposition to Lynch and Turcot's syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. Lastly, the structure shares a high degree of similarity with previously determined prokaryoticMLH1homologs; however, this structure affords a more accurate platform for the classification ofMLH1variants.

Accurate Determination of the Frequency Response Function of Submerged and Confined Structures by Using PZT-Patches †

PubMed Central

Presas, Alexandre; Valentin, David; Egusquiza, Eduard; Valero, Carme; Egusquiza, Mònica; Bossio, Matias

2017-01-01

To accurately determine the dynamic response of a structure is of relevant interest in many engineering applications. Particularly, it is of paramount importance to determine the Frequency Response Function (FRF) for structures subjected to dynamic loads in order to avoid resonance and fatigue problems that can drastically reduce their useful life. One challenging case is the experimental determination of the FRF of submerged and confined structures, such as hydraulic turbines, which are greatly affected by dynamic problems as reported in many cases in the past. The utilization of classical and calibrated exciters such as instrumented hammers or shakers to determine the FRF in such structures can be very complex due to the confinement of the structure and because their use can disturb the boundary conditions affecting the experimental results. For such cases, Piezoelectric Patches (PZTs), which are very light, thin and small, could be a very good option. Nevertheless, the main drawback of these exciters is that the calibration as dynamic force transducers (relationship voltage/force) has not been successfully obtained in the past. Therefore, in this paper, a method to accurately determine the FRF of submerged and confined structures by using PZTs is developed and validated. The method consists of experimentally determining some characteristic parameters that define the FRF, with an uncalibrated PZT exciting the structure. These parameters, which have been experimentally determined, are then introduced in a validated numerical model of the tested structure. In this way, the FRF of the structure can be estimated with good accuracy. With respect to previous studies, where only the natural frequencies and mode shapes were considered, this paper discuss and experimentally proves the best excitation characteristic to obtain also the damping ratios and proposes a procedure to fully determine the FRF. The method proposed here has been validated for the structure vibrating in air comparing the FRF experimentally obtained with a calibrated exciter (impact Hammer) and the FRF obtained with the described method. Finally, the same methodology has been applied for the structure submerged and close to a rigid wall, where it is extremely important to not modify the boundary conditions for an accurate determination of the FRF. As experimentally shown in this paper, in such cases, the use of PZTs combined with the proposed methodology gives much more accurate estimations of the FRF than other calibrated exciters typically used for the same purpose. Therefore, the validated methodology proposed in this paper can be used to obtain the FRF of a generic submerged and confined structure, without a previous calibration of the PZT. PMID:28327501

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

Conserved Binding Mode of Human [beta subscript 2] Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography

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

Wacker, Daniel; Fenalti, Gustavo; Brown, Monica A.

2010-11-15

G protein-coupled receptors (GPCRs) represent a large fraction of current pharmaceutical targets, and of the GPCRs, the {beta}{sub 2} adrenergic receptor ({beta}{sub 2}AR) is one of the most extensively studied. Previously, the X-ray crystal structure of {beta}{sub 2}AR has been determined in complex with two partial inverse agonists, but the global impact of additional ligands on the structure or local impacts on the binding site are not well-understood. To assess the extent of such ligand-induced conformational differences, we determined the crystal structures of a previously described engineered {beta}{sub 2}AR construct in complex with two inverse agonists: ICI 118,551 (2.8 {angstrom}),more » a recently described compound (2.8 {angstrom}) (Kolb et al, 2009), and the antagonist alprenolol (3.1 {angstrom}). The structures show the same overall fold observed for the previous {beta}{sub 2}AR structures and demonstrate that the ligand binding site can accommodate compounds of different chemical and pharmacological properties with only minor local structural rearrangements. All three compounds contain a hydroxy-amine motif that establishes a conserved hydrogen bond network with the receptor and chemically diverse aromatic moieties that form distinct interactions with {beta}{sub 2}AR. Furthermore, receptor ligand cross-docking experiments revealed that a single {beta}{sub 2}AR complex can be suitable for docking of a range of antagonists and inverse agonists but also indicate that additional ligand-receptor structures may be useful to further improve performance for in-silico docking or lead-optimization in drug design.« less

Team assembly mechanisms determine collaboration network structure and team performance.

PubMed

Guimerà, Roger; Uzzi, Brian; Spiro, Jarrett; Amaral, Luís A Nunes

2005-04-29

Agents in creative enterprises are embedded in networks that inspire, support, and evaluate their work. Here, we investigate how the mechanisms by which creative teams self-assemble determine the structure of these collaboration networks. We propose a model for the self-assembly of creative teams that has its basis in three parameters: team size, the fraction of newcomers in new productions, and the tendency of incumbents to repeat previous collaborations. The model suggests that the emergence of a large connected community of practitioners can be described as a phase transition. We find that team assembly mechanisms determine both the structure of the collaboration network and team performance for teams derived from both artistic and scientific fields.

Vascular structure determines pulmonary blood flow distribution

NASA Technical Reports Server (NTRS)

Hlastala, M. P.; Glenny, R. W.

1999-01-01

Scientific knowledge develops through the evolution of new concepts. This process is usually driven by new methodologies that provide observations not previously available. Understanding of pulmonary blood flow determinants advanced significantly in the 1960s and is now changing rapidly again, because of increased spatial resolution of regional pulmonary blood flow measurements.

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.

Distinct Ubiquitin Binding Modes Exhibited by SH3 Domains: Molecular Determinants and Functional Implications

PubMed Central

Ortega Roldan, Jose L.; Casares, Salvador; Ringkjøbing Jensen, Malene; Cárdenes, Nayra; Bravo, Jerónimo; Blackledge, Martin; Azuaga, Ana I.; van Nuland, Nico A. J.

2013-01-01

SH3 domains constitute a new type of ubiquitin-binding domains. We previously showed that the third SH3 domain (SH3-C) of CD2AP binds ubiquitin in an alternative orientation. We have determined the structure of the complex between first CD2AP SH3 domain and ubiquitin and performed a structural and mutational analysis to decipher the determinants of the SH3-C binding mode to ubiquitin. We found that the Phe-to-Tyr mutation in CD2AP and in the homologous CIN85 SH3-C domain does not abrogate ubiquitin binding, in contrast to previous hypothesis and our findings for the first two CD2AP SH3 domains. The similar alternative binding mode of the SH3-C domains of these related adaptor proteins is characterised by a higher affinity to C-terminal extended ubiquitin molecules. We conclude that CD2AP/CIN85 SH3-C domain interaction with ubiquitin constitutes a new ubiquitin-binding mode involved in a different cellular function and thus changes the previously established mechanism of EGF-dependent CD2AP/CIN85 mono-ubiquitination. PMID:24039852

Quality Matters: Extension of Clusters of Residues with Good Hydrophobic Contacts Stabilize (Hyper)Thermophilic Proteins

PubMed Central

2015-01-01

Identifying determinant(s) of protein thermostability is key for rational and data-driven protein engineering. By analyzing more than 130 pairs of mesophilic/(hyper)thermophilic proteins, we identified the quality (residue-wise energy) of hydrophobic interactions as a key factor for protein thermostability. This distinguishes our study from previous ones that investigated predominantly structural determinants. Considering this key factor, we successfully discriminated between pairs of mesophilic/(hyper)thermophilic proteins (discrimination accuracy: ∼80%) and searched for structural weak spots in E. coli dihydrofolate reductase (classification accuracy: 70%). PMID:24437522

On the correlation between hydrogen bonding and melting points in the inositols

PubMed Central

Bekö, Sándor L.; Alig, Edith; Schmidt, Martin U.; van de Streek, Jacco

2014-01-01

Inositol, 1,2,3,4,5,6-hexahydroxycyclohexane, exists in nine stereoisomers with different crystal structures and melting points. In a previous paper on the relationship between the melting points of the inositols and the hydrogen-bonding patterns in their crystal structures [Simperler et al. (2006 ▶). CrystEngComm 8, 589], it was noted that although all inositol crystal structures known at that time contained 12 hydrogen bonds per molecule, their melting points span a large range of about 170 °C. Our preliminary investigations suggested that the highest melting point must be corrected for the effect of molecular symmetry, and that the three lowest melting points may need to be revised. This prompted a full investigation, with additional experiments on six of the nine inositols. Thirteen new phases were discovered; for all of these their crystal structures were examined. The crystal structures of eight ordered phases could be determined, of which seven were obtained from laboratory X-ray powder diffraction data. Five additional phases turned out to be rotator phases and only their unit cells could be determined. Two previously unknown melting points were measured, as well as most enthalpies of melting. Several previously reported melting points were shown to be solid-to-solid phase transitions or decomposition points. Our experiments have revealed a complex picture of phases, rotator phases and phase transitions, in which a simple correlation between melting points and hydrogen-bonding patterns is not feasible. PMID:25075320

Nanoscale structure in AgSbTe2 determined by diffuse elastic neutron scattering

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

Specht, Eliot D; Ma, Jie; Delaire, Olivier A

2015-01-01

Diffuse elastic neutron scattering measurements confirm that AgSbTe2 has a hierarchical structure, with defects on length scales from nanometers to microns. While scattering from mesoscale structure is consistent with previously-proposed structures in which Ag and Sb order on a NaCl lattice, more diffuse scattering from nanoscale structure suggests a structural rearrangement in which hexagonal layers form a combination of (ABC), (ABA), and (AAB) stacking sequences. The AgCrSe2 structure is the best-fitting model for the local atomic arrangements.

Glycine glycinium picrate—Reinvestigation of the structure and vibrational spectra

NASA Astrophysics Data System (ADS)

Ghazaryan, V. V.; Fleck, M.; Petrosyan, A. M.

2011-01-01

The crystal of diglycine picrate (glycine glycinum picrate) has been obtained from an aqueous solution containing stoichiometric quantities of the components. The species crystallizes in the monoclinic system (space group P2 1/ c). The crystal structure was determined with high accuracy, IR and Raman spectra are discussed and compared with previous results, and the molecular structure is presented. It was shown that crystals of diglycine picrate obtained from the solution containing equimolar quantities may contain picric acid as impurity, which is the reason for the previously reported observation of second harmonic generation in this centrosymmetric crystal. With this example we want to point out the risk of misinterpretation of SHG signals in general.

Development of an Onboard Strain Recorder

DTIC Science & Technology

1990-01-01

Investigations ...................... .910 2-3 Strain Sensors of Previous Investigations ..................... 11 2-4 Signal Conditioning of Previous...the time the strain sensor is installed or calibrated. If a maximum stress or force is to be determined, careful structural analysis is required to...such as deckhouse edges have been instrumented as cracks appear. Extreme care concerning placement and orientation of sensor installation is required

Prediction of new ground-state crystal structure of T a2O5

NASA Astrophysics Data System (ADS)

Yang, Yong; Kawazoe, Yoshiyuki

2018-03-01

Tantalum pentoxide (T a2O5 ) is a wide-gap semiconductor which has important technological applications. Despite the enormous efforts from both experimental and theoretical studies, the ground-state crystal structure of T a2O5 is not yet uniquely determined. Based on first-principles calculations in combination with evolutionary algorithm, we identify a triclinic phase of T a2O5 , which is energetically much more stable than any phases or structural models reported previously. Characterization of the static and dynamical properties of the phase reveals the common features shared with previous metastable phases of T a2O5 . In particular, we show that the d spacing of ˜3.8 Å found in the x-ray diffraction patterns of many previous experimental works is actually the radius of the second Ta-Ta coordination shell as defined by radial distribution functions.

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…

Analysis and improvement of the cavity structure of steam receiver of 1MWe solar tower power plant

NASA Astrophysics Data System (ADS)

Yu, Qiang; Wang, Zhifeng; Zhu, Lingzhi

2017-06-01

The central receiver, which plays a dominant role in the radiation-heat conversion, is one of the most important components in the solar tower power plants. Its performance can directly affect the efficiency of the entire solar power generation system. In general, the performance of the central receiver is mainly determined by two aspects: the first is the receiver structure and arrangement of heating pipes, the other is the integral control and operation strategy. The former is the internal essence of the receiver and the latter is extrinsic. In this paper, the latter is temporarily not in the scope of the discussion. According to the previous cavity structure and arrangement of the heating pipes, it is found that there are varying degrees of deformation to the heating pipes, especially for the superheated pipes. In order to make some improvement for the cavity receiver, firstly, the most likely causes were analyzed according to the previous structure. Secondly, a possible cavity structure was proposed according to the calculation results. The results show that the performance of the receiver is better than the previous one.

Diode laser spectroscopy of the MnD radical ( 7Σ) and the determination of mass-independent parameters

NASA Astrophysics Data System (ADS)

Urban, Rolf-Dieter; Jones, Harold

1991-03-01

The infrared spectrum of the manganese deuteride radical has been observed in its ground electronic state ( 7Σ) using a diode-laser spectrometer. The hyperfine structure of a number of infrared transitions in the bands ν=1←0, ν=2←1 and ν=3←2 were measured with a nominal accuracy of ±0.001 cm -1. In all cases, the complete structure was easily resolved. Dunham parameters, spin—rotation and spin—spin coupling parameters were determined from the MnD data. A simultaneous fit of these data with those determined previously for MnH was carried out to determine mass-independent parameters and mass-scaling coefficients.

Reconsideration of F-layer seismic model in the south polar region

NASA Astrophysics Data System (ADS)

Ohtaki, T.; Kaneshima, S.

2017-12-01

Previously, we analyzed the seismic structure near the inner core boundary beneath Antarctica (Ohtaki et al., 2012). In the study, we determined the velocity of the lowermost outer core (F-layer) using amplitude ratio observations between the inner-core phase (PKIKP) and the inner-core grazing/diffracted phase (PKPbc/c-diff). Because the observations are not so sensitive to the F-layer structure, a constant velocity is assumed in the layer to simplify the model. The obtained model (SPR) has a flat velocity zone with a 75 km thick on the inner core boundary. With this F-layer structure and using travel times of these phases as well as the phase that reflects at the boundary, we determined the seismic structure of the inner core in the south polar region. However, a constant velocity layer is unrealistic, although it is reasonable assumption.Recently, we determined F-layer velocity structures more accurately using the combined observations of PKiKP-PKPbc differential travel times and of PKPbc/c-diff dispersion (Ohtaki et al., 2015, 2016). The former observation is sensitive to average velocity in the F-layer; the latter to velocity gradient in the layer. By analyzing these two observations together, we can determine the detailed velocity structure in the F-layer. The surveyed areas are beneath the Northeast Pacific and Australia. The seismic velocity models obtained are quite different between the two regions. Thus our results require laterally heterogeneous F-layer, and show that F-layer is more complicated than we ever imagined.Then there is one question; which structure is that of the south polar region close to? Unfortunately, the seismic waveforms that we analyzed in the previous study may not have quality high enough to analyze the PKiKP-PKPbc or PKPbc dispersion. However, it would be meaningful to reanalyze the amplitude data and reconsider the F-layer velocity there. And we also estimate how large slope of velocity can be acceptable for the F-layer velocity structure in this region.

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.

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

Wu, Hong; Zeng, Hong; Lam, Robert

The crystal structure of the human MLH1 N-terminus is reported at 2.30 Å resolution. The overall structure is described along with an analysis of two clinically important mutations. Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson–Crick base pairs in the genome. Pathogenic mutations in the MLH1 gene are associated with a predisposition to Lynch and Turcot’s syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. The structure shares a high degree ofmore » similarity with previously determined prokaryotic MLH1 homologs; however, this structure affords a more accurate platform for the classification of MLH1 variants.« less

Inelastic behavior of structural components

NASA Technical Reports Server (NTRS)

Hussain, N.; Khozeimeh, K.; Toridis, T. G.

1980-01-01

A more accurate procedure was developed for the determination of the inelastic behavior of structural components. The actual stress-strain curve for the mathematical of the structure was utilized to generate the force-deformation relationships for the structural elements, rather than using simplified models such as elastic-plastic, bilinear and trilinear approximations. relationships were generated for beam elements with various types of cross sections. In the generational of these curves, stress or load reversals, kinematic hardening and hysteretic behavior were taken into account. Intersections between loading and unloading branches were determined through an iterative process. Using the inelastic properties obtained, the plastic static response of some simple structural systems composed of beam elements was computed. Results were compared with known solutions, indicating a considerable improvement over response predictions obtained by means of simplified approximations used in previous investigations.

Review of gestational diabetes mellitus effects on vascular structure and function.

PubMed

Jensen, Louise A; Chik, Constance L; Ryan, Edmond A

2016-05-01

Vascular dysfunction has been described in women with a history of gestational diabetes mellitus. Furthermore, previous gestational diabetes mellitus increases the risk of developing Type 2 diabetes mellitus, a risk factor for cardiovascular disease. Factors contributing to vascular changes remain uncertain. The aim of this review was to summarize vascular structure and function changes found to occur in women with previous gestational diabetes mellitus and to identify factors that contribute to vascular dysfunction. A systematic search of electronic databases yielded 15 publications from 1998 to March 2014 that met the inclusion criteria. Our review confirmed that previous gestational diabetes mellitus contributes to vascular dysfunction, and the most consistent risk factor associated with previous gestational diabetes mellitus and vascular dysfunction was elevated body mass index. Heterogeneity existed across studies in determining the relationship of glycaemic levels and insulin resistance to vascular dysfunction. © The Author(s) 2016.

Non-Linear Seismic Velocity Estimation from Multiple Waveform Functionals and Formal Assessment of Constraints

DTIC Science & Technology

2011-09-01

tectonically active regions such as the Middle East. For example, we previously applied the code to determine the crust and upper mantle structure...Objective Optimization (MOO) for Multiple Datasets The primary goal of our current project is to develop a tool for estimating crustal structure that...be used to obtain crustal velocity structures by modeling broadband waveform, receiver function, and surface wave dispersion data. The code has been

Integrated Structural Biology for α-Helical Membrane Protein Structure Determination.

PubMed

Xia, Yan; Fischer, Axel W; Teixeira, Pedro; Weiner, Brian; Meiler, Jens

2018-04-03

While great progress has been made, only 10% of the nearly 1,000 integral, α-helical, multi-span membrane protein families are represented by at least one experimentally determined structure in the PDB. Previously, we developed the algorithm BCL::MP-Fold, which samples the large conformational space of membrane proteins de novo by assembling predicted secondary structure elements guided by knowledge-based potentials. Here, we present a case study of rhodopsin fold determination by integrating sparse and/or low-resolution restraints from multiple experimental techniques including electron microscopy, electron paramagnetic resonance spectroscopy, and nuclear magnetic resonance spectroscopy. Simultaneous incorporation of orthogonal experimental restraints not only significantly improved the sampling accuracy but also allowed identification of the correct fold, which is demonstrated by a protein size-normalized transmembrane root-mean-square deviation as low as 1.2 Å. The protocol developed in this case study can be used for the determination of unknown membrane protein folds when limited experimental restraints are available. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction.

PubMed

Pittman, Nikéa; Misseldine, Adam; Geilen, Lorena; Halder, Sujata; Smith, J Kennon; Kurian, Justin; Chipman, Paul; Janssen, Mandy; Mckenna, Robert; Baker, Timothy S; D'Abramo, Anthony; Cotmore, Susan; Tattersall, Peter; Agbandje-McKenna, Mavis

2017-10-30

LuIII, a protoparvovirus pathogenic to rodents, replicates in human mitotic cells, making it applicable for use to kill cancer cells. This virus group includes H-1 parvovirus (H-1PV) and minute virus of mice (MVM). However, LuIII displays enhanced oncolysis compared to H-1PV and MVM, a phenotype mapped to the major capsid viral protein 2 (VP2). This suggests that within LuIII VP2 are determinants for improved tumor lysis. To investigate this, the structure of the LuIII virus-like-particle was determined using single particle cryo-electron microscopy and image reconstruction to 3.17 Å resolution, and compared to the H-1PV and MVM structures. The LuIII VP2 structure, ordered from residue 37 to 587 (C-terminal), had the conserved VP topology and capsid morphology previously reported for other protoparvoviruses. This includes a core β-barrel and α-helix A, a depression at the icosahedral 2-fold and surrounding the 5-fold axes, and a single protrusion at the 3-fold axes. Comparative analysis identified surface loop differences among LuIII, H-1PV, and MVM at or close to the capsid 2- and 5-fold symmetry axes, and the shoulder of the 3-fold protrusions. The 2-fold differences cluster near the previously identified MVM sialic acid receptor binding pocket, and revealed potential determinants of protoparvovirus tumor tropism.

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

Structure of ganglioside with CAD blood group antigen activity

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

Gillard, B.K.; Blanchard, D.; Cartron, J.P.

1986-05-01

The novel erythrocyte ganglioside which carries the blood group Cad determinant has been isolated, and its structure has been determined. The ganglioside contained Glu:Gal:GalNAc:GlcNAc in a molar ratio of 1.00:1.94:0.93:0.95. The ganglioside binds Helix pomatia lectin and its chromatographic mobility is similar to G/sub D3/. After treatment with ..beta..-hexosaminidase (human placenta HexA) the product migrated with sialosylparagloboside (SPG), no longer binds Helix lectin, and binds a human anti-SPG antibody. Treatment of this material with neuraminidase (V. cholera) yielded a product with the mobility of paragloboside that bound monoclonal antibody 1B2. NMR analysis revealed that the terminal GalNAc is linked ..beta..1-4more » to Gal, and confirms the structure proposed previously: GalNAc..beta..1-4(NeuAc..cap alpha..2-3)Gal..beta..1-4GlcNAc..beta..1-3Gal..beta..1-4Glc-Cer. This structure is consistent with the previous demonstration that a compound with the same chromatographic mobility as the Cad ganglioside could be synthesized by enzymatic transfer of GalNAc to sialosylparagloboside.« less

Surface buckling of black phosphorus: Determination, origin, and influence on electronic structure

NASA Astrophysics Data System (ADS)

Dai, Zhongwei; Jin, Wencan; Yu, Jie-Xiang; Grady, Maxwell; Sadowski, Jerzy T.; Kim, Young Duck; Hone, James; Dadap, Jerry I.; Zang, Jiadong; Osgood, Richard M.; Pohl, Karsten

2017-12-01

The surface structure of black phosphorus materials is determined using surface-sensitive dynamical microspot low energy electron diffraction (μ LEED ) analysis using a high spatial resolution low energy electron microscopy (LEEM) system. Samples of (i) crystalline cleaved black phosphorus (BP) at 300 K and (ii) exfoliated few-layer phosphorene (FLP) of about 10 nm thickness which were annealed at 573 K in vacuum were studied. In both samples, a significant surface buckling of 0.22 Å and 0.30 Å, respectively, is measured, which is one order of magnitude larger than previously reported. As direct evidence for large buckling, we observe a set of (for the flat surface forbidden) diffraction spots. Using first-principles calculations, we find that the presence of surface vacancies is responsible for the surface buckling in both BP and FLP, and is related to the intrinsic hole doping of phosphoresce materials previously reported.

Surface buckling of black phosphorus: Determination, origin, and influence on electronic structure

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

Dai, Zhongwei; Jin, Wencan; Yu, Jie-Xiang

The surface structure of black phosphorus materials is determined using surface-sensitive dynamical microspot low energy electron diffraction ( μ LEED ) analysis using a high spatial resolution low energy electron microscopy (LEEM) system. Samples of (i) crystalline cleaved black phosphorus (BP) at 300 K and (ii) exfoliated few-layer phosphorene (FLP) of about 10 nm thickness which were annealed at 573 K in vacuum were studied. In both samples, a significant surface buckling of 0.22 Å and 0.30 Å, respectively, is measured, which is one order of magnitude larger than previously reported. As direct evidence for large buckling, we observe amore » set of (for the flat surface forbidden) diffraction spots. Using first-principles calculations, we find that the presence of surface vacancies is responsible for the surface buckling in both BP and FLP, and is related to the intrinsic hole doping of phosphoresce materials previously reported.« less

Surface buckling of black phosphorus: Determination, origin, and influence on electronic structure

DOE PAGES

Dai, Zhongwei; Jin, Wencan; Yu, Jie-Xiang; ...

2017-12-29

The surface structure of black phosphorus materials is determined using surface-sensitive dynamical microspot low energy electron diffraction ( μ LEED ) analysis using a high spatial resolution low energy electron microscopy (LEEM) system. Samples of (i) crystalline cleaved black phosphorus (BP) at 300 K and (ii) exfoliated few-layer phosphorene (FLP) of about 10 nm thickness which were annealed at 573 K in vacuum were studied. In both samples, a significant surface buckling of 0.22 Å and 0.30 Å, respectively, is measured, which is one order of magnitude larger than previously reported. As direct evidence for large buckling, we observe amore » set of (for the flat surface forbidden) diffraction spots. Using first-principles calculations, we find that the presence of surface vacancies is responsible for the surface buckling in both BP and FLP, and is related to the intrinsic hole doping of phosphoresce materials previously reported.« less

Structure determination of 3-O-caffeoyl-epi-gamma-quinide, an orphan bitter lactone in roasted coffee.

PubMed

Frank, Oliver; Blumberg, Simone; Krümpel, Gudrun; Hofmann, Thomas

2008-10-22

Recent investigations on the bitterness of coffee as well as 5- O-caffeoyl quinic acid roasting mixtures indicated the existence of another, yet unknown, bitter lactone besides the previously identified bitter compounds 5- O-caffeoyl- muco-gamma-quinide, 3- O-caffeoyl-gamma-quinide, 4- O-caffeoyl- muco-gamma-quinide, 5- O-caffeoyl- epi-delta-quinide, and 4- O-caffeoyl-gamma-quinide. In the present study, this orphan bitter lactone was isolated from the reaction products generated by dry heating of 5- O-caffeoylquinic acid model, and its structure was determined as the previously unreported 3- O-caffeoyl- epi-gamma-quinide by means of liquid chromatography-mass spectrometry (LC-MS) and one-/two-dimensional NMR experiments. The occurrence of this bitter lactone, exhibiting a low bitter recognition threshold of 58 micromol/L, in coffee beverages could be confirmed by LC-MS/MS (negative electrospray ionization) operating in the multiple reaction monitoring mode.

Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129Xe NMR Spectroscopy

PubMed Central

Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J.; Laitinen, Risto; Jokisaari, Jukka

2017-01-01

Abstract An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o‐ and m‐fluorophenol, whose previously unknown clathrate structures have been studied by 129Xe NMR spectroscopy. The high sensitivity of the 129Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures. PMID:28111848

Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles.

PubMed

Snyder, David A; Montelione, Gaetano T

2005-06-01

An important open question in the field of NMR-based biomolecular structure determination is how best to characterize the precision of the resulting ensemble of structures. Typically, the RMSD, as minimized in superimposing the ensemble of structures, is the preferred measure of precision. However, the presence of poorly determined atomic coordinates and multiple "RMSD-stable domains"--locally well-defined regions that are not aligned in global superimpositions--complicate RMSD calculations. In this paper, we present a method, based on a novel, structurally defined order parameter, for identifying a set of core atoms to use in determining superimpositions for RMSD calculations. In addition we present a method for deciding whether to partition that core atom set into "RMSD-stable domains" and, if so, how to determine partitioning of the core atom set. We demonstrate our algorithm and its application in calculating statistically sound RMSD values by applying it to a set of NMR-derived structural ensembles, superimposing each RMSD-stable domain (or the entire core atom set, where appropriate) found in each protein structure under consideration. A parameter calculated by our algorithm using a novel, kurtosis-based criterion, the epsilon-value, is a measure of precision of the superimposition that complements the RMSD. In addition, we compare our algorithm with previously described algorithms for determining core atom sets. The methods presented in this paper for biomolecular structure superimposition are quite general, and have application in many areas of structural bioinformatics and structural biology.

Structural Studies of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Tetramer in Complex with Its Receptor, Sialyllactose

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

Yuan, Ping; Thompson, Thomas B.; Wurzburg, Beth A.

2010-03-08

The paramyxovirus hemagglutinin-neuraminidase (HN) functions in virus attachment to cells, cleavage of sialic acid from oligosaccharides, and stimulating membrane fusion during virus entry into cells. The structural basis for these diverse functions remains to be fully understood. We report the crystal structures of the parainfluenza virus 5 (SV5) HN and its complexes with sialic acid, the inhibitor DANA, and the receptor sialyllactose. SV5 HN shares common structural features with HN of Newcastle disease virus (NDV) and human parainfluenza 3 (HPIV3), but unlike the previously determined HN structures, the SV5 HN forms a tetramer in solution, which is thought to bemore » the physiological oligomer. The sialyllactose complex reveals intact receptor within the active site, but no major conformational changes in the protein. The SV5 HN structures do not support previously proposed models for HN action in membrane fusion and suggest alternative mechanisms by which HN may promote virus entry into cells.« less

A comparative study of the N-linked oligosaccharide structures of human IgG subclass proteins.

PubMed Central

Jefferis, R; Lund, J; Mizutani, H; Nakagawa, H; Kawazoe, Y; Arata, Y; Takahashi, N

1990-01-01

Quantitative oligosaccharide profiles were determined for each of 18 human IgG paraproteins representing the four subclasses. Each paraprotein exhibits a unique profile that may be substantially different from that observed for polyclonal IgG. The IgG2 and some IgG3 proteins analysed exhibit a predominance of oligosaccharide moieties having galactose on the Man(alpha 1----3) arm rather than the Man(alpha 1----6) arm; it was previously held that galactosylation of the Man(alpha 1----6) arm is preferred, as observed for IgG1, IgG4 and polyclonal IgG. An IgG4 protein is reported that has galactosylated Man(alpha 1----3) and Man(alpha 1----6) arms on both Fc-localized carbohydrate moieties; previous findings suggested that such fully glycosylated structures could not be accommodated within the internal space of the C gamma 2 domains. Unusual monoantennary oligosaccharides present in IgG2 and IgG3 proteins were isolated and their structures determined. Images Fig. 1. PMID:2363690

Integral equation model for warm and hot dense mixtures.

PubMed

Starrett, C E; Saumon, D; Daligault, J; Hamel, S

2014-09-01

In a previous work [C. E. Starrett and D. Saumon, Phys. Rev. E 87, 013104 (2013)] a model for the calculation of electronic and ionic structures of warm and hot dense matter was described and validated. In that model the electronic structure of one atom in a plasma is determined using a density-functional-theory-based average-atom (AA) model and the ionic structure is determined by coupling the AA model to integral equations governing the fluid structure. That model was for plasmas with one nuclear species only. Here we extend it to treat plasmas with many nuclear species, i.e., mixtures, and apply it to a carbon-hydrogen mixture relevant to inertial confinement fusion experiments. Comparison of the predicted electronic and ionic structures with orbital-free and Kohn-Sham molecular dynamics simulations reveals excellent agreement wherever chemical bonding is not significant.

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.

Structural study of (N{sub 2}H{sub 5},H){sub 2.9}U{sub 1.1}Ce{sub 0.9}(C{sub 2}O{sub 4}){sub 5}·10H{sub 2}O from a conventional X-ray diffraction diagram obtained on a powder synthesized by a fast vortex process

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

Brackx, E., E-mail: Emmanuelle.brackx@cea.fr; Laval, J.P.; Dugne, O.

2015-01-15

In the context of research on U/minor actinides for nuclear fuel reprocessing in the transmutation process, developments are first studied with surrogates containing uranium and lanthanides to facilitate testing. The tests consist of precipitating and calcining a hydrazinium uranium/cerium oxalate. The structure of this oxalate had not been previously determined, but was necessary to validate the physicochemical mechanisms involved. The present study, firstly demonstrates the structural similarity of the U/Ce oxalate phase (N{sub 2}H{sub 5},H){sub 2.9}U{sub 1.1}Ce{sub 0.9}(C{sub 2}O{sub 4}){sub 5}·10H{sub 2}O, synthesized using a vortex precipitator for continuous synthesis of actinide oxalates, with previously known oxalates, crystallizing in P6{submore » 3}/mmc symmetry, obtained by more classical methods. This fast precipitation process induces massive nucleation of fine powders. Their structural and microstructural determination confirms that the raw and dried phases belong to the same structural family as (NH{sub 4}){sub 2}U{sub 2}(C{sub 2}O{sub 4}){sub 5}·0.7H{sub 2}O whose structure was described by Chapelet-Arab in P6{sub 3}/mmc symmetry, using single crystal data. However, they present an extended disorder inside the tunnels of the structure, even after drying at 100 °C, between water and hydrazinium ions. This disorder is directly related to the fast vortex method. This structure determination can be used as a basis for further semi-quantitative analysis on the U/minor actinides products formed under various experimental conditions. - Highlights: • Uranium cerium oxalate precipitate characterization by X-ray powder diffraction. • Morphology characterization by SEM analysis. • Structure determination by unit cell Rietveld refinement.« less

Computing approximate solutions of the protein structure determination problem using global constraints on discrete crystal lattices.

PubMed

Dal Palù, Alessandro; Dovier, Agostino; Pontelli, Enrico

2010-01-01

Crystal lattices are discrete models of the three-dimensional space that have been effectively employed to facilitate the task of determining proteins' natural conformation. This paper investigates alternative global constraints that can be introduced in a constraint solver over discrete crystal lattices. The objective is to enhance the efficiency of lattice solvers in dealing with the construction of approximate solutions of the protein structure determination problem. Some of them (e.g., self-avoiding-walk) have been explicitly or implicitly already used in previous approaches, while others (e.g., the density constraint) are new. The intrinsic complexities of all of them are studied and preliminary experimental results are discussed.

New measurement of the electron magnetic moment and the fine structure constant.

PubMed

Hanneke, D; Fogwell, S; Gabrielse, G

2008-03-28

A measurement using a one-electron quantum cyclotron gives the electron magnetic moment in Bohr magnetons, g/2=1.001 159 652 180 73 (28) [0.28 ppt], with an uncertainty 2.7 and 15 times smaller than for previous measurements in 2006 and 1987. The electron is used as a magnetometer to allow line shape statistics to accumulate, and its spontaneous emission rate determines the correction for its interaction with a cylindrical trap cavity. The new measurement and QED theory determine the fine structure constant, with alpha{-1}=137.035 999 084 (51) [0.37 ppb], and an uncertainty 20 times smaller than for any independent determination of alpha.

An integrated geophysical study of north African and Mediterranean lithospheric structure

NASA Astrophysics Data System (ADS)

Dial, Paul Joseph

1998-07-01

This dissertation utilizes gravity and seismic waveform modeling techniques to: (1) determine models of lithospheric structure across northern African through gravity modeling and (2) determine lithospheric and crustal structure and seismic wave propagation characteristics across northern Africa and the Mediterranean region. The purpose of the gravity investigation was to construct models of lithospheric structure across northern Africa through the analysis of gravity data constrained by previous geological and geophysical studies. Three lithospheric models were constructed from Bouguer gravity data using computer modeling, and the gravity data was wavelength-filtered to investigate the relative depth and extent of the structures associated with the major anomalies. In the Atlas Mountains area, the resulting earth models showed slightly greater crustal thickness than those of previous studies if a low density mantle region is not included in the models. However, if a low density mantle region (density = 3.25 g/cm3) was included beneath the Atlas, the earth models showed little crustal thickening (38 km), in accord with previous seismic studies. The second portion of the research consisted of seismic waveform modeling of regional and teleseismic events to determine crustal and lithospheric structure across northern Africa and the Mediterranean. A total of 174 seismograms (145 at regional distances (200--1400 km) and 29 with epicentral distances exceeding 1900 km) were modeled using 1-D velocity models and a reflectivity code. At regional distances from four stations surrounding the western Mediterranean basin (MAL, TOL, PTO and AQU) and one station near the Red Sea (HLW), 1-D velocity models can satisfactorily model the relative amplitudes of both the Pnl and surface wave portions of the seismograms. Modeling of propagation paths greater than 1900 km was also conducted across northern Africa and the Mediterranean. The results indicate that the S-wave velocity model of Corchete et al. (1995) is more appropriate for the Iberian Peninsula, southwestern Mediterranean basin and northwest African coast than the other models tested. This model was better able to predict both the timing and amplitudes of the observed Sn and surface wave components on the observed seismograms. (Abstract shortened by UMI.)

Reinvestigation of structure of porritoxin, a phytotoxin of Alternaria porri.

PubMed

Horiuchi, Masayuki; Maoka, Takashi; Iwase, Noriyasu; Ohnishi, Keiichiro

2002-08-01

The structure of porritoxin, a phytotoxin of Alternaria porri, was reinvestigated by detailed 2D NMR analysis including (1)H-(13)C and (1)H-(15)N HMBC experiments. The structure of porritoxin was determined to be 2-(2'-hydroxyethyl)-4-methoxy-5-methyl-6-(3' '-methyl-2' '-butenyloxy)-2,3-dihydro-1H-isoindol-1-one (1). Thus our previous proposed structure, 8-(3',3'-dimethylallyloxy)-10-methoxy-9-methyl-1H-3,4-dihydro-2,5-benzoxazocin-6(5H)-one (2), is incorrect.

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography.

PubMed

Bhardwaj, Anshul; Casjens, Sherwood R; Cingolani, Gino

2014-02-01

Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.

Structures, phase stabilities, and electrical potentials of Li-Si battery anode materials

NASA Astrophysics Data System (ADS)

Tipton, William W.; Bealing, Clive R.; Mathew, Kiran; Hennig, Richard G.

2013-05-01

The Li-Si materials system holds promise for use as an anode in Li-ion battery applications. For this system, we determine the charge capacity, voltage profiles, and energy storage density solely by ab initio methods without any experimental input. We determine the energetics of the stable and metastable Li-Si phases likely to form during the charging and discharging of a battery. Ab initio molecular dynamics simulations are used to model the structure of amorphous Li-Si as a function of composition, and a genetic algorithm coupled to density-functional theory searches the Li-Si binary phase diagram for small-cell, metastable crystal structures. Calculations of the phonon densities of states using density-functional perturbation theory for selected structures determine the importance of vibrational, including zero-point, contributions to the free energies. The energetics and local structural motifs of these metastable Li-Si phases closely resemble those of the amorphous phases, making these small unit cell crystal phases good approximants of the amorphous phase for use in further studies. The charge capacity is estimated, and the electrical potential profiles and the energy density of Li-Si anodes are predicted. We find, in good agreement with experimental measurements, that the formation of amorphous Li-Si only slightly increases the anode potential. Additionally, the genetic algorithm identifies a previously unreported member of the Li-Si binary phase diagram with composition Li5Si2 which is stable at 0 K with respect to previously known phases. We discuss its relationship to the partially occupied Li7Si3 phase.

Hyperfine structure measurements of neutral vanadium by laser-induced fluorescence spectroscopy in the wavelength range from 750 nm to 860 nm

NASA Astrophysics Data System (ADS)

Başar, Gü.; Güzelçimen, F.; Öztürk, I. K.; Er, A.; Bingöl, D.; Kröger, S.; Başar, Gö.

2017-11-01

The hyperfine structure of 57 spectral lines of neutral vanadium has been investigated using a hollow cathode lamp by laser-induced fluorescence spectroscopy in the wavelength range from 750 nm to 860 nm. New magnetic dipole hyperfine structure constants A have been determined for 14 atomic energy levels and new electric quadrupole hyperfine structure constants B for two levels. Additionally previously published hyperfine structure constants A of 56 levels have been measured again. In five cases, the old A values have been rejected and replaced by improved values.

Mass spectrometry combinations for structural characterization of sulfated-steroid metabolites.

PubMed

Yan, Yuetian; Rempel, Don L; Holy, Timothy E; Gross, Michael L

2014-05-01

Steroid conjugates, which often occur as metabolites, are challenging to characterize. One application is female-mouse urine, where steroid conjugates serve as important ligands for the pheromone-sensing neurons. Although the two with the highest abundance in mouse urine were previously characterized with mass spectrometry (MS) and NMR to be sulfated steroids, many more exist but remain structurally unresolved. Given that their physical and chemical properties are similar, they are likely to have a sulfated steroid ring structure. Because these compounds occur in trace amounts in mouse urine and elsewhere, their characterization by NMR will be difficult. Thus, MS methods become the primary approach for determining structure. Here, we show that a combination of MS tools is effective for determining the structures of sulfated steroids. Using 4-pregnene analogs, we explored high-resolving power MS (HR-MS) to determine chemical formulae; HD exchange MS (HDX-MS) to determine number of active, exchangeable hydrogens (e.g., OH groups); methoxyamine hydrochloride (MOX) derivatization MS, or reactive desorption electrospray ionization with hydroxylamine to determine the number of carbonyl groups; and tandem MS (MS(n)), high-resolution tandem MS (HRMS/MS), and GC-MS to obtain structural details of the steroid ring. From the fragmentation studies, we deduced three major fragmentation rules for this class of sulfated steroids. We also show that a combined MS approach is effective for determining structure of steroid metabolites, with important implications for targeted metabolomics in general and for the study of mouse social communication in particular.

Mass Spectrometry Combinations for Structural Characterization of Sulfated-Steroid Metabolites

NASA Astrophysics Data System (ADS)

Yan, Yuetian; Rempel, Don L.; Holy, Timothy E.; Gross, Michael L.

2014-05-01

Steroid conjugates, which often occur as metabolites, are challenging to characterize. One application is female-mouse urine, where steroid conjugates serve as important ligands for the pheromone-sensing neurons. Although the two with the highest abundance in mouse urine were previously characterized with mass spectrometry (MS) and NMR to be sulfated steroids, many more exist but remain structurally unresolved. Given that their physical and chemical properties are similar, they are likely to have a sulfated steroid ring structure. Because these compounds occur in trace amounts in mouse urine and elsewhere, their characterization by NMR will be difficult. Thus, MS methods become the primary approach for determining structure. Here, we show that a combination of MS tools is effective for determining the structures of sulfated steroids. Using 4-pregnene analogs, we explored high-resolving power MS (HR-MS) to determine chemical formulae; HD exchange MS (HDX-MS) to determine number of active, exchangeable hydrogens (e.g., OH groups); methoxyamine hydrochloride (MOX) derivatization MS, or reactive desorption electrospray ionization with hydroxylamine to determine the number of carbonyl groups; and tandem MS (MSn), high-resolution tandem MS (HRMS/MS), and GC-MS to obtain structural details of the steroid ring. From the fragmentation studies, we deduced three major fragmentation rules for this class of sulfated steroids. We also show that a combined MS approach is effective for determining structure of steroid metabolites, with important implications for targeted metabolomics in general and for the study of mouse social communication in particular.

Mass spectrometry combinations for structural characterization of sulfated-steroid metabolites

PubMed Central

Yan, Yuetian; Rempel, Don; Holy, Timothy E.; Gross, Michael L.

2015-01-01

Steroid conjugates, which often occur as metabolites, are challenging to characterize. One application is female-mouse urine, where steroid conjugates serve as important ligands for the pheromone-sensing neurons. Although the two with the highest abundance in mouse urine were previously characterized with mass spectrometry (MS) and NMR to be sulfated steroids, many more exist but remain structurally unresolved. Given that their physical and chemical properties are similar, they are likely to have a sulfated steroid ring structure. Because these compounds occur in trace amounts in mouse urine and elsewhere, their characterization by NMR will be difficult. Thus, MS methods become the primary approach for determining structure. Here, we show that a combination of MS tools is effective for determining the structures of sulfated steroids. Using 4-pregnene analogs, we explored high-resolving power MS (HR-MS) to determine chemical formulae; HD exchange MS (HDX-MS) to determine number of active, exchangeable hydrogens (e.g., OH groups); methoxyamine hydrochloride (MOX) derivatization MS, or reactive desorption electrospray ionization with hydroxylamine to determine the number of carbonyl groups; and tandem MS (MSn), high-resolution tandem MS (HRMS/MS), and GC-MS to obtain structural details of the steroid ring. From the fragmentation studies, we deduced three major fragmentation rules for this class of sulfated steroids. We also show that a combined MS approach is effective for determining structure of steroid metabolites, with important implications for targeted metabolomics in general and for the study of mouse social communication in particular. PMID:24658800

Secoiridoid components from Jasminum grandiflorum.

PubMed

Sadhu, Samir Kumar; Khan, Md Sojib; Ohtsuki, Takashi; Ishibashi, Masami

2007-07-01

Secoiridoid glucosides, 2''-epifraxamoside and demethyl-2''-epifraxamoside, and the secoiridoid, jasminanhydride were isolated from Jasminum grandiflorum together with four previously known phenolics and a triterpene. Structures were elucidated by detailed spectroscopic analysis. Stereochemistry of the compounds was determined by differential NOE experiment.

Preliminary crystallographic studies of four crystal forms of serum albumin

NASA Technical Reports Server (NTRS)

Carter, D. C.; Chang, B.; Ho, J. X.; Keeling, K.; Krishnasami, Z.

1994-01-01

Several crystal forms of serum albumin suitable for three-dimensional structure determination have been grown. These forms include crystals of recombinant and wild-type human serum albumin, baboon serum albumin, and canine serum albumin. The intrinsic limits of X-ray diffraction for these crystals are in the range 0.28-0.22 nm. Two of the crystal forms produced from human and canine albumin include incorporated long-chain fatty acids. Molecular replacement experiments have been successfully conducted on each crystal form using the previously determined atomic coordinates of human serum albumin illustrating the conserved tertiary structure.

Geometric structure of anatase Ti O2(101 )

NASA Astrophysics Data System (ADS)

Treacy, Jon P. W.; Hussain, Hadeel; Torrelles, Xavier; Grinter, David C.; Cabailh, Gregory; Bikondoa, Oier; Nicklin, Christopher; Selcuk, Sencer; Selloni, Annabella; Lindsay, Robert; Thornton, Geoff

2017-02-01

Surface x-ray diffraction has been used to determine the quantitative structure of the (101) termination of anatase Ti O2 . The atomic displacements from the bulk-terminated structure are significantly different from those previously calculated with density functional theory (DFT) methods with discrepancies for the Ti displacements in the [10 1 ¯] direction of up to 0.3 Å . DFT calculations carried out as part of the current paper provide a much better agreement through improved accuracy and thicker slab models.

Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction

PubMed Central

Misseldine, Adam; Geilen, Lorena; Halder, Sujata; Smith, J. Kennon; Kurian, Justin; Chipman, Paul; Janssen, Mandy; Mckenna, Robert; Baker, Timothy S.; D’Abramo, Anthony; Cotmore, Susan; Tattersall, Peter; Agbandje-McKenna, Mavis

2017-01-01

LuIII, a protoparvovirus pathogenic to rodents, replicates in human mitotic cells, making it applicable for use to kill cancer cells. This virus group includes H-1 parvovirus (H-1PV) and minute virus of mice (MVM). However, LuIII displays enhanced oncolysis compared to H-1PV and MVM, a phenotype mapped to the major capsid viral protein 2 (VP2). This suggests that within LuIII VP2 are determinants for improved tumor lysis. To investigate this, the structure of the LuIII virus-like-particle was determined using single particle cryo-electron microscopy and image reconstruction to 3.17 Å resolution, and compared to the H-1PV and MVM structures. The LuIII VP2 structure, ordered from residue 37 to 587 (C-terminal), had the conserved VP topology and capsid morphology previously reported for other protoparvoviruses. This includes a core β-barrel and α-helix A, a depression at the icosahedral 2-fold and surrounding the 5-fold axes, and a single protrusion at the 3-fold axes. Comparative analysis identified surface loop differences among LuIII, H-1PV, and MVM at or close to the capsid 2- and 5-fold symmetry axes, and the shoulder of the 3-fold protrusions. The 2-fold differences cluster near the previously identified MVM sialic acid receptor binding pocket, and revealed potential determinants of protoparvovirus tumor tropism. PMID:29084163

Use of conserved key amino acid positions to morph protein folds.

PubMed

Reddy, Boojala V B; Li, Wilfred W; Bourne, Philip E

2002-07-15

By using three-dimensional (3D) structure alignments and a previously published method to determine Conserved Key Amino Acid Positions (CKAAPs) we propose a theoretical method to design mutations that can be used to morph the protein folds. The original Paracelsus challenge, met by several groups, called for the engineering of a stable but different structure by modifying less than 50% of the amino acid residues. We have used the sequences from the Protein Data Bank (PDB) identifiers 1ROP, and 2CRO, which were previously used in the Paracelsus challenge by those groups, and suggest mutation to CKAAPs to morph the protein fold. The total number of mutations suggested is less than 40% of the starting sequence theoretically improving the challenge results. From secondary structure prediction experiments of the proposed mutant sequence structures, we observe that each of the suggested mutant protein sequences likely folds to a different, non-native potentially stable target structure. These results are an early indicator that analyses using structure alignments leading to CKAAPs of a given structure are of value in protein engineering experiments. Copyright 2002 Wiley Periodicals, Inc.

The Cryoelectron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod.

PubMed

Hospenthal, Manuela K; Zyla, Dawid; Costa, Tiago R D; Redzej, Adam; Giese, Christoph; Lillington, James; Glockshuber, Rudi; Waksman, Gabriel

2017-12-05

Adhesive chaperone-usher pili are long, supramolecular protein fibers displayed on the surface of many bacterial pathogens. The type 1 and P pili of uropathogenic Escherichia coli (UPEC) play important roles during urinary tract colonization, mediating attachment to the bladder and kidney, respectively. The biomechanical properties of the helical pilus rods allow them to reversibly uncoil in response to flow-induced forces, allowing UPEC to retain a foothold in the unique and hostile environment of the urinary tract. Here we provide the 4.2-Å resolution cryo-EM structure of the type 1 pilus rod, which together with the previous P pilus rod structure rationalizes the remarkable "spring-like" properties of chaperone-usher pili. The cryo-EM structure of the type 1 pilus rod differs in its helical parameters from the structure determined previously by a hybrid approach. We provide evidence that these structural differences originate from different quaternary structures of pili assembled in vivo and in vitro. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Legacy effects overwhelm the short-term effects of exotic plant invasion and restoration on soil microbial community structure, enzyme activities, and nitrogen cycling.

PubMed

Elgersma, Kenneth J; Ehrenfeld, Joan G; Yu, Shen; Vor, Torsten

2011-11-01

Plant invasions can have substantial consequences for the soil ecosystem, altering microbial community structure and nutrient cycling. However, relatively little is known about what drives these changes, making it difficult to predict the effects of future invasions. In addition, because most studies compare soils from uninvaded areas to long-established dense invasions, little is known about the temporal dependence of invasion impacts. We experimentally manipulated forest understory vegetation in replicated sites dominated either by exotic Japanese barberry (Berberis thunbergii), native Viburnums, or native Vacciniums, so that each vegetation type was present in each site-type. We compared the short-term effect of vegetation changes to the lingering legacy effects of the previous vegetation type by measuring soil microbial community structure (phospholipid fatty acids) and function (extracellular enzymes and nitrogen mineralization). We also replaced the aboveground litter in half of each plot with an inert substitute to determine if changes in the soil microbial community were driven by aboveground or belowground plant inputs. We found that after 2 years, the microbial community structure and function was largely determined by the legacy effect of the previous vegetation type, and was not affected by the current vegetation. Aboveground litter removal had only weak effects, suggesting that changes in the soil microbial community and nutrient cycling were driven largely by belowground processes. These results suggest that changes in the soil following either invasion or restoration do not occur quickly, but rather exhibit long-lasting legacy effects from previous belowground plant inputs.

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

Crystal Structures of MEK1 Binary and Ternary Complexes with Nucleotides and Inhibitors

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

Fischmann, Thierry O.; Smith, Catherine K.; Mayhood, Todd W.

MEK1 is a member of the MAPK signal transduction pathway that responds to growth factors and cytokines. We have determined that the kinase domain spans residues 35-382 by proteolytic cleavage. The complete kinase domain has been crystallized and its X-ray crystal structure as a complex with magnesium and ATP-{gamma}S determined at 2.1 {angstrom}. Unlike crystals of a truncated kinase domain previously published, the crystals of the intact domain can be grown either as a binary complex with a nucleotide or as a ternary complex with a nucleotide and one of a multitude of allosteric inhibitors. Further, the crystals allow formore » the determination of costructures with ATP competitive inhibitors. We describe the structures of nonphosphorylated MEK1 (npMEK1) binary complexes with ADP and K252a, an ATP-competitive inhibitor (see Table 1), at 1.9 and 2.7 {angstrom} resolution, respectively. Ternary complexes have also been solved between npMEK1, a nucleotide, and an allosteric non-ATP competitive inhibitor: ATP-{gamma}S with compound 1 and ADP with either U0126 or the MEK1 clinical candidate PD325089 at 1.8, 2.0, and 2.5 {angstrom}, respectively. Compound 1 is structurally similar to PD325901. These structures illustrate fundamental differences among various mechanisms of inhibition at the molecular level. Residues 44-51 have previously been shown to play a negative regulatory role in MEK1 activity. The crystal structure of the integral kinase domain provides a structural rationale for the role of these residues. They form helix A and repress enzymatic activity by stabilizing an inactive conformation in which helix C is displaced from its active state position. Finally, the structure provides for the first time a molecular rationale that explains how mutations in MEK may lead to the cardio-facio-cutaneous syndrome.« less

A complete, multi-level conformational clustering of antibody complementarity-determining regions

PubMed Central

Nikoloudis, Dimitris; Pitts, Jim E.

2014-01-01

Classification of antibody complementarity-determining region (CDR) conformations is an important step that drives antibody modelling and engineering, prediction from sequence, directed mutagenesis and induced-fit studies, and allows inferences on sequence-to-structure relations. Most of the previous work performed conformational clustering on a reduced set of structures or after application of various structure pre-filtering criteria. In this study, it was judged that a clustering of every available CDR conformation would produce a complete and redundant repertoire, increase the number of sequence examples and allow better decisions on structure validity in the future. In order to cope with the potential increase in data noise, a first-level statistical clustering was performed using structure superposition Root-Mean-Square Deviation (RMSD) as a distance-criterion, coupled with second- and third-level clustering that employed Ramachandran regions for a deeper qualitative classification. The classification of a total of 12,712 CDR conformations is thus presented, along with rich annotation and cluster descriptions, and the results are compared to previous major studies. The present repertoire has procured an improved image of our current CDR Knowledge-Base, with a novel nesting of conformational sensitivity and specificity that can serve as a systematic framework for improved prediction from sequence as well as a number of future studies that would aid in knowledge-based antibody engineering such as humanisation. PMID:25071986

Deep Internal Structure of Mars and the Geophysical Package of Netlander

NASA Technical Reports Server (NTRS)

Lognonne, P.; Giardini, D.; Banerdt, B.; Dehant, V.; Barriot, J. P.; Musmann, G.; Menvielle, M.

2000-01-01

Our present understanding of the interior structure of Mars is mostly based on the interpretation of gravity and rotation data, the chemistry of the SNC (shergottites, nakhlites, chassignites) meteoroids, and a comparison with the much better-known interior structure of the Earth. However geophysical information from previous missions have been insufficient to determine the deep internal structure of the planet. Therefore the state and size of the core and the depth and type of mantle discontinuities are unknown. Most previous seismic experiments have indeed failed, either due to a launch failure (as for the Optimism seismometer onboard the small surface stations of Mars 96) or after failure on Mars (as for the Viking 1 seismometer). The remaining Viking 2 seismometer did not produce a convincing marsquake detection, basically due to too strong wind sensitivity and too low resolution in the teleseismic frequency band. After almost a decade of continuous activity and proposals, the first network mission to Mars, NetLander (NL), is expected to be launched between 2005 and 2007. One of the main scientific objectives of this four-lander network mission will be the determination of the internal structure of the planet using a geophysical package. This package will have a seismometer, a magnetometer, and a geodetic experiment, allowing a complementary approach that will yield many new constraints on the mineralogy and temperature of the mantle and core of the planet.

Structure and Thermodynamics of Polyolefin Melts

NASA Astrophysics Data System (ADS)

Weinhold, J. D.; Curro, J. G.; Habenschuss, A.; Londono, J. D.

1997-03-01

Subtle differences in the intermolecular packing of various polyolefins can create dissimilar permeability and mixing behavior. We have used a combination of the Polymer Reference Interaction Site Model (PRISM) and Monte Carlo simulation to study the structural and thermodynamic properties of realistic models for polyolefins. Results for polyisobutylene and syndiotactic polypropylene will be presented along with comparisons to wide-angle x-ray scattering experiments and properties determined from previous studies of polyethylene and isotactic polypropylene. Our technique uses a Monte Carlo simulation on an isolated molecule to determine the polymer's intramolecular structure. With this information, PRISM theory can predict the intermolecular packing for any liquid density and/or mixture composition in a computationally efficient manner. This approach will then be used to explore the mixing behavior of these polyolefins.

A new feruloyl amide derivative from the fruits of Tribulus terrestris.

PubMed

Zhang, Xiaopo; Wei, Na; Huang, Jian; Tan, Yinfeng; Jin, Dejun

2012-01-01

A new feruloyl amide derivative, named tribulusamide C, was isolated from the fruits of Tribulus terrestris. Its structure was determined on the basis of spectroscopic analysis including IR, 1-D-, 2-D-NMR and HR-ESI-MS. The structure of tribulusamide C was characterised by a unit of pyrrolidine-2,5-dione, which distinguished it from other lignanamides previously isolated from the fruits of T. terrestris.

TEM and TED investigation of Ag/PbTe thin film bilayers.

NASA Astrophysics Data System (ADS)

Mandrino, Đorđe; Marinković, V.

Morphology and phase structure of Ag/PbTe thin film bilayers were investigated. This system was of particular interest because of interfacial reaction observed previously in an analogous Ag/SnTe system. Reaction products due to the interdiffusion of Ag with the substrate were determined as well as their orientations. They were discussed in view of the reaction products' structural relations to the PbTe.

Structural consequences of metallothionein dimerization: solution structure of the isolated Cd4-alpha-domain and comparison with the holoprotein dimer.

PubMed

Ejnik, John W; Muñoz, Amalia; DeRose, Eugene; Shaw, C Frank; Petering, David H

2003-07-22

The NMR determination of the structure of Cd(7)-metallothionein was done previously using a relatively large protein concentration that favors dimer formation. The reactivity of the protein is also affected under this condition. To examine the influence of protein concentration on metallothionein conformation, the isolated Cd(4)-alpha-domain was prepared from rabbit metallothionein-2 (MT 2), and its three-dimensional structure was determined by heteronuclear, (1)H-(111)Cd, and homonuclear, (1)H-(1)H NMR, correlation experiments. The three-dimensional structure was refined using distance and angle constraints derived from these two-dimensional NMR data sets and a distance geometry/simulated annealing protocol. The backbone superposition of the alpha-domain from rabbit holoprotein Cd(7)-MT 2 and the isolated rabbit Cd(4)-alpha was measured at a RMSD of 2.0 A. Nevertheless, the conformations of the two Cd-thiolate clusters were distinctly different at two of the cadmium centers. In addition, solvent access to the sulfhydryl ligands of the isolated Cd(4)-alpha cluster was 130% larger due to this small change in cluster geometry. To probe whether these differences were an artifact of the structure calculation, the Cd(4)-alpha-domain structure in rabbit Cd(7)-MT 2 was redetermined, using the previously defined set of NOEs and the present calculation protocol. All calculations employed the same ionic radius for Cd(2+) and same cadmium-thiolate bond distance. The newly calculated structure matched the original with an RMSD of 1.24 A. It is hypothesized that differences in the two alpha-domain structures result from a perturbation of the holoprotein structure because of head-to-tail dimerization under the conditions of the NMR experiments.

Reply to “Structural and magnetic behavior of the cubic oxyfluoride SrFeO{sub 2}F studied by neutron diffraction”

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

Clemens, Oliver, E-mail: oliver.clemens@kit.edu; Karlsruher Institut für Technologie, Institut für Nanotechnologie, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen; Berry, Frank J.

2015-03-15

In this article we comment on the results published by Thompson et al. (, J. Solid State Chem. 219 (2014) 173–178) on the crystal structure of SrFeO{sub 2}F, who claim the compound to crystallize in the cubic space group Pm-3m. We give a more detailed explanation of the determination of our previously reported structural model with Imma symmetry (Clemens et al., J. Solid State Chem. 206 (2013) 158–169), with addition of variable temperature XRD measurements with high counting time to provide unambiguous evidence for the Imma model being correct for our sample. - Graphical abstract: The crystal structure of SrFeO{submore » 2}F is discussed with regards to previous reports. - Highlights: • SrFeO{sub 2}F was synthesized by polymer based fluorination of SrFeO{sub 3}. • Evaluation of the diffraction data shows a pseudocubic cell metric. • Superstructure reflections at low d-spacings indicate deviation from cubic symmetry. • The phase transition temperature from orthorhombic to cubic was determined using variable temperature X-ray diffraction. • Results published by Thompson et al. are critically discussed with respect to those observations.« less

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

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

[A quantitative approach to sports training-adapted social determinants concerning sport].

PubMed

Alvis-Gómez, Martina K; Neira-Tolosa, Nury A

2013-01-01

Identifying and quantitatively analysing social determinants affecting disabled teenagers' inclusion/exclusion in high-performance sports. This was a descriptive cross-sectional study involving 19 12- to 19-year-old athletes suffering physical and sensory disability and 17 staff from the District Institute of Recreation and Sport. Likert-type rating scales were used, based on four analysis categories, i.e. social structure, socio-economic, educational and living condition determinants. Social inequity pervades the national paralympic sports' system. This is because 74 % of individuals only become recognised as sportspeople when they have obtained meritorious results in set competition without appropriate conditions having been previously provided by such paralympic sports institution to enable them to overcome structural and intermediate barriers. The social structure imposed on district-based paralympic sport stigmatises individuals regarding their individual abilities, affects their empowerment and freedom due to the discrimination experienced by disabled teenagers regarding their competitive achievements.

Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination.

PubMed

Bailey, Lucas J; Sheehy, Kimberly M; Dominik, Pawel K; Liang, Wenguang G; Rui, Huan; Clark, Michael; Jaskolowski, Mateusz; Kim, Yejoon; Deneka, Dawid; Tang, Wei-Jen; Kossiakoff, Anthony A

2018-02-02

Antibody Fab fragments have been exploited with significant success to facilitate the structure determination of challenging macromolecules as crystallization chaperones and as molecular fiducial marks for single particle cryo-electron microscopy approaches. However, the inherent flexibility of the "elbow" regions, which link the constant and variable domains of the Fab, can introduce disorder and thus diminish their effectiveness. We have developed a phage display engineering strategy to generate synthetic Fab variants that significantly reduces elbow flexibility, while maintaining their high affinity and stability. This strategy was validated using previously recalcitrant Fab-antigen complexes where introduction of an engineered elbow region enhanced crystallization and diffraction resolution. Furthermore, incorporation of the mutations appears to be generally portable to other synthetic antibodies and may serve as a universal strategy to enhance the success rates of Fabs as structure determination chaperones. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluating MEDEVAC Force Structure Requirements Using an Updated Army Scenario, Total Army Analysis Admission Data, Monte Carlo Simulation, and Theater Structure.

PubMed

Fulton, Lawrence; Kerr, Bernie; Inglis, James M; Brooks, Matthew; Bastian, Nathaniel D

2015-07-01

In this study, we re-evaluate air ambulance requirements (rules of allocation) and planning considerations based on an Army-approved, Theater Army Analysis scenario. A previous study using workload only estimated a requirement of 0.4 to 0.6 aircraft per admission, a significant bolus over existence-based rules. In this updated study, we estimate requirements for Phase III (major combat operations) using a simulation grounded in previously published work and Phase IV (stability operations) based on four rules of allocation: unit existence rules, workload factors, theater structure (geography), and manual input. This study improves upon previous work by including the new air ambulance mission requirements of Department of Defense 51001.1, Roles and Functions of the Services, by expanding the analysis over two phases, and by considering unit rotation requirements known as Army Force Generation based on Department of Defense policy. The recommendations of this study are intended to inform future planning factors and already provided decision support to the Army Aviation Branch in determining force structure requirements. Reprint & Copyright © 2015 Association of Military Surgeons of the U.S.

Magnetic and electromagnetic prospections at the Roman city of Hadrianopolis, southern Albania

NASA Astrophysics Data System (ADS)

Schettino, Antonio; Perna, Roberto; Pierantoni, Pietro Paolo; Ghezzi, Annalisa; Tassi, Luca; Sforzini, David

2017-04-01

We report on a combined magnetic-GPR survey performed in 2015-2017 at the ancient Roman city of Hadrianopolis, located in southern Albania, in the context of the project Teatri Antichi Riuniti (TAU). The collected data supplemented previous archaeological surveys performed by the University of Macerata with the aim of promoting the valley and starting the realization of an archaeological park. Hadrianopolis was founded through a reorganization of a previous Hellenistic settlement. Starting from 2015, magnetic and GPR surveys were carried out in Hadrianopolis in order to determine the urban framework. The collected data revealed the existence of structures organized along two main different patterns, which have been interpreted as due to the superposition of Roman buildings and Late Antiquity structures. In fact, the arrangement of structures in the studied area shows a regular urban organization of Roman type separated by a less regular disposition of the buildings that can be attributed to the Byzantine age. The latter arrangement is superimposed on the previous Roman structures. A stone wall, clearly identified by the combination of magnetic anomalies and GPR images, separates the Byzantine seattlement from the genuine Roman sector.

Sphericity determination using resonant ultrasound spectroscopy

DOEpatents

Dixon, Raymond D.; Migliori, Albert; Visscher, William M.

1994-01-01

A method is provided for grading production quantities of spherical objects, such as roller balls for bearings. A resonant ultrasound spectrum (RUS) is generated for each spherical object and a set of degenerate sphere-resonance frequencies is identified. From the degenerate sphere-resonance frequencies and known relationships between degenerate sphere-resonance frequencies and Poisson's ratio, a Poisson's ratio can be determined, along with a "best" spherical diameter, to form spherical parameters for the sphere. From the RUS, fine-structure resonant frequency spectra are identified for each degenerate sphere-resonance frequency previously selected. From each fine-structure spectrum and associated sphere parameter values an asphericity value is determined. The asphericity value can then be compared with predetermined values to provide a measure for accepting or rejecting the sphere.

Sphericity determination using resonant ultrasound spectroscopy

DOEpatents

Dixon, R.D.; Migliori, A.; Visscher, W.M.

1994-10-18

A method is provided for grading production quantities of spherical objects, such as roller balls for bearings. A resonant ultrasound spectrum (RUS) is generated for each spherical object and a set of degenerate sphere-resonance frequencies is identified. From the degenerate sphere-resonance frequencies and known relationships between degenerate sphere-resonance frequencies and Poisson's ratio, a Poisson's ratio can be determined, along with a 'best' spherical diameter, to form spherical parameters for the sphere. From the RUS, fine-structure resonant frequency spectra are identified for each degenerate sphere-resonance frequency previously selected. From each fine-structure spectrum and associated sphere parameter values an asphericity value is determined. The asphericity value can then be compared with predetermined values to provide a measure for accepting or rejecting the sphere. 14 figs.

Structural transition of (InSb)n clusters at n = 6-10

NASA Astrophysics Data System (ADS)

Lu, Qi Liang; Luo, Qi Quan; Huang, Shou Guo; Li, Yi De

2016-10-01

An optimization strategy combining global semi-empirical quantum mechanical search with all-electron density functional theory was adopted to determine the lowest energy structure of (InSb)n clusters with n = 6-10. A new structural growth pattern of the clusters was observed. The lowest energy structures of (InSb)6 and (InSb)8 were different from that of previously reported results. Competition existed between core-shell and cage-like structures of (InSb)8. The structural transition of (InSb)n clusters occurred at size n = 8-9. For (InSb)9 and (InSb)10 clusters, core-shell structure were more energetically favorable than the cage. The corresponding electronic properties were investigated.

Structure and Dynamics of Type III Secretion Effector Protein ExoU As determined by SDSL-EPR Spectroscopy in Conjunction with De Novo Protein Folding

PubMed Central

2017-01-01

ExoU is a 74 kDa cytotoxin that undergoes substantial conformational changes as part of its function, that is, it has multiple thermodynamically stable conformations that interchange depending on its environment. Such flexible proteins pose unique challenges to structural biology: (1) not only is it often difficult to determine structures by X-ray crystallography for all biologically relevant conformations because of the flat energy landscape (2) but also experimental conditions can easily perturb the biologically relevant conformation. The first challenge can be overcome by applying orthogonal structural biology techniques that are capable of observing alternative, biologically relevant conformations. The second challenge can be addressed by determining the structure in the same biological state with two independent techniques under different experimental conditions. If both techniques converge to the same structural model, the confidence that an unperturbed biologically relevant conformation is observed increases. To this end, we determine the structure of the C-terminal domain of the effector protein, ExoU, from data obtained by electron paramagnetic resonance spectroscopy in conjunction with site-directed spin labeling and in silico de novo structure determination. Our protocol encompasses a multimodule approach, consisting of low-resolution topology sampling, clustering, and high-resolution refinement. The resulting model was compared with an ExoU model in complex with its chaperone SpcU obtained previously by X-ray crystallography. The two models converged to a minimal RMSD100 of 3.2 Å, providing evidence that the unbound structure of ExoU matches the fold observed in complex with SpcU. PMID:28691114

47 CFR 90.159 - Temporary and conditional permits.

Code of Federal Regulations, 2010 CFR

2010-10-01

... proposed antenna structure has been previously studied by the Federal Aviation Administration and determined to pose no hazard to aviation safety as required by § 17.4 of the Commission's Rules; or the... Section 90.159 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO...

Plasma pressure distribution in the equatorial plane of the Earth's magnetosphere at geocentric distances of 6-10 R E according to the international THEMIS mission data

NASA Astrophysics Data System (ADS)

Kirpichev, I. P.; Antonova, E. E.

2011-08-01

The structure of the averaged plasma pressure distribution in the plasma ring around the Earth at geocentric distances of ˜6-10 R E has been determined. The distribution function moments measured on the international THEMIS mission satellites have been used. The plasma pressure distribution in the equatorial plane at 15 R E > XSM > -15 R E and 15 R E > YSM > -15 R E has been statistically studied. The radial dependence of the plasma pressure at the day-night and morning-evening meridians has been analyzed. It has been indicated that the plasma ring around the Earth has a structure, which is close to being azimuthally symmetric. The achieved results have been compared with the pressure distributions obtained previously. It has been indicated that in the overlapping regions, the achieved results agree with the previously obtained data within the pressure determination errors.

The 2.3-Angstrom Structure of Porcine Circovirus 2

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

Khayat, Reza; Brunn, Nicholas; Speir, Jeffrey A.

Porcine circovirus 2 (PCV2) is a T = 1 nonenveloped icosahedral virus that has had severe impact on the swine industry. Here we report the crystal structure of an N-terminally truncated PCV2 virus-like particle at 2.3-{angstrom} resolution, and the cryo-electron microscopy (cryo-EM) image reconstruction of a full-length PCV2 virus-like particle at 9.6-{angstrom} resolution. This is the first atomic structure of a circovirus. The crystal structure revealed that the capsid protein fold is a canonical viral jelly roll. The loops connecting the strands of the jelly roll define the limited features of the surface. Sulfate ions interacting with the surface andmore » electrostatic potential calculations strongly suggest a heparan sulfate binding site that allows PCV2 to gain entry into the cell. The crystal structure also allowed previously determined epitopes of the capsid to be visualized. The cryo-EM image reconstruction showed that the location of the N terminus, absent in the crystal structure, is inside the capsid. As the N terminus was previously shown to be antigenic, it may externalize through viral 'breathing'.« less

Isolation and characterization of novel endogenous digitalis-like factors in the ovary of the giant toad, Bufo marinus.

PubMed

Matsukawa, M; Mukai, T; Akizawa, T; Miyatake, S; Yoshioka, M; Morris, J F; Butler, V P

1998-12-01

We have previously described the structures of four novel unconjugated bufadienolides in the ovary of the toad, Bufo marinus. In this study, we report the separation and characterization of three novel bufadienolide conjugates. These compounds were purified by HPLC, and their structures were determined to be 11alpha, 19-dihydroxytelocinobufagin-3-(12-hydroxydodecanoic acid) ester, 11alpha,19-dihydroxytelocinobufagin-3-(14-hydroxy-7-tetra decenoic acid) ester, and 11alpha, 19-dihydroxytelocinobufagin-3-(14-hydroxytetradecanoic acid) ester on the basis of NMR and MS data. Numerous dicarboxylic acid esters of bufadienolides have previously been described, but the three bufadienolide conjugates described in this report differ from previously described esters in that they contain hydroxylated monocarboxylic acids. The function of these three conjugates is not known but they are, like bufotoxins, potent inhibitors of Na+, K+-ATPase and may play a developmental role in the differentiation of toad oocytes.

Relationship of PrPSc molecular properties with incubation time in a natural prion disease host: a characterization of three isolates of U.S. sheep scrapie

USDA-ARS?s Scientific Manuscript database

Determination of aspects of tertiary and quaternary structure of PrPSc associated with differences in disease presentation in the host is a key area of interest in the prion field. Previously, we determined that a U.S. scrapie isolate (136-VDEP) with a short incubation time upon passage in sheep als...

The role of the AT pairs in the acid denaturation of DNA.

PubMed Central

Hermann, P; Fredericq, E

1977-01-01

It has been determined previously that the protonation of the GC pairs induces a DNA conformation change which leads to a "metastable" structure. The role of the AT pairs, however, is no well known because the protonation does not modify their spectral properties. By means of an indirect method based on the binding of proflavine, it has been determined that the AT pairs are protonated before the acid-induced denaturation and that they seem to be unable to assume a conformation change when protonated. These results would indicate that the protonated AT pairs may be responsible for the induction of the acid denaturation and not the GC pairs as it was thought previously. PMID:20604

Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes

PubMed Central

Yesudhas, Dhanusha; Anwar, Muhammad Ayaz; Panneerselvam, Suresh; Durai, Prasannavenkatesh; Shah, Masaud; Choi, Sangdun

2016-01-01

The octamer-binding transcription factor 4 (Oct4) and sex-determining region Y (SRY)-box 2 (Sox2) proteins induce various transcriptional regulators to maintain cellular pluripotency. Most Oct4/Sox2 complexes have either 0 base pairs (Oct4/Sox20bp) or 3 base pairs (Oct4/Sox23bp) separation between their DNA-binding sites. Results from previous biochemical studies have shown that the complexes separated by 0 base pairs are associated with a higher pluripotency rate than those separated by 3 base pairs. Here, we performed molecular dynamics (MD) simulations and calculations to determine the binding free energy and per-residue free energy for the Oct4/Sox20bp and Oct4/Sox23bp complexes to identify structural differences that contribute to differences in induction rate. Our MD simulation results showed substantial differences in Oct4/Sox2 domain movements, as well as secondary-structure changes in the Oct4 linker region, suggesting a potential reason underlying the distinct efficiencies of these complexes during reprogramming. Moreover, we identified key residues and hydrogen bonds that potentially facilitate protein-protein and protein-DNA interactions, in agreement with previous experimental findings. Consequently, our results confess that differential spacing of the Oct4/Sox2 DNA binding sites can determine the magnitude of transcription of the targeted genes during reprogramming. PMID:26790000

Structural test of the parameterized-backbone method for protein design.

PubMed

Plecs, Joseph J; Harbury, Pehr B; Kim, Peter S; Alber, Tom

2004-09-03

Designing new protein folds requires a method for simultaneously optimizing the conformation of the backbone and the side-chains. One approach to this problem is the use of a parameterized backbone, which allows the systematic exploration of families of structures. We report the crystal structure of RH3, a right-handed, three-helix coiled coil that was designed using a parameterized backbone and detailed modeling of core packing. This crystal structure was determined using another rationally designed feature, a metal-binding site that permitted experimental phasing of the X-ray data. RH3 adopted the intended fold, which has not been observed previously in biological proteins. Unanticipated structural asymmetry in the trimer was a principal source of variation within the RH3 structure. The sequence of RH3 differs from that of a previously characterized right-handed tetramer, RH4, at only one position in each 11 amino acid sequence repeat. This close similarity indicates that the design method is sensitive to the core packing interactions that specify the protein structure. Comparison of the structures of RH3 and RH4 indicates that both steric overlap and cavity formation provide strong driving forces for oligomer specificity.

nextPARS: parallel probing of RNA structures in Illumina

PubMed Central

Saus, Ester; Willis, Jesse R.; Pryszcz, Leszek P.; Hafez, Ahmed; Llorens, Carlos; Himmelbauer, Heinz

2018-01-01

RNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining the secondary structures of RNAs is central to understanding their function and evolution. In recent years several sequencing-based approaches have been developed that allow probing structural features of thousands of RNA molecules present in a sample. Here, we describe nextPARS, a novel Illumina-based implementation of in vitro parallel probing of RNA structures. Our approach achieves comparable accuracy to previous implementations, while enabling higher throughput and sample multiplexing. PMID:29358234

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.

Electronic structure of lanthanide scandates

NASA Astrophysics Data System (ADS)

Mizzi, Christopher A.; Koirala, Pratik; Marks, Laurence D.

2018-02-01

X-ray photoelectron spectroscopy, ultraviolet photoelectron spectroscopy, and density functional theory calculations were used to study the electronic structure of three lanthanide scandates: GdSc O3,TbSc O3 , and DySc O3 . X-ray photoelectron spectra simulated from first-principles calculations using a combination of on-site hybrid and GGA +U methods were found to be in good agreement with experimental x-ray photoelectron spectra. The hybrid method was used to model the ground state electronic structure and the GGA +U method accounted for the shift of valence state energies due to photoelectron emission via a Slater-Janak transition state approach. From these results, the lanthanide scandate valence bands were determined to be composed of Ln 4 f ,O 2 p , and Sc 3 d states, in agreement with previous work. However, contrary to previous work the minority Ln 4 f states were found to be located closer to, and in some cases at, the valence band maximum. This suggests that minority Ln 4 f electrons may play a larger role in lanthanide scandate properties than previously thought.

Crystal structure of the toxin Msmeg_6760, the structural homolog of Mycobacterium tuberculosis Rv2035, a novel type II toxin involved in the hypoxic response

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

Bajaj, R. Alexandra; Arbing, Mark A.; Shin, Annie

The structure of Msmeg_6760, a protein of unknown function, has been determined. Biochemical and bioinformatics analyses determined that Msmeg_6760 interacts with a protein encoded in the same operon, Msmeg_6762, and predicted that the operon is a toxin–antitoxin (TA) system. Structural comparison of Msmeg_6760 with proteins of known function suggests that Msmeg_6760 binds a hydrophobic ligand in a buried cavity lined by large hydrophobic residues. Access to this cavity could be controlled by a gate–latch mechanism. The function of the Msmeg_6760 toxin is unknown, but structure-based predictions revealed that Msmeg_6760 and Msmeg_6762 are homologous to Rv2034 and Rv2035, a predicted novelmore » TA system involved inMycobacterium tuberculosislatency during macrophage infection. The Msmeg_6760 toxin fold has not been previously described for bacterial toxins and its unique structural features suggest that toxin activation is likely to be mediated by a novel mechanism.« less

Janthinocins A, B and C, novel peptide lactone antibiotics produced by Janthinobacterium lividum. II. Structure elucidation.

PubMed

Johnson, J H; Tymiak, A A; Bolgar, M S

1990-08-01

The structures of janthinocins A, B and C, three novel macrocyclic peptide lactone antibiotics isolated from fermentations of Janthinobacterium lividum, were determined. The janthinocins are of particular interest because they contain three amino acid residues that have not previously been reported in natural products: Each contains erythro-beta-hydroxy-D-leucine while janthinocins A and B also contain beta-hydroxytryptophan and beta-ketotryptophan, respectively.

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

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

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

Bhardwaj, Anshul; Casjens, Sherwood R.; Cingolani, Gino, E-mail: gino.cingolani@jefferson.edu

2014-02-01

This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identifiedmore » in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.« less

Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus

PubMed Central

Huynh, Nhung T.; Hesketh, Emma L.; Saxena, Pooja; Meshcheriakova, Yulia; Ku, You-Chan; Hoang, Linh T.; Johnson, John E.; Ranson, Neil A.; Lomonossoff, George P.; Reddy, Vijay S.

2016-01-01

SUMMARY Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed. PMID:27021160

On the internal structure of relativistic jets collimated by ambient gas pressure

NASA Astrophysics Data System (ADS)

Beskin, V. S.; Chernoglazov, A. V.; Kiselev, A. M.; Nokhrina, E. E.

2017-12-01

Recent progress in very long baseline interferometry (VLBI) observations of relativistic jets outflowing from active galactic nuclei gives us direct information about jet width rjet(l) dependence on the distance l from the 'central engine'. Being the missing link in previous works, this relation opens the possibility of determining the internal structure of a jet. In this article, we consider a relativistic jet submerged in an external medium with finite gas pressure Pext. Neither an external magnetic field nor an infinitely thin current sheet will be assumed. This approach allows us to construct a reasonable solution in which both the magnetic field and the flow velocity vanish at the jet boundary r = rjet. In particular, the connection between external gas pressure and internal structure of a relativistic jet is determined.

Extending existing structural identifiability analysis methods to mixed-effects models.

PubMed

Janzén, David L I; Jirstrand, Mats; Chappell, Michael J; Evans, Neil D

2018-01-01

The concept of structural identifiability for state-space models is expanded to cover mixed-effects state-space models. Two methods applicable for the analytical study of the structural identifiability of mixed-effects models are presented. The two methods are based on previously established techniques for non-mixed-effects models; namely the Taylor series expansion and the input-output form approach. By generating an exhaustive summary, and by assuming an infinite number of subjects, functions of random variables can be derived which in turn determine the distribution of the system's observation function(s). By considering the uniqueness of the analytical statistical moments of the derived functions of the random variables, the structural identifiability of the corresponding mixed-effects model can be determined. The two methods are applied to a set of examples of mixed-effects models to illustrate how they work in practice. Copyright © 2017 Elsevier Inc. All rights reserved.

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

PubMed Central

Kinjo, Akira R.; Bekker, Gert-Jan; Suzuki, Hirofumi; Tsuchiya, Yuko; Kawabata, Takeshi; Ikegawa, Yasuyo; Nakamura, Haruki

2017-01-01

The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described. PMID:27789697

Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn 2+/Mn 2+ heterobinucleation

DOE PAGES

Ransey, Elizabeth; Paredes, Eduardo; Dey, Sourav K.; ...

2017-05-17

Here, the RNA lariat debranching enzyme, Dbr1, is a metallophosphoesterase that cleaves 2'-5' phosphodiester bonds within intronic lariats. Previous reports have indicated that Dbr1 enzymatic activity is supported by diverse metal ions including Ni 2+, Mn 2+, Mg 2+, Fe 2+, and Zn 2+. While in initial structures of the Entamoeba histolytica Dbr1 only one of the two catalytic metal-binding sites were observed to be occupied (with a Mn 2+ ion), recent structures determined a Zn 2+/Fe 2+ heterobinucleation. We solved a high-resolution X-ray crystal structure (1.8 Å) of the E. histolytica Dbr1 and determined a Zn 2+/Mn 2+ occupancy.more » ICP-AES corroborate this finding, and in vitro debranching assays with fluorescently labeled branched substrates confirm activity.« less

Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn 2+/Mn 2+ heterobinucleation

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

Ransey, Elizabeth; Paredes, Eduardo; Dey, Sourav K.

Here, the RNA lariat debranching enzyme, Dbr1, is a metallophosphoesterase that cleaves 2'-5' phosphodiester bonds within intronic lariats. Previous reports have indicated that Dbr1 enzymatic activity is supported by diverse metal ions including Ni 2+, Mn 2+, Mg 2+, Fe 2+, and Zn 2+. While in initial structures of the Entamoeba histolytica Dbr1 only one of the two catalytic metal-binding sites were observed to be occupied (with a Mn 2+ ion), recent structures determined a Zn 2+/Fe 2+ heterobinucleation. We solved a high-resolution X-ray crystal structure (1.8 Å) of the E. histolytica Dbr1 and determined a Zn 2+/Mn 2+ occupancy.more » ICP-AES corroborate this finding, and in vitro debranching assays with fluorescently labeled branched substrates confirm activity.« less

Improvement of determinating seafloor benchmark position with large-scale horizontal heterogeneity in the ocean area

NASA Astrophysics Data System (ADS)

Uemura, Y.; Tadokoro, K.; Matsuhiro, K.; Ikuta, R.

2015-12-01

The most critical issue in reducing the accuracy of seafloor positioning system, GPS/Acoustic technique, is large-scale thermal gradient of sound-speed structure [Muto et al., 2008] due to the ocean current. For example, Kuroshio Current, near our observation station, forms this structure. To improve the accuracy of seafloor benchmark position (SBP), we need to directly measure the structure frequently, or estimate it from travel time residual. The former, we repeatedly measure the sound-speed at Kuroshio axis using Underway CTD and try to apply analysis method of seafloor positioning [Yasuda et al., 2015 AGU meeting]. The latter, however, we cannot estimate the structure using travel time residual until now. Accordingly, in this study, we focus on azimuthal dependence of Estimated Mean Sound-Speed (EMSS). EMSS is defined as distance between vessel position and estimated SBP divided by travel time. If thermal gradient exists and SBP is true, EMSS should have azimuthal dependence with the assumption of horizontal layered sound-speed structure in our previous analysis method. We use the data at KMC located on the central part of Nankai Trough, Japan on Jan. 28, 2015, because on that day KMC was on the north edge of Kuroshio, where we expect that thermal gradient exists. In our analysis method, the hyper parameter (μ value) weights travel time residual and rate of change of sound speed structure. However, EMSS derived from μ value determined by Ikuta et al. [2008] does not have azimuthal dependence, that is, we cannot estimate thermal gradient. Thus, we expect SBP has a large bias. Therefore, in this study, we use another μ value and examine whether EMSS has azimuthal dependence or not. With the μ value of this study, which is 1 order of magnitude smaller than the previous value, EMSS has azimuthal dependence that is consistent with observation day's thermal gradient. This result shows that we can estimate the thermal gradient adequately. This SBP displaces 25.6 cm to the north and 11.8 cm to the east compared to previous SBP. This displacement reduces the bias of SBP and RMS of horizontal component in time series to 1/3. Therefore, determination of SBP is suitable when the thermal gradient exists on observation day and EMSS has azimuthal dependence for redetermination of μ value.

Structural Insights into Bound Water in Crystalline Amino Acids: Experimental and Theoretical (17)O NMR.

PubMed

Michaelis, Vladimir K; Keeler, Eric G; Ong, Ta-Chung; Craigen, Kimberley N; Penzel, Susanne; Wren, John E C; Kroeker, Scott; Griffin, Robert G

2015-06-25

We demonstrate here that the (17)O NMR properties of bound water in a series of amino acids and dipeptides can be determined with a combination of nonspinning and magic-angle spinning experiments using a range of magnetic field strengths from 9.4 to 21.1 T. Furthermore, we propose a (17)O chemical shift fingerprint region for bound water molecules in biological solids that is well outside the previously determined ranges for carbonyl, carboxylic, and hydroxyl oxygens, thereby offering the ability to resolve multiple (17)O environments using rapid one-dimensional NMR techniques. Finally, we compare our experimental data against quantum chemical calculations using GIPAW and hybrid-DFT, finding intriguing discrepancies between the electric field gradients calculated from structures determined by X-ray and neutron diffraction.

Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat induced point mutations

USDA-ARS?s Scientific Manuscript database

The genome sequence of the phytopathogenic fungus Leptosphaeria maculans has been determined. It has a unique bipartite structure, divided between distinct GC-equilibrated and AT-rich regions (isochores), reminiscent of some plants and animals but not previously observed in fungi. The GC-equilibrate...

A Multivariate Model of Achievement in Geometry

ERIC Educational Resources Information Center

Bailey, MarLynn; Taasoobshirazi, Gita; Carr, Martha

2014-01-01

Previous studies have shown that several key variables influence student achievement in geometry, but no research has been conducted to determine how these variables interact. A model of achievement in geometry was tested on a sample of 102 high school students. Structural equation modeling was used to test hypothesized relationships among…

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

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

A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography.

PubMed

Chatake, Toshiyuki; Fujiwara, Satoru

2016-01-01

A difference in the neutron scattering length between hydrogen and deuterium leads to a high density contrast in neutron Fourier maps. In this study, a technique for determining the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography is developed and evaluated using ribonuclease A. The contrast map between the D2O-solvent and H2O-solvent crystals is calculated in real space, rather than in reciprocal space as performed in previous neutron D/H contrast crystallography. The present technique can thus utilize all of the amplitudes of the neutron structure factors for both D2O-solvent and H2O-solvent crystals. The neutron D/H contrast maps clearly demonstrate the powerful detectability of H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at medium resolution (1.8 Å). Moreover, water molecules can be categorized into three types according to their tendency towards rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. This technique is suitable for incorporation into the standard structure-determination process used in neutron protein crystallography; consequently, more precise and efficient determination of the D-atom positions is possible using a combination of this D/H contrast technique and standard neutron structure-determination protocols.

Frequency measurement of the 2 S10-3 D12 two-photon transition in atomic 4He

NASA Astrophysics Data System (ADS)

Huang, Yi-Jan; Guan, Yu-Chan; Huang, Yao-Chin; Suen, Te-Hwei; Peng, Jin-Long; Wang, Li-Bang; Shy, Jow-Tsong

2018-03-01

We present precise frequency measurement of the 2 S10-3 D12 two-photon transition in 4He at 1009 nm. The laser source at 1009 nm is stabilized on an optical frequency comb to perform the absolute frequency measurement. The absolute frequency of 2 S10-3 D12 transition is experimentally determined to be 594 414 291.803(13) MHz with a relative uncertainty of 1.6 ×10-11 , which is more precise than previous determinations by a factor of 25. In combination with the theoretical ionization energy of the 3 D12 state, the ionization energy of the 2 S10 state is determined to be 960 332 040.823(24) MHz. In addition, the deduced 2 S10 and 2 S31 Lamb shifts are 2806.864(24) MHz and 4058.130(24) MHz, respectively, which are 1.6 times better than previous determinations, and the fine structure 3 D31-3 D12 is determined to be 101 143.889(29) MHz, improving the precedent determination by a factor of 11.

Distributed biotin–streptavidin transcription roadblocks for mapping cotranscriptional RNA folding

PubMed Central

Strobel, Eric J.; Nedialkov, Yuri; Artsimovitch, Irina

2017-01-01

Abstract RNA folding during transcription directs an order of folding that can determine RNA structure and function. However, the experimental study of cotranscriptional RNA folding has been limited by the lack of easily approachable methods that can interrogate nascent RNA structure at nucleotide resolution. To address this, we previously developed cotranscriptional selective 2΄-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) to simultaneously probe all intermediate RNA transcripts during transcription by stalling elongation complexes at catalytically dead EcoRIE111Q roadblocks. While effective, the distribution of elongation complexes using EcoRIE111Q requires laborious PCR using many different oligonucleotides for each sequence analyzed. Here, we improve the broad applicability of cotranscriptional SHAPE-Seq by developing a sequence-independent biotin–streptavidin (SAv) roadblocking strategy that simplifies the preparation of roadblocking DNA templates. We first determine the properties of biotin–SAv roadblocks. We then show that randomly distributed biotin–SAv roadblocks can be used in cotranscriptional SHAPE-Seq experiments to identify the same RNA structural transitions related to a riboswitch decision-making process that we previously identified using EcoRIE111Q. Lastly, we find that EcoRIE111Q maps nascent RNA structure to specific transcript lengths more precisely than biotin–SAv and propose guidelines to leverage the complementary strengths of each transcription roadblock in cotranscriptional SHAPE-Seq. PMID:28398514

Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.

PubMed

Strobel, Eric J; Watters, Kyle E; Nedialkov, Yuri; Artsimovitch, Irina; Lucks, Julius B

2017-07-07

RNA folding during transcription directs an order of folding that can determine RNA structure and function. However, the experimental study of cotranscriptional RNA folding has been limited by the lack of easily approachable methods that can interrogate nascent RNA structure at nucleotide resolution. To address this, we previously developed cotranscriptional selective 2΄-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) to simultaneously probe all intermediate RNA transcripts during transcription by stalling elongation complexes at catalytically dead EcoRIE111Q roadblocks. While effective, the distribution of elongation complexes using EcoRIE111Q requires laborious PCR using many different oligonucleotides for each sequence analyzed. Here, we improve the broad applicability of cotranscriptional SHAPE-Seq by developing a sequence-independent biotin-streptavidin (SAv) roadblocking strategy that simplifies the preparation of roadblocking DNA templates. We first determine the properties of biotin-SAv roadblocks. We then show that randomly distributed biotin-SAv roadblocks can be used in cotranscriptional SHAPE-Seq experiments to identify the same RNA structural transitions related to a riboswitch decision-making process that we previously identified using EcoRIE111Q. Lastly, we find that EcoRIE111Q maps nascent RNA structure to specific transcript lengths more precisely than biotin-SAv and propose guidelines to leverage the complementary strengths of each transcription roadblock in cotranscriptional SHAPE-Seq. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

PubMed Central

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

2012-01-01

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

PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.

PubMed

Lee, Woonghee; Kim, Jin Hae; Westler, William M; Markley, John L

2011-06-15

PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY ((13)C-edited and/or (15)N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/.

The periplasmic domain of Escherichia coli outer membrane protein A can undergo a localized temperature dependent structural transition.

PubMed

Ishida, Hiroaki; Garcia-Herrero, Alicia; Vogel, Hans J

2014-12-01

Gram-negative bacteria such as Escherichia coli are surrounded by two membranes with a thin peptidoglycan (PG)-layer located in between them in the periplasmic space. The outer membrane protein A (OmpA) is a 325-residue protein and it is the major protein component of the outer membrane of E. coli. Previous structure determinations have focused on the N-terminal fragment (residues 1-171) of OmpA, which forms an eight stranded transmembrane β-barrel in the outer membrane. Consequently it was suggested that OmpA is composed of two independently folded domains in which the N-terminal β-barrel traverses the outer membrane and the C-terminal domain (residues 180-325) adopts a folded structure in the periplasmic space. However, some reports have proposed that full-length OmpA can instead refold in a temperature dependent manner into a single domain forming a larger transmembrane pore. Here, we have determined the NMR solution structure of the C-terminal periplasmic domain of E. coli OmpA (OmpA(180-325)). Our structure reveals that the C-terminal domain folds independently into a stable globular structure that is homologous to the previously reported PG-associated domain of Neisseria meningitides RmpM. Our results lend credence to the two domain structure model and a PG-binding function for OmpA, and we could indeed localize the PG-binding site on the protein through NMR chemical shift perturbation experiments. On the other hand, we found no evidence for binding of OmpA(180-325) with the TonB protein. In addition, we have also expressed and purified full-length OmpA (OmpA(1-325)) to study the structure of the full-length protein in micelles and nanodiscs by NMR spectroscopy. In both membrane mimetic environments, the recombinant OmpA maintains its two domain structure that is connected through a flexible linker. A series of temperature-dependent HSQC experiments and relaxation dispersion NMR experiments detected structural destabilization in the bulge region of the periplasmic domain of OmpA above physiological temperatures, which may induce dimerization and play a role in triggering the previously reported larger pore formation. Copyright © 2014 Elsevier B.V. All rights reserved.

Structure of Toxoplasma gondii fructose-1,6-bisphosphate aldolase

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

Boucher, Lauren E.; Bosch, Jürgen, E-mail: jbosch@jhu.edu; Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205

The structure of T. gondii fructose-1,6-bisphosphate aldolase, a glycolytic enzyme and structural component of the invasion machinery, was determined to a resolution of 2.0 Å. The apicomplexan parasite Toxoplasma gondii must invade host cells to continue its lifecycle. It invades different cell types using an actomyosin motor that is connected to extracellular adhesins via the bridging protein fructose-1,6-@@bisphosphate aldolase. During invasion, aldolase serves in the role of a structural bridging protein, as opposed to its normal enzymatic role in the glycolysis pathway. Crystal structures of the homologous Plasmodium falciparum fructose-1,6-bisphosphate aldolase have been described previously. Here, T. gondii fructose-1,6-bisphosphate aldolasemore » has been crystallized in space group P22{sub 1}2{sub 1}, with the biologically relevant tetramer in the asymmetric unit, and the structure has been determined via molecular replacement to a resolution of 2.0 Å. An analysis of the quality of the model and of the differences between the four chains in the asymmetric unit and a comparison between the T. gondii and P. falciparum aldolase structures is presented.« less

TAP score: torsion angle propensity normalization applied to local protein structure evaluation

PubMed Central

Tosatto, Silvio CE; Battistutta, Roberto

2007-01-01

Background Experimentally determined protein structures may contain errors and require validation. Conformational criteria based on the Ramachandran plot are mainly used to distinguish between distorted and adequately refined models. While the readily available criteria are sufficient to detect totally wrong structures, establishing the more subtle differences between plausible structures remains more challenging. Results A new criterion, called TAP score, measuring local sequence to structure fitness based on torsion angle propensities normalized against the global minimum and maximum is introduced. It is shown to be more accurate than previous methods at estimating the validity of a protein model in terms of commonly used experimental quality parameters on two test sets representing the full PDB database and a subset of obsolete PDB structures. Highly selective TAP thresholds are derived to recognize over 90% of the top experimental structures in the absence of experimental information. Both a web server and an executable version of the TAP score are available at . Conclusion A novel procedure for energy normalization (TAP) has significantly improved the possibility to recognize the best experimental structures. It will allow the user to more reliably isolate problematic structures in the context of automated experimental structure determination. PMID:17504537

Methods for Determining the Optimum Design of Structures Protected from Aerodynamic Heating and Application to Typical Boost-Glide or Reentry Flight Paths

NASA Technical Reports Server (NTRS)

Harris, Robert S., Jr.; Davidson, John R.

1962-01-01

General equations are developed for the design of efficient structures protected from thermal environments typical of those encountered in boost-glide or atmospheric-reentry conditions. The method is applied to insulated heat-sink stressed-skin structures and to internally cooled insulated structures. Plates loaded in compression are treated in detail. Under limited conditions of plate buckling, high loading, and short flight periods, and for aluminum structures only, the weights of both configurations are nearly equal. Load parameters are found and are similar to those derived in previous investigations for the restricted case of a constant equilibrium temperature at the outside surface of the insulation.

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

Third Structure Determination by Powder Diffractometery Round Robin (SDPDRR-3)

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

Le Bail, A.; Cranswick, L; Adil, K

2009-01-01

The results from a third structure determination by powder diffractometry (SDPD) round robin are discussed. From the 175 potential participants having downloaded the powder data, nine sent a total of 12 solutions (8 and 4 for samples 1 and 2, respectively, a tetrahydrated calcium tartrate and a lanthanum tungstate). Participants used seven different computer programs for structure solution (ESPOIR, EXPO, FOX, PSSP, SHELXS, SUPERFLIP, and TOPAS), applying Patterson, direct methods, direct space methods, and charge flipping approach. It is concluded that solving a structure from powder data remains a challenge, at least one order of magnitude more difficult than solvingmore » a problem with similar complexity from single-crystal data. Nevertheless, a few more steps in the direction of increasing the SDPD rate of success were accomplished since the two previous round robins: this time, not only the computer program developers were successful but also some users. No result was obtained from crystal structure prediction experts.« less

DNA bending-induced phase transition of encapsidated genome in phage λ

PubMed Central

Lander, Gabriel C.; Johnson, John E.; Rau, Donald C.; Potter, Clinton S.; Carragher, Bridget; Evilevitch, Alex

2013-01-01

The DNA structure in phage capsids is determined by DNA–DNA interactions and bending energy. The effects of repulsive interactions on DNA interaxial distance were previously investigated, but not the effect of DNA bending on its structure in viral capsids. By varying packaged DNA length and through addition of spermine ions, we transform the interaction energy from net repulsive to net attractive. This allowed us to isolate the effect of bending on the resulting DNA structure. We used single particle cryo-electron microscopy reconstruction analysis to determine the interstrand spacing of double-stranded DNA encapsidated in phage λ capsids. The data reveal that stress and packing defects, both resulting from DNA bending in the capsid, are able to induce a long-range phase transition in the encapsidated DNA genome from a hexagonal to a cholesteric packing structure. This structural observation suggests significant changes in genome fluidity as a result of a phase transition affecting the rates of viral DNA ejection and packaging. PMID:23449219

Optimization of fluorimetric lipid membrane biosensor sensitivity through manipulation of membrane structure and nitrobenzoxadiazole dipalmitoylphosphatidylethanolamine concentration

NASA Astrophysics Data System (ADS)

Shrive, Jason D. A.; Krull, Ulrich J.

1995-01-01

In the work reported here, surface concentrations of 0.027 and 0.073 molecules nm-2 of the fluorescent membrane probe molecule nitrobenzoxadiazole dipalmitoylphosphatidylethanolamine (NBD-PE) were shown to yield optimum sensitivity for fluorimetric transduction of membrane structural perturbations for lipid membrane-based biosensor development. These optima were obtained through correlation of experimental data with theoretical predictions of optimum surface concentrations based on a model for NBD-PE self quenching previously published by our group. It was also determined that membrane structural heterogeneity improves the sensitivity of NBD-PE labeled membrane transducers. Together with fluorescence microscopy, observations of surface potential change upon compression or expansion of phosphatidylcholine (PC)/phosphatidic acid (PA) monolayers were used to qualitatively indicate the degree of structural heterogeneity in these membranes. It was determined that sub-microscopic domains must exist in microscopically homogeneous egg PC/egg PA membranes in order to facilitate the observed NBD-PE self-quenching responses upon alteration of bulk pH and therefore, membrane surface electrostatics and structure.

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

Crystallographic Studies of Prion Protein (PrP) Segments Suggest How Structural Changes Encoded by Polymorphism at Residue 129 Modulate Susceptibility to Human Prion Disease

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

Apostol, Marcin I.; Sawaya, Michael R.; Cascio, Duilio

2010-09-23

A single nucleotide polymorphism (SNP) in codon 129 of the human prion gene, leading to a change from methionine to valine at residue 129 of prion protein (PrP), has been shown to be a determinant in the susceptibility to prion disease. However, the molecular basis of this effect remains unexplained. In the current study, we determined crystal structures of prion segments having either Met or Val at residue 129. These 6-residue segments of PrP centered on residue 129 are 'steric zippers,' pairs of interacting {beta}-sheets. Both structures of these 'homozygous steric zippers' reveal direct intermolecular interactions between Met or Valmore » in one sheet and the identical residue in the mating sheet. These two structures, plus a structure-based model of the heterozygous Met-Val steric zipper, suggest an explanation for the previously observed effects of this locus on prion disease susceptibility and progression.« less

Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.

PubMed

Sborgi, Lorenzo; Verma, Abhinav; Muñoz, Victor; de Alba, Eva

2011-01-01

GpW is a 68-residue protein from bacteriophage λ that participates in virus head morphogenesis. Previous NMR studies revealed a novel α+β fold for this protein. Recent experiments have shown that gpW folds in microseconds by crossing a marginal free energy barrier (i.e., downhill folding). These features make gpW a highly desirable target for further experimental and computational folding studies. As a step in that direction, we have re-determined the high-resolution structure of gpW by multidimensional NMR on a construct that eliminates the purification tags and unstructured C-terminal tail present in the prior study. In contrast to the previous work, we have obtained a full manual assignment and calculated the structure using only unambiguous distance restraints. This new structure confirms the α+β topology, but reveals important differences in tertiary packing. Namely, the two α-helices are rotated along their main axis to form a leucine zipper. The β-hairpin is orthogonal to the helical interface rather than parallel, displaying most tertiary contacts through strand 1. There also are differences in secondary structure: longer and less curved helices and a hairpin that now shows the typical right-hand twist. Molecular dynamics simulations starting from both gpW structures, and calculations with CS-Rosetta, all converge to our gpW structure. This confirms that the original structure has strange tertiary packing and strained secondary structure. A comparison of NMR datasets suggests that the problems were mainly caused by incomplete chemical shift assignments, mistakes in NOE assignment and the inclusion of ambiguous distance restraints during the automated procedure used in the original study. The new gpW corrects these problems, providing the appropriate structural reference for future work. Furthermore, our results are a cautionary tale against the inclusion of ambiguous experimental information in the determination of protein structures.

The structure of Tim50(164–361) suggests the mechanism by which Tim50 receives mitochondrial presequences

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

Li, Jingzhi; Sha, Bingdong, E-mail: bdsha@uab.edu

2015-08-25

The Tim50 crystal structure indicates that the IMS domain of Tim50 exhibits significant structural plasticity within the putative presequence-binding groove. Mitochondrial preproteins are transported through the translocase of the outer membrane (TOM) complex. Tim50 and Tim23 then transfer preproteins with N-terminal targeting presequences through the intermembrane space (IMS) across the inner membrane. The crystal structure of the IMS domain of Tim50 [Tim50(164–361)] has previously been determined to 1.83 Å resolution. Here, the crystal structure of Tim50(164–361) at 2.67 Å resolution that was crystallized using a different condition is reported. Compared with the previously determined Tim50(164–361) structure, significant conformational changes occurmore » within the protruding β-hairpin of Tim50 and the nearby helix A2. These findings indicate that the IMS domain of Tim50 exhibits significant structural plasticity within the putative presequence-binding groove, which may play important roles in the function of Tim50 as a receptor protein in the TIM complex that interacts with the presequence and multiple other proteins. More interestingly, the crystal packing indicates that helix A1 from the neighboring monomer docks into the putative presequence-binding groove of Tim50(164–361), which may mimic the scenario of Tim50 and the presequence complex. Tim50 may recognize and bind the presequence helix by utilizing the inner side of the protruding β-hairpin through hydrophobic interactions. Therefore, the protruding β-hairpin of Tim50 may play critical roles in receiving the presequence and recruiting Tim23 for subsequent protein translocations.« less

Crystal structure of heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96

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

Ida, Koh; E-mail: idakoh@sci.kitasato-u.ac.jp; Moriguchi, Tomotaka

2005-07-29

Sarcosine oxidase from Corynebacterium sp. U-96 is a heterotetrameric enzyme. Here we report the crystal structures of the enzyme in complex with dimethylglycine and folinic acid. The {alpha} subunit is composed of two domains, contains NAD{sup +}, and binds folinic acid. The {beta} subunit contains dimethylglycine, FAD, and FMN, and these flavins are approximately 10 A apart. The {gamma} subunit is in contact with two domains of {alpha} subunit and has possibly a folate-binding structure. The {delta} subunit contains a single atom of zinc and has a Cys{sub 3}His zinc finger structure. Based on the structures determined and on themore » previous works, the structure-function relationship on the heterotetrameric sarcosine oxidase is discussed.« less

Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole at 2.0-A resolution.

PubMed

Gay, Sean C; Shah, Manish B; Talakad, Jyothi C; Maekawa, Keiko; Roberts, Arthur G; Wilderman, P Ross; Sun, Ling; Yang, Jane Y; Huelga, Stephanie C; Hong, Wen-Xu; Zhang, Qinghai; Stout, C David; Halpert, James R

2010-04-01

The structure of the K262R genetic variant of human cytochrome P450 2B6 in complex with the inhibitor 4-(4-chlorophenyl)imidazole (4-CPI) has been determined using X-ray crystallography to 2.0-A resolution. Production of diffraction quality crystals was enabled through a combination of protein engineering, chaperone coexpression, modifications to the purification protocol, and the use of unique facial amphiphiles during crystallization. The 2B6-4-CPI complex is virtually identical to the rabbit 2B4 structure bound to the same inhibitor with respect to the arrangement of secondary structural elements and the placement of active site residues. The structure supports prior P450 2B6 homology models based on other mammalian cytochromes P450 and is consistent with the limited site-directed mutagenesis studies on 2B6 and extensive studies on P450 2B4 and 2B1. Although the K262R genetic variant shows unaltered binding of 4-CPI, altered binding affinity, kinetics, and/or product profiles have been previously shown with several other ligands. On the basis of new P450 2B6 crystal structure and previous 2B4 structures, substitutions at residue 262 affect a hydrogen-bonding network connecting the G and H helices, where subtle differences could be transduced to the active site. Docking experiments indicate that the closed protein conformation allows smaller ligands such as ticlopidine to bind to the 2B6 active site in the expected orientation. However, it is unknown whether 2B6 undergoes structural reorganization to accommodate bulkier molecules, as previously inferred from multiple P450 2B4 crystal structures.

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.

Determinants of Chronic Respiratory Symptoms among Pharmaceutical Factory Workers

PubMed Central

Enquselassie, Fikre; Tefera, Yifokire; Gizaw, Muluken; Wakuma, Samson; Woldemariam, Messay

2018-01-01

Background Chronic respiratory symptoms including chronic cough, chronic phlegm, wheezing, shortness of breath, and chest pain are manifestations of respiratory problems which are mainly evolved as a result of occupational exposures. This study aims to assess determinants of chronic respiratory symptoms among pharmaceutical factory workers. Methods A case control study was carried out among 453 pharmaceutical factory workers with 151 cases and 302 controls. Data was collected using pretested and structured questionnaire. The data was analyzed using descriptive statistics and bivariate and multivariate analysis. Result Previous history of chronic respiratory diseases (AOR = 3.36, 95% CI = 1.85–6.12), family history of chronic respiratory diseases (AOR = 2.55, 95% CI = 1.51–4.32), previous dusty working environment (AOR = 2.26, 95% CI = 1.07–4.78), ever smoking (AOR = 3.66, 95% CI = 1.05–12.72), and service years (AOR = 1.86, 95% CI = 1.16–2.99) showed statistically significant association with chronic respiratory symptoms. Conclusion Previous history of respiratory diseases, family history of chronic respiratory diseases, previous dusty working environment, smoking, and service years were determinants of chronic respiratory symptoms. Public health endeavors to prevent the burden of chronic respiratory symptoms among pharmaceutical factory workers should target the reduction of adverse workplace exposures and discouragement of smoking. PMID:29666655

Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif.

PubMed

Oshima, Kosuke; Gao, Xuzhu; Hayashi, Seiichiro; Ueda, Toshifumi; Nakashima, Takashi; Kimura, Makoto

2018-01-01

A characteristic feature of archaeal ribonuclease P (RNase P) RNAs is that they have extended helices P12.1 and P12.2 containing kink-turn (K-turn) motifs to which the archaeal RNase P protein Rpp38, a homologue of the human RNase P protein Rpp38, specifically binds. PhoRpp38 from the hyperthermophilic archaeon Pyrococcus horikoshii is involved in the elevation of the optimum temperature of the reconstituted RNase P by binding the K-turns in P12.1 and P12.2. Previously, the crystal structure of PhoRpp38 in complex with the K-turn in P12.2 was determined at 3.4 Å resolution. In this study, the crystal structure of PhoRpp38 in complex with the K-turn in P12.2 was improved to 2.1 Å resolution and the structure of PhoRpp38 in complex with the K-turn in P12.1 was also determined at a resolution of 3.1 Å. Both structures revealed that Lys35, Asn38 and Glu39 in PhoRpp38 interact with characteristic G·A and A·G pairs in the K-turn, while Thr37, Asp59, Lys84, Glu94, Ala96 and Ala98 in PhoRpp38 interact with the three-nucleotide bulge in the K-turn. Moreover, an extended stem-loop containing P10-P12.2 in complex with PhoRpp38, as well as PhoRpp21 and PhoRpp29, which are the archaeal homologues of the human proteins Rpp21 and Rpp29, respectively, was affinity-purified and crystallized. The crystals thus grown diffracted to a resolution of 6.35 Å. Structure determination of the crystals will demonstrate the previously proposed secondary structure of stem-loops including helices P12.1 and P12.2 and will also provide insight into the structural organization of the specificity domain in P. horikoshii RNase P RNA.

Crystal Structure of a Phosphorylated Light Chain Domain of Scallop Smooth-Muscle Myosin

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

Kumar, V.S.; Robinson, H.; O-Neall-Hennessey, E.

2011-11-02

We have determined the crystal structure of a phosphorylated smooth-muscle myosin light chain domain (LCD). This reconstituted LCD is of a sea scallop catch muscle myosin with its phosphorylatable regulatory light chain (RLC SmoA). In the crystal structure, Arg{sup 16}, an arginine residue that is present in this isoform but not in vertebrate smooth-muscle RLC, stabilizes the phosphorylation site. This arginine interacts with the carbonyl group of the phosphorylation-site serine in the unphosphorylated LCD (determined previously), and with the phosphate group when the serine is phosphorylated. However, the overall conformation of the LCD is essentially unchanged upon phosphorylation. This resultmore » provides additional evidence that phosphorylation of the RLC is unlikely to act as an on-switch in regulation of scallop catch muscle myosin.« less

Bedrock geologic and structural map through the western Candor Colles region of Mars

USGS Publications Warehouse

Okubo, Chris H.

2014-01-01

The structure and geology of the layered deposits in the Candor Colles region corresponding to units Avfs, Avme, and Hvl of Witbeck and others (1991) are reevaluated in this 1:18,000-scale map. The objectives herein are to gather high-resolution structural measurements to (1) refine the previous unit boundaries in this area established by Witbeck and others (1991), (2) revise the local stratigraphy where necessary, (3) characterize bed forms to help constrain depositional processes, and (4) determine the styles and extent of deformation to better inform reconstructions of the local post-depositional geologic history.

Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing.

PubMed

Suzuki, Toshifumi; Tsurusaki, Yoshinori; Nakashima, Mitsuko; Miyake, Noriko; Saitsu, Hirotomo; Takeda, Satoru; Matsumoto, Naomichi

2014-12-01

Structural variations (SVs), including translocations, inversions, deletions and duplications, are potentially associated with Mendelian diseases and contiguous gene syndromes. Determination of SV-related breakpoints at the nucleotide level is important to reveal the genetic causes for diseases. Whole-genome sequencing (WGS) by next-generation sequencers is expected to determine structural abnormalities more directly and efficiently than conventional methods. In this study, 14 SVs (9 balanced translocations, 1 inversion and 4 microdeletions) in 9 patients were analyzed by WGS with a shallow (5 × ) to moderate read coverage (20 × ). Among 28 breakpoints (as each SV has two breakpoints), 19 SV breakpoints had been determined previously at the nucleotide level by any other methods and 9 were uncharacterized. BreakDancer and Integrative Genomics Viewer determined 20 breakpoints (16 translocation, 2 inversion and 2 deletion breakpoints), but did not detect 8 breakpoints (2 translocation and 6 deletion breakpoints). These data indicate the efficacy of WGS for the precise determination of translocation and inversion breakpoints.

Terahertz laser vibration-rotation-tunneling spectrum of the water pentamer-d 10. . Constraints on the bifurcation tunneling dynamics

NASA Astrophysics Data System (ADS)

Cruzan, Jeff D.; Viant, Mark R.; Brown, Mac G.; Lucas, Don D.; Liu, Kun; Saykally, Richard J.

1998-08-01

The vibration-rotation-tunneling (VRT) spectrum of a low-frequency intermolecular vibration of (D 2O) 5 was recorded near 0.9 THz (30.2 cm -1). From an analysis of the relative intensities in the compact Q-branch region, the ground-state C-rotational constant is estimated to be 975±60 MHz, consistent with ab initio structural predictions. The precisely determined B-rotational constant ( B=1750.96±0.20 MHz) agrees well with previous results. Efforts to resolve possible bifurcation tunneling fine structure, such as that observed in VRT spectra of (D 2O) 3, revealed no such effects. This constrains the splittings to be less than 450 kHz, or roughly 3 times smaller than required by previous results.

Adsorption of O_{2} on Ag(111): Evidence of Local Oxide Formation.

PubMed

Andryushechkin, B V; Shevlyuga, V M; Pavlova, T V; Zhidomirov, G M; Eltsov, K N

2016-07-29

The atomic structure of the disordered phase formed by oxygen on Ag(111) at low coverage is determined by a combination of low-temperature scanning tunneling microscopy and density functional theory. We demonstrate that the previous assignment of the dark objects in STM to chemisorbed oxygen atoms is incorrect and incompatible with trefoil-like structures observed in atomic-resolution images in current work. In our model, each object is an oxidelike ring formed by six oxygen atoms around the vacancy in Ag(111).

Developments in signal processing and interpretation in laser tapping

NASA Astrophysics Data System (ADS)

Perton, M.; Neron, C.; Blouin, A.; Monchalin, J.-P.

2013-01-01

A novel technique, called laser-tapping, based on the thermoelastic excitation by laser like laser-ultrasonics has been previously introduced for inspecting honeycomb and foam core structures. If the top skin is delaminated or detached from the substrate, the detached layer is driven into vibration. The interpretation of the vibrations in terms of Lamb wave resonances is first discussed for a flat bottom hole configuration and then used to determine appropriate signal processing for samples such as honeycomb structures.

Determination of HART I Blade Structural Properties by Laboratory Testing

NASA Technical Reports Server (NTRS)

Jung, Sung N.; Lau, Benton H.

2012-01-01

The structural properties of higher harmonic Aeroacoustic Rotor Test (HART I) blades were measured using the original set of blades tested in the German-dutch wind tunnel (DNW) in 1994. the measurements include bending and torsion stiffness, geometric offsets, and mass and inertia properties of the blade. the measured properties were compared to the estimated values obtained initially from the blade manufacturer. The previously estimated blade properties showed consistently higher stiffness, up to 30 percent for the flap bending in the blade inboard root section.

Physical characteristics of Medicago truncatula calcium oxalate crystals determine their effectiveness in insect defense

USDA-ARS?s Scientific Manuscript database

Plant structural traits can act as defense against herbivorous insects, causing them to avoid feeding on a given plant or tissue. Mineral crystals of calcium oxalate in leaves of Medicago truncatula Gaertn. have previously been shown to be effective deterrents of lepidopteran insect feeding. They ar...

Classification of the College Instructor's Professional and Personal Competencies

ERIC Educational Resources Information Center

Isaeva, T. E.

2007-01-01

At the beginning of the twenty-first century, the issue of the instructor's professional and personal competencies has taken on features not previously characteristic of it. The problem of determining the content and structuring of the professional and personal competencies of instructors in higher education is conditioned not only by social,…

Confirmatory Factor Analysis of the WISC-IV in a Hospital Referral Sample

ERIC Educational Resources Information Center

Devena, Sarah E.; Gay, Catherine E.; Watkins, Marley W.

2013-01-01

Confirmatory factor analysis was used to determine the factor structure of the Wechsler Intelligence Scale for Children-Fourth Edition (WISC-IV) scores of 297 children referred to a children's hospital in the Southwestern United States. Results support previous findings that indicate the WISC-IV is best represented by a direct hierarchical…

Determinants of the Attempting and Outcome of Coups d'etat

ERIC Educational Resources Information Center

Powell, Jonathan

2012-01-01

Previous studies have attested to leaders "coup-proofing" their regimes by reducing the ability or disposition of their armies to seek their removal. The following article tests the utility of these efforts. "Structural" coup-proofing such as counterbalancing is expected to reduce the ability to organize a coup plot by creating substantial…

Effects of risk attitudes on extended attack fire management decisionmaking

Treesearch

Donald G. MacGregor; Armando González-Cabán

2009-01-01

Fire management inherently involves the assessment and management of risk, and decision making under uncertainty. Although organizational standards and guides are an important determinant of how decision problems are structured and framed, decision makers may view risk-based decisions from a perspective that is unique to their background and experience. Previous...

Multiple band structures in 70Ge

NASA Astrophysics Data System (ADS)

Haring-Kaye, R. A.; Morrow, S. I.; Döring, J.; Tabor, S. L.; Le, K. Q.; Allegro, P. R. P.; Bender, P. C.; Elder, R. M.; Medina, N. H.; Oliveira, J. R. B.; Tripathi, Vandana

2018-02-01

High-spin states in 70Ge were studied using the 55Mn(18O,p 2 n ) fusion-evaporation reaction at a beam energy of 50 MeV. Prompt γ -γ coincidences were measured using the Florida State University Compton-suppressed Ge array consisting of three Clover detectors and seven single-crystal detectors. An investigation of these coincidences resulted in the addition of 31 new transitions and the rearrangement of four others in the 70Ge level scheme, providing a more complete picture of the high-spin decay pattern involving both positive- and negative-parity states with multiple band structures. Spins were assigned based on directional correlation of oriented nuclei ratios, which many times also led to unambiguous parity determinations based on the firm assignments for low-lying states made in previous work. Total Routhian surface calculations, along with the observed trends in the experimental kinematic moment of inertia with rotational frequency, support the multiquasiparticle configurations of the various crossing bands proposed in recent studies. The high-spin excitation spectra predicted by previous shell-model calculations compare favorably with the experimental one determined from this study.

Bond-strength inversion in (In,Ga)As semiconductor alloys

NASA Astrophysics Data System (ADS)

Eckner, Stefanie; Ritter, Konrad; Schöppe, Philipp; Haubold, Erik; Eckner, Erich; Rensberg, Jura; Röder, Robert; Ridgway, Mark C.; Schnohr, Claudia S.

2018-05-01

The atomic-scale structure and vibrational properties of semiconductor alloys are determined by the energy required for stretching and bending the individual bonds. Using temperature-dependent extended x-ray absorption fine-structure spectroscopy, we have determined the element-specific In-As and Ga-As effective bond-stretching force constants in (In,Ga)As as a function of the alloy composition. The results reveal a striking inversion of the bond strength where the originally stiffer bond in the parent materials becomes the softer bond in the alloy and vice versa. Our findings clearly demonstrate that changes of both the individual bond length and the surrounding matrix affect the bond-stretching force constants. We thus show that the previously used common assumptions about the element-specific force constants in semiconductor alloys do not reproduce the composition dependence determined experimentally for (In,Ga)As.

Electrostatic interactions and binding orientation of HIV-1 matrix studied by neutron reflectivity.

PubMed

Nanda, Hirsh; Datta, Siddhartha A K; Heinrich, Frank; Lösche, Mathias; Rein, Alan; Krueger, Susan; Curtis, Joseph E

2010-10-20

The N-terminal matrix (MA) domain of the HIV-1 Gag protein is responsible for binding to the plasma membrane of host cells during viral assembly. The putative membrane-binding interface of MA was previously mapped by means of mutagenesis and analysis of its trimeric crystal structure. However, the orientation of MA on membranes has not been directly determined by experimental measurements. We present neutron reflectivity measurements that resolve the one-dimensional scattering length density profile of MA bound to a biomimetic of the native viral membrane. A molecular refinement procedure was developed using atomic structures of MA to determine the orientation of the protein on the membrane. The orientation defines a lipid-binding interface consistent with previous mutagenesis results. The MA protein maintains this orientation without the presence of a myristate group, driven only by electrostatic interactions. Furthermore, MA is found to penetrate the membrane headgroup region peripherally such that only the side chains of specific Lys and Arg residues interact with the surface. The results suggest that electrostatic interactions are sufficient to favorably orient MA on viral membrane mimics. The spatial determination of the membrane-bound protein demonstrates the ability of neutron reflectivity to discern orientation and penetration under physiologically relevant conditions. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination

PubMed Central

Kazmier, Kelli; Alexander, Nathan S.; Meiler, Jens; Mchaourab, Hassane S.

2010-01-01

A hybrid protein structure determination approach combining sparse Electron Paramagnetic Resonance (EPR) distance restraints and Rosetta de novo protein folding has been previously demonstrated to yield high quality models (Alexander et al., 2008). However, widespread application of this methodology to proteins of unknown structures is hindered by the lack of a general strategy to place spin label pairs in the primary sequence. In this work, we report the development of an algorithm that optimally selects spin labeling positions for the purpose of distance measurements by EPR. For the α-helical subdomain of T4 lysozyme (T4L), simulated restraints that maximize sequence separation between the two spin labels while simultaneously ensuring pairwise connectivity of secondary structure elements yielded vastly improved models by Rosetta folding. 50% of all these models have the correct fold compared to only 21% and 8% correctly folded models when randomly placed restraints or no restraints are used, respectively. Moreover, the improvements in model quality require a limited number of optimized restraints, the number of which is determined by the pairwise connectivities of T4L α-helices. The predicted improvement in Rosetta model quality was verified by experimental determination of distances between spin labels pairs selected by the algorithm. Overall, our results reinforce the rationale for the combined use of sparse EPR distance restraints and de novo folding. By alleviating the experimental bottleneck associated with restraint selection, this algorithm sets the stage for extending computational structure determination to larger, traditionally elusive protein topologies of critical structural and biochemical importance. PMID:21074624

Salvage of failed protein targets by reductive alkylation.

PubMed

Tan, Kemin; Kim, Youngchang; Hatzos-Skintges, Catherine; Chang, Changsoo; Cuff, Marianne; Chhor, Gekleng; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; An, Hao; Babnigg, Gyorgy; Bigelow, Lance; Joachimiak, Grazyna; Li, Hui; Mack, Jamey; Makowska-Grzyska, Magdalena; Maltseva, Natalia; Mulligan, Rory; Tesar, Christine; Zhou, Min; Joachimiak, Andrzej

2014-01-01

The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins.

Salvage of Failed Protein Targets by Reductive Alkylation

PubMed Central

Tan, Kemin; Kim, Youngchang; Hatzos-Skintges, Catherine; Chang, Changsoo; Cuff, Marianne; Chhor, Gekleng; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; An, Hao; Babnigg, Gyorgy; Bigelow, Lance; Joachimiak, Grazyna; Li, Hui; Mack, Jamey; Makowska-Grzyska, Magdalena; Maltseva, Natalia; Mulligan, Rory; Tesar, Christine; Zhou, Min; Joachimiak, Andrzej

2014-01-01

The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins. PMID:24590719

Helix handedness of Leptospira interrogans as determined by scanning electron microscopy.

PubMed Central

Carleton, O; Charon, N W; Allender, P; O'Brien, S

1979-01-01

Representative serovars and strains of the seven genetic groups of Leptospira interrogans, and two previously studied serovars, were all found to form exclusively right-handed helices as determined by scanning electron microscopy. No change in handedness occurred in cells grown in a minimal medium (Tween-80 albumin) compared to cells grown in a rich medium (rabbit serum). The right-handedness of the organisms was related to the evolution, cell wall structure, and the mechanism of motility of L. interrogans. Images PMID:438122

Light-extraction enhancement for light-emitting diodes: a firefly-inspired structure refined by the genetic algorithm

NASA Astrophysics Data System (ADS)

Bay, Annick; Mayer, Alexandre

2014-09-01

The efficiency of light-emitting diodes (LED) has increased significantly over the past few years, but the overall efficiency is still limited by total internal reflections due to the high dielectric-constant contrast between the incident and emergent media. The bioluminescent organ of fireflies gave incentive for light-extraction enhance-ment studies. A specific factory-roof shaped structure was shown, by means of light-propagation simulations and measurements, to enhance light extraction significantly. In order to achieve a similar effect for light-emitting diodes, the structure needs to be adapted to the specific set-up of LEDs. In this context simulations were carried out to determine the best geometrical parameters. In the present work, the search for a geometry that maximizes the extraction of light has been conducted by using a genetic algorithm. The idealized structure considered previously was generalized to a broader variety of shapes. The genetic algorithm makes it possible to search simultaneously over a wider range of parameters. It is also significantly less time-consuming than the previous approach that was based on a systematic scan on parameters. The results of the genetic algorithm show that (1) the calculations can be performed in a smaller amount of time and (2) the light extraction can be enhanced even more significantly by using optimal parameters determined by the genetic algorithm for the generalized structure. The combination of the genetic algorithm with the Rigorous Coupled Waves Analysis method constitutes a strong simulation tool, which provides us with adapted designs for enhancing light extraction from light-emitting diodes.

Crystal structure of LGR4-Rspo1 complex: insights into the divergent mechanisms of ligand recognition by leucine-rich repeat G-protein-coupled receptors (LGRs).

PubMed

Xu, Jin-Gen; Huang, Chunfeng; Yang, Zhengfeng; Jin, Mengmeng; Fu, Panhan; Zhang, Ni; Luo, Jian; Li, Dali; Liu, Mingyao; Zhou, Yan; Zhu, Yongqun

2015-01-23

Leucine-rich repeat G-protein-coupled receptors (LGRs) are a unique class of G-protein-coupled receptors characterized by a large extracellular domain to recognize ligands and regulate many important developmental processes. Among the three groups of LGRs, group B members (LGR4-6) recognize R-spondin family proteins (Rspo1-4) to stimulate Wnt signaling. In this study, we successfully utilized the "hybrid leucine-rich repeat technique," which fused LGR4 with the hagfish VLR protein, to obtain two recombinant human LGR4 proteins, LGR415 and LGR49. We determined the crystal structures of ligand-free LGR415 and the LGR49-Rspo1 complex. LGR4 exhibits a twisted horseshoe-like structure. Rspo1 adopts a flat and β-fold architecture and is bound in the concave surface of LGR4 in the complex through electrostatic and hydrophobic interactions. All the Rspo1-binding residues are conserved in LGR4-6, suggesting that LGR4-6 bind R-spondins through an identical surface. Structural analysis of our LGR4-Rspo1 complex with the previously determined LGR4 and LGR5 structures revealed that the concave surface of LGR4 is the sole binding site for R-spondins, suggesting a one-site binding model of LGR4-6 in ligand recognition. The molecular mechanism of LGR4-6 is distinct from the two-step mechanism of group A receptors LGR1-3 and the multiple-interface binding model of group C receptors LGR7-8, suggesting LGRs utilize the divergent mechanisms for ligand recognition. Our structures, together with previous reports, provide a comprehensive understanding of the ligand recognition by LGRs. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

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

DOE PAGES

Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio; ...

2016-09-19

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 obstaclemore » 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 showwith 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.« less

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

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

Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio

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 obstaclemore » 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 showwith 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.« less

Surface structure of bulk 2H-MoS2(0001) and exfoliated suspended monolayer MoS2: A selected area low energy electron diffraction study

NASA Astrophysics Data System (ADS)

Dai, Zhongwei; Jin, Wencan; Grady, Maxwell; Sadowski, Jerzy T.; Dadap, Jerry I.; Osgood, Richard M.; Pohl, Karsten

2017-06-01

We have used selected area low energy electron diffraction intensity-voltage (μLEED-IV) analysis to investigate the surface structure of crystalline 2H molybdenum disulfide (MoS2) and mechanically exfoliated and suspended monolayer MoS2. Our results show that the surface structure of bulk 2H-MoS2 is distinct from its bulk and that it has a slightly smaller surface relaxation at 320 K than previously reported at 95 K. We concluded that suspended monolayer MoS2 shows a large interlayer relaxation compared to the MoS2 sandwich layer terminating the bulk surface. The Debye temperature of MoS2 was concluded to be about 600 K, which agrees with a previous theoretical study. Our work has shown that the dynamical μLEED-IV analysis performed with a low energy electron microscope (LEEM) is a powerful technique for determination of the local atomic structures of currently extensively studied two-dimensional (2-D) materials.

Surface structure of bulk 2H-MoS 2 (0001) and exfoliated suspended monolayer MoS 2 : A selected area low energy electron diffraction study

DOE PAGES

Dai, Zhongwei; Jin, Wencan; Grady, Maxwell; ...

2017-02-10

Here, we used selected area low energy electron diffraction intensity-voltage (μLEED-IV) analysis to investigate the surface structure of crystalline 2H molybdenum disulfide (MoS 2) and mechanically exfoliated and suspended monolayer MoS 2. Our results show that the surface structure of bulk 2H-MoS 2 is distinct from its bulk and that it has a slightly smaller surface relaxation at 320 K than previously reported at 95 K. We concluded that suspended monolayer MoS 2 shows a large interlayer relaxation compared to the MoS 2 sandwich layer terminating the bulk surface. The Debye temperature of MoS 2 was concluded to be aboutmore » 600 K, which agrees with a previous theoretical study. Our work has shown that the dynamical μLEED-IV analysis performed with a low energy electron microscope (LEEM) is a powerful technique for determination of the local atomic structures of currently extensively studied two-dimensional (2-D) materials.« less

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

PubMed

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

2010-08-14

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

Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus.

PubMed

Huynh, Nhung T; Hesketh, Emma L; Saxena, Pooja; Meshcheriakova, Yulia; Ku, You-Chan; Hoang, Linh T; Johnson, John E; Ranson, Neil A; Lomonossoff, George P; Reddy, Vijay S

2016-04-05

Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Predicting binding modes of reversible peptide-based inhibitors of falcipain-2 consistent with structure-activity relationships.

PubMed

Hernández González, Jorge Enrique; Hernández Alvarez, Lilian; Pascutti, Pedro Geraldo; Valiente, Pedro A

2017-09-01

Falcipain-2 (FP-2) is a major hemoglobinase of Plasmodium falciparum, considered an important drug target for the development of antimalarials. A previous study reported a novel series of 20 reversible peptide-based inhibitors of FP-2. However, the lack of tridimensional structures of the complexes hinders further optimization strategies to enhance the inhibitory activity of the compounds. Here we report the prediction of the binding modes of the aforementioned inhibitors to FP-2. A computational approach combining previous knowledge on the determinants of binding to the enzyme, docking, and postdocking refinement steps, is employed. The latter steps comprise molecular dynamics simulations and free energy calculations. Remarkably, this approach leads to the identification of near-native ligand conformations when applied to a validation set of protein-ligand structures. Overall, we proposed substrate-like binding modes of the studied compounds fulfilling the structural requirements for FP-2 binding and yielding free energy values that correlated well with the experimental data. Proteins 2017; 85:1666-1683. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Phenetic Comparison of Prokaryotic Genomes Using k-mers

PubMed Central

Déraspe, Maxime; Raymond, Frédéric; Boisvert, Sébastien; Culley, Alexander; Roy, Paul H.; Laviolette, François; Corbeil, Jacques

2017-01-01

Abstract Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated the methodology using simulated genomes and previously published phylogenomic studies of Streptococcus pneumoniae and Pseudomonas aeruginosa. We also investigated the relationship of specific genetic determinants with bacterial population structures. By comparing clusters from the complete genomic content of a genome population with clusters from specific functional categories of genes, we can determine how the population structures are correlated. Indeed, the strain clustering based on a subset of k-mers allows determination of its similarity with the whole genome clusters. We also applied this methodology on 42 species of bacteria to determine the correlational significance of five important bacterial genomic characteristics. For example, intrinsic resistance is more important in P. aeruginosa than in S. pneumoniae, and the former has increased correlation of its population structure with antibiotic resistance genes. The global view of the pangenome of bacteria also demonstrated the taxa-dependent interaction of population structure with antibiotic resistance, bacteriophage, plasmid, and mobile element k-mer data sets. PMID:28957508

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.

Coastal oceanography sets the pace of rocky intertidal community dynamics.

PubMed

Menge, B A; Lubchenco, J; Bracken, M E S; Chan, F; Foley, M M; Freidenburg, T L; Gaines, S D; Hudson, G; Krenz, C; Leslie, H; Menge, D N L; Russell, R; Webster, M S

2003-10-14

The structure of ecological communities reflects a tension among forces that alter populations. Marine ecologists previously emphasized control by locally operating forces (predation, competition, and disturbance), but newer studies suggest that inputs from large-scale oceanographically modulated subsidies (nutrients, particulates, and propagules) can strongly influence community structure and dynamics. On New Zealand rocky shores, the magnitude of such subsidies differs profoundly between contrasting oceanographic regimes. Community structure, and particularly the pace of community dynamics, differ dramatically between intermittent upwelling regimes compared with relatively persistent down-welling regimes. We suggest that subsidy rates are a key determinant of the intensity of species interactions, and thus of structure in marine systems, and perhaps also nonmarine communities.

A Benchmark Problem for Development of Autonomous Structural Modal Identification

NASA Technical Reports Server (NTRS)

Pappa, Richard S.; Woodard, Stanley E.; Juang, Jer-Nan

1996-01-01

This paper summarizes modal identification results obtained using an autonomous version of the Eigensystem Realization Algorithm on a dynamically complex, laboratory structure. The benchmark problem uses 48 of 768 free-decay responses measured in a complete modal survey test. The true modal parameters of the structure are well known from two previous, independent investigations. Without user involvement, the autonomous data analysis identified 24 to 33 structural modes with good to excellent accuracy in 62 seconds of CPU time (on a DEC Alpha 4000 computer). The modal identification technique described in the paper is the baseline algorithm for NASA's Autonomous Dynamics Determination (ADD) experiment scheduled to fly on International Space Station assembly flights in 1997-1999.

Structures of cage, prism, and book isomers of water hexamer from broadband rotational spectroscopy.

PubMed

Pérez, Cristóbal; Muckle, Matt T; Zaleski, Daniel P; Seifert, Nathan A; Temelso, Berhane; Shields, George C; Kisiel, Zbigniew; Pate, Brooks H

2012-05-18

Theory predicts the water hexamer to be the smallest water cluster with a three-dimensional hydrogen-bonding network as its minimum energy structure. There are several possible low-energy isomers, and calculations with different methods and basis sets assign them different relative stabilities. Previous experimental work has provided evidence for the cage, book, and cyclic isomers, but no experiment has identified multiple coexisting structures. Here, we report that broadband rotational spectroscopy in a pulsed supersonic expansion unambiguously identifies all three isomers; we determined their oxygen framework structures by means of oxygen-18-substituted water (H(2)(18)O). Relative isomer populations at different expansion conditions establish that the cage isomer is the minimum energy structure. Rotational spectra consistent with predicted heptamer and nonamer structures have also been identified.

Structural Basis of Neutralization of the Major Toxic Component from the Scorpion Centruroides noxius Hoffmann by a Human-derived Single-chain Antibody Fragment

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

Canul-Tec, Juan Carlos; Riaño-Umbarila, Lidia; Rudiño-Piñera, Enrique

2011-08-09

It has previously been reported that several single-chain antibody fragments of human origin (scFv) neutralize the effects of two different scorpion venoms through interactions with the primary toxins of Centruroides noxius Hoffmann (Cn2) and Centruroides suffusus suffusus (Css2). Here we present the crystal structure of the complex formed between one scFv (9004G) and the Cn2 toxin, determined in two crystal forms at 2.5 and 1.9 {angstrom} resolution. A 15-residue span of the toxin is recognized by the antibody through a cleft formed by residues from five of the complementarity-determining regions of the scFv. Analysis of the interface of the complexmore » reveals three features. First, the epitope of toxin Cn2 overlaps with essential residues for the binding of {beta}-toxins to its Na+ channel receptor site. Second, the putative recognition of Css2 involves mainly residues that are present in both Cn2 and Css2 toxins. Finally, the effect on the increase of affinity of previously reported key residues during the maturation process of different scFvs can be inferred from the structure. Taken together, these results provide the structural basis that explain the mechanism of the 9004G neutralizing activity and give insight into the process of directed evolution that gave rise to this family of neutralizing scFvs.« less

Genetic structure of the crown-of-thorns seastar in the Pacific Ocean, with focus on Guam.

PubMed

Tusso, Sergio; Morcinek, Kerstin; Vogler, Catherine; Schupp, Peter J; Caballes, Ciemon F; Vargas, Sergio; Wörheide, Gert

2016-01-01

Population outbreaks of the corallivorous crown-of-thorns seastar (COTS), Acanthaster 'planci' L., are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared samples from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations sampled were found to be structured in three significantly differentiated groups: (1) all locations immediately around Guam, as well as Kingman Reef and Swains Island; (2) Japan, Philippines, GBR and Vanuatu; and (3) Johnston Atoll, which was significantly different from all other localities. The lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island suggests potential long-distance dispersal of COTS in the Pacific.

Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20

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

McCraw, Dustin M.; O'Donnell, Jason K.; Taylor, Kenneth A.

2012-09-15

The use of adeno-associated virus (AAV) as a gene therapy vector is limited by the host neutralizing immune response. The cryo-electron microscopy (EM) structure at 8.5 A resolution is determined for a complex of AAV-2 with the Fab' fragment of monoclonal antibody (MAb) A20, the most extensively characterized AAV MAb. The binding footprint is determined through fitting the cryo-EM reconstruction with a homology model following sequencing of the variable domain, and provides a structural basis for integrating diverse prior epitope mappings. The footprint extends from the previously implicated plateau to the side of the spike, and into the conserved canyon,more » covering a larger area than anticipated. Comparison with structures of binding and non-binding serotypes indicates that recognition depends on a combination of subtle serotype-specific features. Separation of the neutralizing epitope from the heparan sulfate cell attachment site encourages attempts to develop immune-resistant vectors that can still bind to target cells.« less

A nonlinear viscoelastic approach to durability predictions for polymer based composite structures

NASA Technical Reports Server (NTRS)

Brinson, Hal F.

1991-01-01

Current industry approaches for the durability assessment of metallic structures are briefly reviewed. For polymer based composite structures, it is suggested that new approaches must be adopted to include memory or viscoelastic effects which could lead to delayed failures that might not be predicted using current techniques. A durability or accelerated life assessment plan for fiber reinforced plastics (FRP) developed and documented over the last decade or so is reviewed and discussed. Limitations to the plan are outlined and suggestions to remove the limitations are given. These include the development of a finite element code to replace the previously used lamination theory code and the development of new specimen geometries to evaluate delamination failures. The new DCB model is reviewed and results are presented. Finally, it is pointed out that new procedures are needed to determine interfacial properties and current efforts underway to determine such properties are reviewed. Suggestions for additional efforts to develop a consistent and accurate durability predictive approach for FRP structures are outlined.

In vitro organogenesis of gut-like structures from mouse embryonic stem cells.

PubMed

Kuwahara, M; Ogaeri, T; Matsuura, R; Kogo, H; Fujimoto, T; Torihashi, S

2004-04-01

Embryonic stem (ES) cells have pluripotency and give rise to many cell types and tissues, including representatives of all three germ layers in the embryo. We have reported previously that mouse ES cells formed contracting gut-like organs from embryoid bodies (EBs). These gut-like structures contracted spontaneously, and had large lumens surrounded by three layers, i.e. epithelium, lamina propria and muscularis. Ganglia were scattered along the periphery, and interstitial cells of Cajal (ICC) were distributed among the smooth muscle cells. In the present study, to determine whether they can be a model of gut organogenesis, we investigated the formation process of the gut-like structures in comparison with embryonic gut development. As a result, we found that the fundamental process of formation in vitro was similar to embryonic gut development in vivo. The result indicates that the gut-like structure is a useful tool not only for developmental study to determine the factors that induce gut organogenesis, but also for studies of enteric neurone and ICC development.

A nonlinear viscoelastic approach to durability predictions for polymer based composite structures

NASA Technical Reports Server (NTRS)

Brinson, Hal F.; Hiel, C. C.

1990-01-01

Current industry approaches for the durability assessment of metallic structures are briefly reviewed. For polymer based composite structures, it is suggested that new approaches must be adopted to include memory or viscoelastic effects which could lead to delayed failures that might not be predicted using current techniques. A durability or accelerated life assessment plan for fiber reinforced plastics (FRP) developed and documented over the last decade or so is reviewed and discussed. Limitations to the plan are outlined and suggestions to remove the limitations are given. These include the development of a finite element code to replace the previously used lamination theory code and the development of new specimen geometries to evaluate delamination failures. The new DCB model is reviewed and results are presented. Finally, it is pointed out that new procedures are needed to determine interfacial properties and current efforts underway to determine such properties are reviewed. Suggestions for additional efforts to develop a consistent and accurate durability predictive approach for FRP structures is outlined.

Hyperfine Structure Constants of Energetically High-lying Levels of Odd Parity of Atomic Vanadium

NASA Astrophysics Data System (ADS)

Güzelçimen, F.; Yapıcı, B.; Demir, G.; Er, A.; Öztürk, I. K.; Başar, Gö.; Kröger, S.; Tamanis, M.; Ferber, R.; Docenko, D.; Başar, Gü.

2014-09-01

High-resolution Fourier transform spectra of a vanadium-argon plasma have been recorded in the wavelength range of 365-670 nm (15,000-27,400 cm-1). Optical bandpass filters were used in the experimental setup to enhance the sensitivity of the Fourier transform spectrometer. In total, 138 atomic vanadium spectral lines showing resolved or partially resolved hyperfine structure have been analyzed to determine the magnetic dipole hyperfine structure constants A of the involved energy levels. One of the investigated lines has not been previously classified. As a result, the magnetic dipole hyperfine structure constants A for 90 energy levels are presented: 35 of them belong to the configuration 3d 34s4p and 55 to the configuration 3d 44p. Of these 90 constants, 67 have been determined for the first time, with 23 corresponding to the configuration 3d 34s4p and 44 to 3d 44p.

Rotational temperatures of Venus upper atmosphere as measured by SOIR on board Venus Express

NASA Astrophysics Data System (ADS)

Mahieux, A.; Vandaele, A. C.; Robert, S.; Wilquet, V.; Drummond, R.; López Valverde, M. A.; López Puertas, M.; Funke, B.; Bertaux, J. L.

2015-08-01

SOIR is a powerful infrared spectrometer flying on board the Venus Express spacecraft since mid-2006. It sounds the Venus atmosphere above the cloud layer using the solar occultation technique. In the recorded spectra, absorption structures from many species are observed, among them carbon dioxide, the main constituent of the Venus atmosphere. Previously, temperature vertical profiles were derived from the carbon dioxide density retrieved from the SOIR spectra by assuming hydrostatic equilibrium. These profiles show a permanent cold layer at 125 km with temperatures of ~100 K, surrounded by two warmer layers at 90 and 140 km, reaching temperatures of ~200 K and 250-300 K, respectively. In this work, temperature profiles are derived from the SOIR spectra using another technique based on the ro-vibrational structure of carbon dioxide observed in the spectra. The error budget is extensively investigated. Temperature profiles obtained by both techniques are comparable within their respective uncertainties and they confirm the vertical structure previously determined from SOIR spectra.

Evolutionary characterization of the West Nile Virus complete genome.

PubMed

Gray, R R; Veras, N M C; Santos, L A; Salemi, M

2010-07-01

The spatial dynamics of the West Nile Virus epidemic in North America are largely unknown. Previous studies that investigated the evolutionary history of the virus used sequence data from the structural genes (prM and E); however, these regions may lack phylogenetic information and obscure true evolutionary relationships. This study systematically evaluated the evolutionary patterns in the eleven genes of the WNV genome in order to determine which region(s) were most phylogenetically informative. We found that while the E region lacks resolution and can potentially result in misleading conclusions, the full NS3 or NS5 regions have strong phylogenetic signal. Furthermore, we show that geographic structure of WNV infection within the US is more pronounced than previously reported in studies that used the structural genes. We conclude that future evolutionary studies should focus on NS3 and NS5 in order to maximize the available sequences while retaining maximal interpretative power to infer temporal and geographic trends among WNV strains. Copyright 2010 Elsevier Inc. All rights reserved.

Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid–base catalysis

PubMed Central

Schultz, Eric P.; Vasquez, Ernesto E.; Scott, William G.

2014-01-01

The hammerhead ribozyme catalyzes RNA cleavage via acid–base catalysis. Whether it does so by general acid–base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid–base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK a of the substituted purine; in both cases inosine, which is similar to G in pK a and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential role of G12 as a general base, indicates that an alternative hammerhead cleavage mechanism involving specific base catalysis may instead explain the observed rate dependence upon purine substitutions at G12. The crystallographic results, contrary to previous assumptions, therefore cannot be interpreted to favor the general base catalysis mecahnism over the specific base catalysis mechanism. Instead, both of these mutually exclusive mechanistic alternatives must be considered in light of the current structural and biochemical data. PMID:25195740

Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis.

PubMed

Schultz, Eric P; Vasquez, Ernesto E; Scott, William G

2014-09-01

The hammerhead ribozyme catalyzes RNA cleavage via acid-base catalysis. Whether it does so by general acid-base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid-base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK(a) of the substituted purine; in both cases inosine, which is similar to G in pK(a) and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential role of G12 as a general base, indicates that an alternative hammerhead cleavage mechanism involving specific base catalysis may instead explain the observed rate dependence upon purine substitutions at G12. The crystallographic results, contrary to previous assumptions, therefore cannot be interpreted to favor the general base catalysis mecahnism over the specific base catalysis mechanism. Instead, both of these mutually exclusive mechanistic alternatives must be considered in light of the current structural and biochemical data.

Aromatic claw: A new fold with high aromatic content that evades structural prediction: Aromatic Claw

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

Sachleben, Joseph R.; Adhikari, Aashish N.; Gawlak, Grzegorz

2016-11-10

We determined the NMR structure of a highly aromatic (13%) protein of unknown function, Aq1974 from Aquifex aeolicus (PDB ID: 5SYQ). The unusual sequence of this protein has a tryptophan content five times the normal (six tryptophan residues of 114 or 5.2% while the average tryptophan content is 1.0%) with the tryptophans occurring in a WXW motif. It has no detectable sequence homology with known protein structures. Although its NMR spectrum suggested that the protein was rich in β-sheet, upon resonance assignment and solution structure determination, the protein was found to be primarily α-helical with a small two-stranded β-sheet withmore » a novel fold that we have termed an Aromatic Claw. As this fold was previously unknown and the sequence unique, we submitted the sequence to CASP10 as a target for blind structural prediction. At the end of the competition, the sequence was classified a hard template based model; the structural relationship between the template and the experimental structure was small and the predictions all failed to predict the structure. CSRosetta was found to predict the secondary structure and its packing; however, it was found that there was little correlation between CSRosetta score and the RMSD between the CSRosetta structure and the NMR determined one. This work demonstrates that even in relatively small proteins, we do not yet have the capacity to accurately predict the fold for all primary sequences. The experimental discovery of new folds helps guide the improvement of structural prediction methods.« less

The Structural Underpinnings of Policy Learning: A Classroom Policy Simulation

NASA Astrophysics Data System (ADS)

Bird, Stephen

This paper investigates the relationship between the centrality of individual actors in a social network structure and their policy learning performance. In a dynamic comparable to real-world policy networks, results from a classroom simulation demonstrate a strong relationship between centrality in social learning networks and grade performance. Previous research indicates that social network centrality should have a positive effect on learning in other contexts and this link is tested in a policy learning context. Second, the distinction between collaborative learning versus information diffusion processes in policy learning is examined. Third, frequency of interaction is analyzed to determine whether consistent, frequent tics have a greater impact on the learning process. Finally, the data arc analyzed to determine if the benefits of centrality have limitations or thresholds when benefits no longer accrue. These results demonstrate the importance of network structure, and support a collaborative conceptualization of the policy learning process.

Modal identification of structures from the responses and random decrement signatures

NASA Technical Reports Server (NTRS)

Brahim, S. R.; Goglia, G. L.

1977-01-01

The theory and application of a method which utilizes the free response of a structure to determine its vibration parameters is described. The time-domain free response is digitized and used in a digital computer program to determine the number of modes excited, the natural frequencies, the damping factors, and the modal vectors. The technique is applied to a complex generalized payload model previously tested using sine sweep method and analyzed by NASTRAN. Ten modes of the payload model are identified. In case free decay response is not readily available, an algorithm is developed to obtain the free responses of a structure from its random responses, due to some unknown or known random input or inputs, using the random decrement technique without changing time correlation between signals. The algorithm is tested using random responses from a generalized payload model and from the space shuttle model.

Fine structure constant and quantized optical transparency of plasmonic nanoarrays.

PubMed

Kravets, V G; Schedin, F; Grigorenko, A N

2012-01-24

Optics is renowned for displaying quantum phenomena. Indeed, studies of emission and absorption lines, the photoelectric effect and blackbody radiation helped to build the foundations of quantum mechanics. Nevertheless, it came as a surprise that the visible transparency of suspended graphene is determined solely by the fine structure constant, as this kind of universality had been previously reserved only for quantized resistance and flux quanta in superconductors. Here we describe a plasmonic system in which relative optical transparency is determined solely by the fine structure constant. The system consists of a regular array of gold nanoparticles fabricated on a thin metallic sublayer. We show that its relative transparency can be quantized in the near-infrared, which we attribute to the quantized contact resistance between the nanoparticles and the metallic sublayer. Our results open new possibilities in the exploration of universal dynamic conductance in plasmonic nanooptics.

Mapping transiently formed and sparsely populated conformations on a complex energy landscape.

PubMed

Wang, Yong; Papaleo, Elena; Lindorff-Larsen, Kresten

2016-08-23

Determining the structures, kinetics, thermodynamics and mechanisms that underlie conformational exchange processes in proteins remains extremely difficult. Only in favourable cases is it possible to provide atomic-level descriptions of sparsely populated and transiently formed alternative conformations. Here we benchmark the ability of enhanced-sampling molecular dynamics simulations to determine the free energy landscape of the L99A cavity mutant of T4 lysozyme. We find that the simulations capture key properties previously measured by NMR relaxation dispersion methods including the structure of a minor conformation, the kinetics and thermodynamics of conformational exchange, and the effect of mutations. We discover a new tunnel that involves the transient exposure towards the solvent of an internal cavity, and show it to be relevant for ligand escape. Together, our results provide a comprehensive view of the structural landscape of a protein, and point forward to studies of conformational exchange in systems that are less characterized experimentally.

Molecular Assembly of Clostridium botulinum progenitor M complex of type E.

PubMed

Eswaramoorthy, Subramaniam; Sun, Jingchuan; Li, Huilin; Singh, Bal Ram; Swaminathan, Subramanyam

2015-12-07

Clostridium botulinum neurotoxin (BoNT) is released as a progenitor complex, in association with a non-toxic-non-hemagglutinin protein (NTNH) and other associated proteins. We have determined the crystal structure of M type Progenitor complex of botulinum neurotoxin E [PTC-E(M)], a heterodimer of BoNT and NTNH. The crystal structure reveals that the complex exists as a tight, interlocked heterodimer of BoNT and NTNH. The crystal structure explains the mechanism of molecular assembly of the complex and reveals several acidic clusters at the interface responsible for association at low acidic pH and disassociation at basic/neutral pH. The similarity of the general architecture between the PTC-E(M) and the previously determined PTC-A(M) strongly suggests that the progenitor M complexes of all botulinum serotypes may have similar molecular arrangement, although the neurotoxins apparently can take very different conformation when they are released from the M complex.

Accommodation of structural rearrangements in the huntingtin-interacting protein 1 coiled-coil domain.

PubMed

Wilbur, Jeremy D; Hwang, Peter K; Brodsky, Frances M; Fletterick, Robert J

2010-03-01

Huntingtin-interacting protein 1 (HIP1) is an important link between the actin cytoskeleton and clathrin-mediated endocytosis machinery. HIP1 has also been implicated in the pathogenesis of Huntington's disease. The binding of HIP1 to actin is regulated through an interaction with clathrin light chain. Clathrin light chain binds to a flexible coiled-coil domain in HIP1 and induces a compact state that is refractory to actin binding. To understand the mechanism of this conformational regulation, a high-resolution crystal structure of a stable fragment from the HIP1 coiled-coil domain was determined. The flexibility of the HIP1 coiled-coil region was evident from its variation from a previously determined structure of a similar region. A hydrogen-bond network and changes in coiled-coil monomer interaction suggest that the HIP1 coiled-coil domain is uniquely suited to allow conformational flexibility.

Structure determination of a major facilitator peptide transporter: Inward facing PepTSt from Streptococcus thermophilus crystallized in space group P3121

PubMed Central

Quistgaard, Esben M.; Martinez Molledo, Maria

2017-01-01

Major facilitator superfamily (MFS) peptide transporters (typically referred to as PepT, POT or PTR transporters) mediate the uptake of di- and tripeptides, and so play an important dietary role in many organisms. In recent years, a better understanding of the molecular basis for this process has emerged, which is in large part due to a steep increase in structural information. Yet, the conformational transitions underlying the transport mechanism are still not fully understood, and additional data is therefore needed. Here we report in detail the detergent screening, crystallization, experimental MIRAS phasing, and refinement of the peptide transporter PepTSt from Streptococcus thermophilus. The space group is P3121, and the protein is crystallized in a monomeric inward facing form. The binding site is likely to be somewhat occluded, as the lobe encompassing transmembrane helices 10 and 11 is markedly bent towards the central pore of the protein, but the extent of this potential occlusion could not be determined due to disorder at the apex of the lobe. Based on structural comparisons with the seven previously determined P212121 and C2221 structures of inward facing PepTSt, the structural flexibility as well as the conformational changes mediating transition between the inward open and inward facing occluded states are discussed. In conclusion, this report improves our understanding of the structure and conformational cycle of PepTSt, and can furthermore serve as a case study, which may aid in supporting future structure determinations of additional MFS transporters or other integral membrane proteins. PMID:28264013

The Structure of Intergenerational Relations in Rural China: A Latent Class Analysis

ERIC Educational Resources Information Center

Guo, Man; Chi, Iris; Silverstein, Merril

2012-01-01

Most existing typology studies of intergenerational relations have used samples in North America and Europe. The present study expands on previous research by determining whether similar family relation typologies could be found using a sample of Chinese rural elders. The data were derived from a survey of 1,224 older adults in China's rural Anhui…

Long-term structural change in uneven-aged northern hardwoods

Treesearch

William B. Leak

1996-01-01

The diameter distributions of 10 previously unmanaged northern hardwood stands on the Bartlett Experimental Forest in New Hampshire were analyzed to determine changes over a 35 yr period since a single cutting by the diameter-limit or single-tree selection methods. The diameter distribution of an uncut old-growth stand (the Bowl) provided a comparison. The cuttings...

Determining the crystal structure of fibrinogen.

PubMed

Doolittle, R F

2004-05-01

Summary. I have enjoyed reading previous historical sketches that have appeared in Journal of Thrombosis and Haemostasis, and especially those by Ted Tuddenham on factor VIII and Bjorn Dahlback on activated protein C resistance. Like those authors, I have tried to capture some of the excitement-as well as the disappointments-that occurred along the way to a long-term goal.

Freezing does not alter multiscale tendon mechanics and damage mechanisms in tension.

PubMed

Lee, Andrea H; Elliott, Dawn M

2017-12-01

It is common in biomechanics to use previously frozen tissues, where it is assumed that the freeze-thaw process does not cause consequential mechanical or structural changes. We have recently quantified multiscale tendon mechanics and damage mechanisms using previously frozen tissue, where damage was defined as an irreversible change in the microstructure that alters the macroscopic mechanical parameters. Because freezing has been shown to alter tendon microstructures, the objective of this study was to determine if freezing alters tendon multiscale mechanics and damage mechanisms. Multiscale testing using a protocol that was designed to evaluate tendon damage (tensile stress-relaxation followed by unloaded recovery) was performed on fresh and previously frozen rat tail tendon fascicles. At both the fascicle and fibril levels, there was no difference between the fresh and frozen groups for any of the parameters, suggesting that there is no effect of freezing on tendon mechanics. After unloading, the microscale fibril strain fully recovered, and interfibrillar sliding only partially recovered, suggesting that the tendon damage is localized to the interfibrillar structures and that mechanisms of damage are the same in both fresh and previously frozen tendons. © 2017 New York Academy of Sciences.

Fundamental and assessment of concrete structure monitoring by using acoustic emission technique testing: A review

NASA Astrophysics Data System (ADS)

Desa, M. S. M.; Ibrahim, M. H. W.; Shahidan, S.; Ghadzali, N. S.; Misri, Z.

2018-04-01

Acoustic emission (AE) technique is one of the non-destructive (NDT) testing, where it can be used to determine the damage of concrete structures such as crack, corrosion, stability, sensitivity, as structure monitoring and energy formed within cracking opening growth in the concrete structure. This article gives a comprehensive review of the acoustic emission (AE) technique testing due to its application in concrete structure for structural health monitoring (SHM). Assessment of AE technique used for structural are reviewed to give the perception of its structural engineering such as dam, bridge and building, where the previous research has been reviewed based on AE application. The assessment of AE technique focusing on basic fundamental of parametric and signal waveform analysis during analysis process and its capability in structural monitoring. Moreover, the assessment and application of AE due to its function have been summarized and highlighted for future references

[Nuclear magnetic resonance of anorectal malformations and persistent postoperative fecal incontinence].

PubMed

de Agustín, J C; Alami, H; Lassaletta, L; Gámez, M; Fernández, A; Fraile, E; Alenda, J G; Rollán, V; Utrilla, J G

1992-07-01

We review our experience with Magnetic Resonance Imaging (MRI) in the evaluation of 6 patients showing anorectal malformation, and 4 more with persistent postoperative fecal incontinence. Preoperative sagittal, axial and coronal planes were studied with special consideration to the pelvic and vertebral structures. The excellent resolution of MRI allowed accurate identification of the pelvic musculature in all patients, including those with bizarre sacral abnormalities. MRI revealed structural anomalies not detected previously, such as teathering cord, intraspinal lipoma, presacral mass and renal malformation. In our institution, MRI has replaced the CT scan in the study of patients suffering of persistent fecal incontinence. In non operated on cases of anorectal malformations, MRI determines with extraordinary accuracy the location of the rectal atretic pouch, the actual pelvic muscular quality, and the detection of previously unsuspected associated anomalies.

Structure of the SnO2(110 ) -(4 ×1 ) Surface

NASA Astrophysics Data System (ADS)

Merte, Lindsay R.; Jørgensen, Mathias S.; Pussi, Katariina; Gustafson, Johan; Shipilin, Mikhail; Schaefer, Andreas; Zhang, Chu; Rawle, Jonathan; Nicklin, Chris; Thornton, Geoff; Lindsay, Robert; Hammer, Bjørk; Lundgren, Edvin

2017-09-01

Using surface x-ray diffraction (SXRD), quantitative low-energy electron diffraction (LEED), and density-functional theory (DFT) calculations, we have determined the structure of the (4 ×1 ) reconstruction formed by sputtering and annealing of the SnO2(110 ) surface. We find that the reconstruction consists of an ordered arrangement of Sn3O3 clusters bound atop the bulk-terminated SnO2(110 ) surface. The model was found by application of a DFT-based evolutionary algorithm with surface compositions based on SXRD, and shows excellent agreement with LEED and with previously published scanning tunneling microscopy measurements. The model proposed previously consisting of in-plane oxygen vacancies is thus shown to be incorrect, and our result suggests instead that Sn(II) species in interstitial positions are the more relevant features of reduced SnO2(110 ) surfaces.

ROY Revisited, Again: The Eighth Solved Structure

DOE PAGES

Tan, Melissa; Shtukenberg, Alexander G.; Zhu, Shengcai; ...

2018-01-01

X-ray powder diffraction and crystal structure prediction (CSP) algorithms were used in synergy to establish the crystal structure of the eighth polymorph of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY), form R05. R05 crystallizes in the monoclinic space group P2_1 with lattice parameters a = 11.479(4) Å, b = 11.030(1) Å, c = 10.840(6) Å, β = 118.23(1)°. This is both the first acentric ROY polymorph, and the first with Z' > 1. The torsion angles defined by the S-C-N-C atom sequence of each molecule in the asymmetric unit are -34.0° and 44.9°. These angles fall between those previously determined for the red and orangemore » forms of ROY. Hirshfeld surface analysis was employed to understand the crystal packing and intermolecular interactions in R05 and an updated energy stability ranking was determined using computational methods. Finally, although the application of CSP was critical to the structure solution of R05, energy stability rankings determined using a series of DFT vdW-inclusive models substantially deviate from experiment, indicating that ROY polymorphism continues to be a challenge for CSP.« less

ROY Revisited, Again: The Eighth Solved Structure

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

Tan, Melissa; Shtukenberg, Alexander G.; Zhu, Shengcai

X-ray powder diffraction and crystal structure prediction (CSP) algorithms were used in synergy to establish the crystal structure of the eighth polymorph of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY), form R05. R05 crystallizes in the monoclinic space group P2_1 with lattice parameters a = 11.479(4) Å, b = 11.030(1) Å, c = 10.840(6) Å, β = 118.23(1)°. This is both the first acentric ROY polymorph, and the first with Z' > 1. The torsion angles defined by the S-C-N-C atom sequence of each molecule in the asymmetric unit are -34.0° and 44.9°. These angles fall between those previously determined for the red and orangemore » forms of ROY. Hirshfeld surface analysis was employed to understand the crystal packing and intermolecular interactions in R05 and an updated energy stability ranking was determined using computational methods. Finally, although the application of CSP was critical to the structure solution of R05, energy stability rankings determined using a series of DFT vdW-inclusive models substantially deviate from experiment, indicating that ROY polymorphism continues to be a challenge for CSP.« less

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal.

PubMed

Clabbers, M T B; van Genderen, E; Wan, W; Wiegers, E L; Gruene, T; Abrahams, J P

2017-09-01

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm 3 , i.e. no more than 6 × 10 5 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal

PubMed Central

Clabbers, M. T. B.; van Genderen, E.; Wiegers, E. L.; Gruene, T.; Abrahams, J. P.

2017-01-01

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm3, i.e. no more than 6 × 105 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures. PMID:28876237

FRET measurements of kinesin neck orientation reveal a structural basis for processivity and asymmetry.

PubMed

Martin, Douglas S; Fathi, Reza; Mitchison, Timothy J; Gelles, Jeff

2010-03-23

As the smallest and simplest motor enzymes, kinesins have served as the prototype for understanding the relationship between protein structure and mechanochemical function of enzymes in this class. Conventional kinesin (kinesin-1) is a motor enzyme that transports cargo toward the plus end of microtubules by a processive, asymmetric hand-over-hand mechanism. The coiled-coil neck domain, which connects the two kinesin motor domains, contributes to kinesin processivity (the ability to take many steps in a row) and is proposed to be a key determinant of the asymmetry in the kinesin mechanism. While previous studies have defined the orientation and position of microtubule-bound kinesin motor domains, the disposition of the neck coiled-coil remains uncertain. We determined the neck coiled-coil orientation using a multidonor fluorescence resonance energy transfer (FRET) technique to measure distances between microtubules and bound kinesin molecules. Microtubules were labeled with a new fluorescent taxol donor, TAMRA-X-taxol, and kinesin derivatives with an acceptor fluorophore attached at positions on the motor and neck coiled-coil domains were used to reconstruct the positions and orientations of the domains. FRET measurements to positions on the motor domain were largely consistent with the domain orientation determined in previous studies, validating the technique. Measurements to positions on the neck coiled-coil were inconsistent with a radial orientation and instead demonstrated that the neck coiled-coil is parallel to the microtubule surface. The measured orientation provides a structural explanation for how neck surface residues enhance processivity and suggests a simple hypothesis for the origin of kinesin step asymmetry and "limping."

Structural studies of naturally occurring toxicogenic compounds

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

Springer, J. P.

1977-10-01

The paralytic shellfish poison (PSP), saxitoxin, is a neurotoxin isolated from Alaska butter clams (Saxidomus giganteus), mussels (Mytilus californianus) and axenic cultures of the dinoflagellate Gonyaulax catenella. The structure of saxitoxin has been determined through the use of single crystal X-ray diffraction. It possesses a unique tricyclic arrangement of atoms containing two guanidinium moieties and also a hydrated ketone. The relative stereochemistry is presented as well as the absolute configuration. The chemical constitution of a tremorgenic metabolite, paxilline, isolated from extracts of the fungus Penicillium paxilli Bainier has been determined. Paxilline represents a previously unreported class of natural compounds formedmore » by the combination of tryptophan and mevalonate subunits. The complete stereostructure of two other fungal metabolites, paspaline and paspalicine, closely related to paxilline but isolated from Claviceps paspali Stammes have also been determined and are presented. The stereochemistries of paxilline, paspaline and paspalicine are identical at corresponding chiral centers.« less

Isolation and identification of three potential impurities of pholcodine bulk drug substance.

PubMed

Denk, O M; Gray, A I; Skellern, G G; Watson, D G

2000-07-01

Three previously unreported manufacturing impurities were isolated from a pholcodine mother liquor using preparative reversed-phase HPLC. The liquor was the residue remaining after recrystallisation of a production batch of pholcodine. The impurities, which are structurally related to pholcodine, were initially detected by thin-layer chromatography (TLC). Their structures were determined after separation by preparative HPLC (Econo-Prep 5 microm C18 column, 30 cm x 21.2 mm i.d.). Structure elucidation was carried out using nuclear magnetic resonance (NMR) spectroscopy, mass spectroscopy (MS) and ultra violet (UV) spectroscopy. The impurities were identified as alkylated derivatives of pholcodine possessing second 2-morpholinoethyl substituents at various positions.

NiO: correlated band structure of a charge-transfer insulator.

PubMed

Kunes, J; Anisimov, V I; Skornyakov, S L; Lukoyanov, A V; Vollhardt, D

2007-10-12

The band structure of the prototypical charge-transfer insulator NiO is computed by using a combination of an ab initio band structure method and the dynamical mean-field theory with a quantum Monte-Carlo impurity solver. Employing a Hamiltonian which includes both Ni d and O p orbitals we find excellent agreement with the energy bands determined from angle-resolved photoemission spectroscopy. This brings an important progress in a long-standing problem of solid-state theory. Most notably we obtain the low-energy Zhang-Rice bands with strongly k-dependent orbital character discussed previously in the context of low-energy model theories.

Testing of Composite Fan Vanes With Erosion-Resistant Coating Accelerated

NASA Technical Reports Server (NTRS)

Bowman, Cheryl L.; Sutter, James K.; Otten, Kim D.; Samorezov, Sergey; Perusek, Gail P.

2004-01-01

The high-cycle fatigue of composite stator vanes provided an accelerated life-state prior to insertion in a test stand engine. The accelerated testing was performed in the Structural Dynamics Laboratory at the NASA Glenn Research Center under the guidance of Structural Mechanics and Dynamics Branch personnel. Previous research on fixturing and test procedures developed at Glenn determined that engine vibratory conditions could be simulated for polymer matrix composite vanes by using the excitation of a combined slip table and electrodynamic shaker in Glenn's Structural Dynamics Laboratory. Bench-top testing gave researchers the confidence to test the coated vanes in a full-scale engine test.

Structure of Dimeric and Tetrameric Complexes of the BAR Domain Protein PICK1 Determined by Small-Angle X-Ray Scattering.

PubMed

Karlsen, Morten L; Thorsen, Thor S; Johner, Niklaus; Ammendrup-Johnsen, Ina; Erlendsson, Simon; Tian, Xinsheng; Simonsen, Jens B; Høiberg-Nielsen, Rasmus; Christensen, Nikolaj M; Khelashvili, George; Streicher, Werner; Teilum, Kaare; Vestergaard, Bente; Weinstein, Harel; Gether, Ulrik; Arleth, Lise; Madsen, Kenneth L

2015-07-07

PICK1 is a neuronal scaffolding protein containing a PDZ domain and an auto-inhibited BAR domain. BAR domains are membrane-sculpting protein modules generating membrane curvature and promoting membrane fission. Previous data suggest that BAR domains are organized in lattice-like arrangements when stabilizing membranes but little is known about structural organization of BAR domains in solution. Through a small-angle X-ray scattering (SAXS) analysis, we determine the structure of dimeric and tetrameric complexes of PICK1 in solution. SAXS and biochemical data reveal a strong propensity of PICK1 to form higher-order structures, and SAXS analysis suggests an offset, parallel mode of BAR-BAR oligomerization. Furthermore, unlike accessory domains in other BAR domain proteins, the positioning of the PDZ domains is flexible, enabling PICK1 to perform long-range, dynamic scaffolding of membrane-associated proteins. Together with functional data, these structural findings are compatible with a model in which oligomerization governs auto-inhibition of BAR domain function. Copyright © 2015 Elsevier Ltd. All rights reserved.

Critical layer thickness in In/sub 0. 2/Ga/sub 0. 8/As/GaAs single strained quantum well structures

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

Fritz, I.J.; Gourley, P.L.; Dawson, L.R.

1987-09-28

We report accurate determination of the critical layer thickness (CLT) for single strained-layer epitaxy in the InGaAs/GaAs system. Our samples were molecular beam epitaxially grown, selectively doped, single quantum well structures comprising a strained In/sub 0.2/Ga/sub 0.8/As layer imbedded in GaAs. We determined the CLT by two sensitive techniques: Hall-effect measurements at 77 K and photoluminescence microscopy. Both techniques indicate a CLT of about 20 nm. This value is close to that determined previously (--15 nm) for comparable strained-layer superlattices, but considerably less than the value of --45 nm suggested by recent x-ray rocking-curve measurements. We show by a simplemore » calculation that photoluminescence microscopy is more than two orders of magnitude more sensitive to dislocations than x-ray diffraction. Our results re-emphasize the necessity of using high-sensitivity techniques for accurate determination of critical layer thicknesses.« less

Three-Dimensional Geometry of Collagenous Tissues by Second Harmonic Polarimetry.

PubMed

Reiser, Karen; Stoller, Patrick; Knoesen, André

2017-06-01

Collagen is a biological macromolecule capable of second harmonic generation, allowing label-free detection in tissues; in addition, molecular orientation can be determined from the polarization dependence of the second harmonic signal. Previously we reported that in-plane orientation of collagen fibrils could be determined by modulating the polarization angle of the laser during scanning. We have now extended this method so that out-of-plane orientation angles can be determined at the same time, allowing visualization of the 3-dimensional structure of collagenous tissues. This approach offers advantages compared with other methods for determining out-of-plane orientation. First, the orientation angles are directly calculated from the polarimetry data obtained in a single scan, while other reported methods require data from multiple scans, use of iterative optimization methods, application of fitting algorithms, or extensive post-optical processing. Second, our method does not require highly specialized instrumentation, and thus can be adapted for use in almost any nonlinear optical microscopy setup. It is suitable for both basic and clinical applications. We present three-dimensional images of structurally complex collagenous tissues that illustrate the power of such 3-dimensional analyses to reveal the architecture of biological structures.

Three-Dimensional Geometry of Collagenous Tissues by Second Harmonic Polarimetry

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

Reiser, Karen; Stoller, Patrick; Knoesen, André

Collagen is a biological macromolecule capable of second harmonic generation, allowing label-free detection in tissues; in addition, molecular orientation can be determined from the polarization dependence of the second harmonic signal. Previously we reported that in-plane orientation of collagen fibrils could be determined by modulating the polarization angle of the laser during scanning. We have now extended this method so that out-of-plane orientation angles can be determined at the same time, allowing visualization of the 3-dimensional structure of collagenous tissues. This approach offers advantages compared with other methods for determining out-of-plane orientation. First, the orientation angles are directly calculated frommore » the polarimetry data obtained in a single scan, while other reported methods require data from multiple scans, use of iterative optimization methods, application of fitting algorithms, or extensive post-optical processing. Second, our method does not require highly specialized instrumentation, and thus can be adapted for use in almost any nonlinear optical microscopy setup. It is suitable for both basic and clinical applications. We present three-dimensional images of structurally complex collagenous tissues that illustrate the power of such 3-dimensional analyses to reveal the architecture of biological structures.« less

Three-Dimensional Geometry of Collagenous Tissues by Second Harmonic Polarimetry

DOE PAGES

Reiser, Karen; Stoller, Patrick; Knoesen, André

2017-06-01

Collagen is a biological macromolecule capable of second harmonic generation, allowing label-free detection in tissues; in addition, molecular orientation can be determined from the polarization dependence of the second harmonic signal. Previously we reported that in-plane orientation of collagen fibrils could be determined by modulating the polarization angle of the laser during scanning. We have now extended this method so that out-of-plane orientation angles can be determined at the same time, allowing visualization of the 3-dimensional structure of collagenous tissues. This approach offers advantages compared with other methods for determining out-of-plane orientation. First, the orientation angles are directly calculated frommore » the polarimetry data obtained in a single scan, while other reported methods require data from multiple scans, use of iterative optimization methods, application of fitting algorithms, or extensive post-optical processing. Second, our method does not require highly specialized instrumentation, and thus can be adapted for use in almost any nonlinear optical microscopy setup. It is suitable for both basic and clinical applications. We present three-dimensional images of structurally complex collagenous tissues that illustrate the power of such 3-dimensional analyses to reveal the architecture of biological structures.« less

Structural basis for antibody recognition in the receptor-binding domains of toxins A and B from Clostridium difficile.

PubMed

Murase, Tomohiko; Eugenio, Luiz; Schorr, Melissa; Hussack, Greg; Tanha, Jamshid; Kitova, Elena N; Klassen, John S; Ng, Kenneth K S

2014-01-24

Clostridium difficile infection is a serious and highly prevalent nosocomial disease in which the two large, Rho-glucosylating toxins TcdA and TcdB are the main virulence factors. We report for the first time crystal structures revealing how neutralizing and non-neutralizing single-domain antibodies (sdAbs) recognize the receptor-binding domains (RBDs) of TcdA and TcdB. Surprisingly, the complexes formed by two neutralizing antibodies recognizing TcdA do not show direct interference with the previously identified carbohydrate-binding sites, suggesting that neutralization of toxin activity may be mediated by mechanisms distinct from steric blockage of receptor binding. A camelid sdAb complex also reveals the molecular structure of the TcdB RBD for the first time, facilitating the crystallization of a strongly negatively charged protein fragment that has resisted previous attempts at crystallization and structure determination. Electrospray ionization mass spectrometry measurements confirm the stoichiometries of sdAbs observed in the crystal structures. These studies indicate how key epitopes in the RBDs from TcdA and TcdB are recognized by sdAbs, providing molecular insights into toxin structure and function and providing for the first time a basis for the design of highly specific toxin-specific therapeutic and diagnostic agents.

Structural Basis for Antibody Recognition in the Receptor-binding Domains of Toxins A and B from Clostridium difficile*

PubMed Central

Murase, Tomohiko; Eugenio, Luiz; Schorr, Melissa; Hussack, Greg; Tanha, Jamshid; Kitova, Elena N.; Klassen, John S.; Ng, Kenneth K. S.

2014-01-01

Clostridium difficile infection is a serious and highly prevalent nosocomial disease in which the two large, Rho-glucosylating toxins TcdA and TcdB are the main virulence factors. We report for the first time crystal structures revealing how neutralizing and non-neutralizing single-domain antibodies (sdAbs) recognize the receptor-binding domains (RBDs) of TcdA and TcdB. Surprisingly, the complexes formed by two neutralizing antibodies recognizing TcdA do not show direct interference with the previously identified carbohydrate-binding sites, suggesting that neutralization of toxin activity may be mediated by mechanisms distinct from steric blockage of receptor binding. A camelid sdAb complex also reveals the molecular structure of the TcdB RBD for the first time, facilitating the crystallization of a strongly negatively charged protein fragment that has resisted previous attempts at crystallization and structure determination. Electrospray ionization mass spectrometry measurements confirm the stoichiometries of sdAbs observed in the crystal structures. These studies indicate how key epitopes in the RBDs from TcdA and TcdB are recognized by sdAbs, providing molecular insights into toxin structure and function and providing for the first time a basis for the design of highly specific toxin-specific therapeutic and diagnostic agents. PMID:24311789

Kamenetsk—A new impact structure in the Ukrainian Shield

NASA Astrophysics Data System (ADS)

Gurov, Eugene; Nikolaenko, Nikolay; Shevchuk, Helena; Yamnichenko, Anatoly

2017-12-01

The Kamenetsk impact structure is a deeply eroded simple crater that formed in crystalline rocks of the Ukrainian Shield. This study presents structural, lithologic, and shock metamorphic evidence for an impact origin of the Kamenetsk structure, which was previously described as a paleovolcano. The Kamenetsk structure is an oval depression that is 1.0-1.2 km in diameter and 130 m deep. The structure is deeply eroded, and only the lower part of the sequence of lithic breccia has been preserved in the deepest part of the crater to recent time, while the predominant part of impact rocks and postimpact sediments was eroded. Manifestations of shock metamorphism of minerals, especially planar deformation features in quartz and feldspars, were determined by petrographic investigations of lithic breccia that allowed us to determine the impact origin of the Kamenetsk structure. The erosion of the crater and surrounding target to a minimal depth of 220 m preceded the deposition of the postimpact sediments. The time of the formation of the Kamenetsk structure is bracketed within a wide interval from 2.0 to 2.1 Ga, the age of the crystalline target rocks, to the Late Miocene age of the sediments overlaying the crater. The deep erosion of the structure suggests it is probably Paleozoic in age.

Morphological Dependence of Element Stoichiometry in the H. americanus Exoskeleton

NASA Astrophysics Data System (ADS)

Mergelsberg, S. T.; Ulrich, R. N.; Dove, P. M.

2016-02-01

The crustacean exoskeleton is a complex biocomposite of inorganic mineral and organic macromolecules that expresses highly divergent morphologies across different taxa. While the structures and compositions of the organic framework show complex links to environmental and developmental pressures, little is known about the mineral chemistry. Previous studies of the cuticle have assumed that magnesium, phosphorous, and other trace metals are largely contained in the inorganic mineral fraction. Due to analytical limitations of structural analyses and in situ spectroscopic methods, the stoichiometry of the organic and inorganic portions could not be resolved. For example, previous Raman and XRD studies conclude the higher concentrations of trace elements, such as P and Mg measured in reinforced structures, e.g. the claw and abdomen, are primarily determined by the mineral fraction. Using the American Lobster (Homarus americanus) as a model organism to establish relationships between body part function and cuticle composition, this study quantified the distributions of Mg and P in the mineral and organic fractions. The experiments were designed to dissolve the exoskeleton of 10 body parts using three types of solutions that were specific to extracting 1) the mineral phase, 2) protein, and 3) polysaccharide. Analysis of the solutions by ICP-OES shows the mineral phase contains magnesium and phosphorous at concentrations sufficient to support the formation of calcium-magnesium and phosphate minerals. The protein fraction of the body parts contains significantly more Mg and P than previously hypothesized, while the levels of P contained in the organic portion are fairly constant. The findings demonstrate the lobster cuticle contains a significant amount of non-mineralized P and Mg that is readily water-soluble in the protein component. However, for those body parts used for defense and food acquisition, such as the claw, the mineral component determines the overall composition of the exoskeleton.

Infrared spectra of C2H4 dimer and trimer

NASA Astrophysics Data System (ADS)

Barclay, A. J.; Esteki, K.; McKellar, A. R. W.; Moazzen-Ahmadi, N.

2018-05-01

Spectra of ethylene dimers and trimers are studied in the ν11 and (for the dimer) ν9 fundamental band regions of C2H4 (≈2990 and 3100 cm-1) using a tunable optical parametric oscillator source to probe a pulsed supersonic slit jet expansion. The deuterated trimer has been observed previously, but this represents the first rotationally resolved spectrum of (C2H4)3. The results support the previously determined cross-shaped (D2d) dimer and barrel-shaped (C3h or C3) trimer structures. However, the dimer spectrum in the ν9 fundamental region of C2H4 is apparently very perturbed and a previous rotational analysis is not well verified.

Investigating middle-atmospheric gravity waves associated with a sprite-producing mesoscale convective event

NASA Astrophysics Data System (ADS)

Vollmer, D. R.; McHarg, M. G.; Harley, J.; Haaland, R. K.; Stenbaek-Nielsen, H.

2016-12-01

On 23 July 2014, a mesoscale convective event over western Nebraska produced a large number of sprites. One frame per second images obtained from a low-noise Andor Scientific CMOS camera showed regularly-spaced horizontal striations in the airglow both before and during several of the sprite events, suggesting the presence of vertically-propagating gravity waves in the middle atmosphere. Previous work hypothesized that the gravity waves were produced by the thunderstorm itself. We compare our observations with previous work, and present numerical simulations conducted to determine source, structure, and propagation of atmospheric gravity waves.

Structure of PA1221, a nonribosomal peptide synthetase containing adenylation and peptidyl carrier protein domains.

PubMed

Mitchell, Carter A; Shi, Ce; Aldrich, Courtney C; Gulick, Andrew M

2012-04-17

Many bacteria use large modular enzymes for the synthesis of polyketide and peptide natural products. These multidomain enzymes contain integrated carrier domains that deliver bound substrates to multiple catalytic domains, requiring coordination of these chemical steps. Nonribosomal peptide synthetases (NRPSs) load amino acids onto carrier domains through the activity of an upstream adenylation domain. Our lab recently determined the structure of an engineered two-domain NRPS containing fused adenylation and carrier domains. This structure adopted a domain-swapped dimer that illustrated the interface between these two domains. To continue our investigation, we now examine PA1221, a natural two-domain protein from Pseudomonas aeruginosa. We have determined the amino acid specificity of this new enzyme and used domain specific mutations to demonstrate that loading the downstream carrier domain within a single protein molecule occurs more quickly than loading of a nonfused carrier domain intermolecularly. Finally, we have determined crystal structures of both apo- and holo-PA1221 proteins, the latter using a valine-adenosine vinylsulfonamide inhibitor that traps the adenylation domain-carrier domain interaction. The protein adopts an interface similar to that seen with the prior adenylation domain-carrier protein construct. A comparison of these structures with previous structures of multidomain NRPSs suggests that a large conformational change within the NRPS adenylation domains guides the carrier domain into the active site for thioester formation.

DNA Nanotubes for NMR Structure Determination of Membrane Proteins

PubMed Central

Bellot, Gaëtan; McClintock, Mark A.; Chou, James J; Shih, William M.

2013-01-01

Structure determination of integral membrane proteins by solution NMR represents one of the most important challenges of structural biology. A Residual-Dipolar-Coupling-based refinement approach can be used to solve the structure of membrane proteins up to 40 kDa in size, however, a weak-alignment medium that is detergent-resistant is required. Previously, availability of media suitable for weak alignment of membrane proteins was severely limited. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400nm-long six-helix bundles each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, towards collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes via counter ions and small DNA binding molecules. This detergent-resistant liquid-crystal media offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility, and structural programmability. Production of sufficient nanotubes for 4–5 NMR experiments can be completed in one week by a single individual. PMID:23518667

The use of radar and visual observations to characterize the surface structure of the planet Mercury

NASA Technical Reports Server (NTRS)

Clark, P. E.; Kobrick, M.; Jurgens, R. F.

1985-01-01

An analysis is conducted of available topographic profiles and scattering parameters derived from earth-based S- and X-band radar observations of Mercury, in order to determine the nature and origin of regional surface variations and structures that are typical of the planet. Attention is given to the proposal that intercrater plains on Mercury formed from extensive volcanic flooding during bombardment, so that most craters were formed on a partially molten surface and were thus obliterated, together with previously formed tectonic features.

Structure-activity relationships of tetramethylpiperidine-substituted phenazines against Mycobacterium leprae in vitro.

PubMed Central

Franzblau, S G; White, K E; O'Sullivan, J F

1989-01-01

In a previous study of structure-activity relationships of selected phenazines against Mycobacterium leprae in vitro, compounds containing a 2,2,6,6-tetramethylpiperidine substitution at the imino nitrogen were most active. Therefore, the effect of substitution at the para positions of the phenyl and anilino groups in tetramethylpiperidine-substituted phenazines was assessed. As determined by radiorespirometry, activity in ascending order was observed in compounds substituted with hydrogens or fluorines, ethoxy groups, methyl groups, chlorines, and bromines and correlated with partition coefficients in octanol-water. PMID:2692516

Evidence for early metamorphosis of sea lampreys in the Chippewa River, Michigan

USGS Publications Warehouse

Morkert, Sidney B.; Swink, William D.; Seelye, James G.

1998-01-01

We determined age at metamorphosis to the juvenile or parasitic phase for sea lampreysPetromyzon marinus in a highly productive Great Lakes tributary to determine if the age at metamorphosis was earlier than expected. Ages determined from statoliths, a structure analogous to otoliths in teleost fishes, indicated that many sea lampreys collected from the Chippewa River, Michigan, in September 1995 were undergoing metamorphosis at age 2, at least 1 year earlier than previously observed. In all, 141 newly metamorphosed lampreys were examined, and 81% were estimated to be only 2 years old. The length-frequency distribution of newly metamorphosed sea lampreys in the Chippewa River also indicated the possibility of metamorphsis at age 2, but to a lesser extent than indicated by statolith aging. The Chippewa River is a highly productive stream that might require more frequent treatment than previously suspected. More careful examination of other highly productive streams is needed to determine if, and to what extent, sea lampreys metamorphose at age 2 in the Chippewa River and other Great Lakes tributaries.

Preliminary results of local earthquake tomography around Bali, Lombok, and Sumbawa regions

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

Nugraha, Andri Dian, E-mail: nugraha@gf.itb.ac.id; Puspito, Nanang T; Yudistira, Tedi

Bali, Sumbawa, and Lombok regions are located in active tectonic influence by Indo-Australia plate subducts beneath Sunda plate in southern part and local back-arc thrust in northern part the region. Some active volcanoes also lie from eastern part of Java, Bali, Lombok and Sumbawa regions. Previous studies have conducted subsurface seismic velocity imaging using regional and global earthquake data around the region. In this study, we used P-arrival time from local earthquake networks compiled by MCGA, Indonesia within time periods of 2009 up to 2013 to determine seismic velocity structure and simultaneously hypocenter adjustment by applying seismic tomography inversion method.more » For the tomographic inversion procedure, we started from 1-D initial velocity structure. We evaluated the resolution of tomography inversion results through checkerboard test and calculating derivative weigh sum. The preliminary results of tomography inversion show fairly clearly high seismic velocity subducting Indo-Australian and low velocity anomaly around volcano regions. The relocated hypocenters seem to cluster around the local fault system such as back-arc thrust fault in northern part of the region and around local fault in Sumbawa regions. Our local earthquake tomography results demonstrated consistent with previous studies and improved the resolution. For future works, we will determine S-wave velocity structure using S-wave arrival time to enhance our understanding of geological processes and for much better interpretation.« less

Preliminary results of local earthquake tomography around Bali, Lombok, and Sumbawa regions

NASA Astrophysics Data System (ADS)

Nugraha, Andri Dian; Kusnandar, Ridwan; Puspito, Nanang T.; Sakti, Artadi Pria; Yudistira, Tedi

2015-04-01

Bali, Sumbawa, and Lombok regions are located in active tectonic influence by Indo-Australia plate subducts beneath Sunda plate in southern part and local back-arc thrust in northern part the region. Some active volcanoes also lie from eastern part of Java, Bali, Lombok and Sumbawa regions. Previous studies have conducted subsurface seismic velocity imaging using regional and global earthquake data around the region. In this study, we used P-arrival time from local earthquake networks compiled by MCGA, Indonesia within time periods of 2009 up to 2013 to determine seismic velocity structure and simultaneously hypocenter adjustment by applying seismic tomography inversion method. For the tomographic inversion procedure, we started from 1-D initial velocity structure. We evaluated the resolution of tomography inversion results through checkerboard test and calculating derivative weigh sum. The preliminary results of tomography inversion show fairly clearly high seismic velocity subducting Indo-Australian and low velocity anomaly around volcano regions. The relocated hypocenters seem to cluster around the local fault system such as back-arc thrust fault in northern part of the region and around local fault in Sumbawa regions. Our local earthquake tomography results demonstrated consistent with previous studies and improved the resolution. For future works, we will determine S-wave velocity structure using S-wave arrival time to enhance our understanding of geological processes and for much better interpretation.

Sum rules across the unpolarized Compton processes involving generalized polarizabilities and moments of nucleon structure functions

NASA Astrophysics Data System (ADS)

Lensky, Vadim; Hagelstein, Franziska; Pascalutsa, Vladimir; Vanderhaeghen, Marc

2018-04-01

We derive two new sum rules for the unpolarized doubly virtual Compton scattering process on a nucleon, which establish novel low-Q2 relations involving the nucleon's generalized polarizabilities and moments of the nucleon's unpolarized structure functions F1(x ,Q2) and F2(x ,Q2). These relations facilitate the determination of some structure constants which can only be accessed in off-forward doubly virtual Compton scattering, not experimentally accessible at present. We perform an empirical determination for the proton and compare our results with a next-to-leading-order chiral perturbation theory prediction. We also show how these relations may be useful for a model-independent determination of the low-Q2 subtraction function in the Compton amplitude, which enters the two-photon-exchange contribution to the Lamb shift of (muonic) hydrogen. An explicit calculation of the Δ (1232 )-resonance contribution to the muonic-hydrogen 2 P -2 S Lamb shift yields -1 ±1 μ eV , confirming the previously conjectured smallness of this effect.

Oximes: Inhibitors of Human Recombinant Acetylcholinesterase. A Structure-Activity Relationship (SAR) Study

PubMed Central

Sepsova, Vendula; Karasova, Jana Zdarova; Korabecny, Jan; Dolezal, Rafael; Zemek, Filip; Bennion, Brian J.; Kuca, Kamil

2013-01-01

Acetylcholinesterase (AChE) reactivators were developed for the treatment of organophosphate intoxication. Standard care involves the use of anticonvulsants (e.g., diazepam), parasympatolytics (e.g., atropine) and oximes that restore AChE activity. However, oximes also bind to the active site of AChE, simultaneously acting as reversible inhibitors. The goal of the present study is to determine how oxime structure influences the inhibition of human recombinant AChE (hrAChE). Therefore, 24 structurally different oximes were tested and the results compared to the previous eel AChE (EeAChE) experiments. Structural factors that were tested included the number of pyridinium rings, the length and structural features of the linker, and the number and position of the oxime group on the pyridinium ring. PMID:23959117

Primary structure of the hemoglobin alpha-chain of rose-ringed parakeet (Psittacula krameri).

PubMed

Islam, A; Beg, O U; Persson, B; Zaidi, Z H; Jörnvall, H

1988-10-01

The structure of the hemoglobin alpha-chain of Rose-ringed Parakeet was determined by sequence degradations of the intact subunit, the CNBr fragments, and peptides obtained by digestion with staphylococcal Glu-specific protease and trypsin. Using this analysis, the complete alpha-chain structure of 21 avian species is known, permitting comparisons of the protein structure and of avian relationships. The structure exhibits differences from previously established avian alpha-chains at a total of 61 positions, five of which have residues unique to those of the parakeet (Ser-12, Gly-65, Ser-67, Ala-121, and Leu-134). The analysis defines hemoglobin variation within an additional avian order (Psittaciformes), demonstrates distant patterns for evaluation of relationships within other avian orders, and lends support to taxonomic conclusions from molecular data.

Apo And Calcium-Bound Crystal Structures of Alpha-11 Giardin, An Unusual Annexin From 'Giardia Lamblia'

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

Pathuri, P.; Nguyen, E.T.; Svard, S.G.

2007-07-12

Alpha-11 giardin is a member of the multi-gene alpha-giardin family in the intestinal protozoan, Giardia lamblia. This gene family shares an ancestry with the annexin super family, whose common characteristic is calcium-dependent binding to membranes that contain acidic phospholipids. Several alpha giardins are highly expressed during parasite-induced diarrhea in humans. Despite being a member of a large family of proteins, little is known about the function and cellular localization of alpha-11 giardin, although giardins are often associated with the cytoskeleton. It has been shown that Giardia exhibits high levels of alpha-11 giardin mRNA transcript throughout its life cycle; however, constitutivemore » over-expression of this protein is lethal to the parasite. Determining the three-dimensional structure of an alpha-giardin is essential to identifying functional domains shared in the alpha-giardin family. Here we report the crystal structures of the apo and Ca{sup 2+}-bound forms of alpha-11 giardin, the first alpha giardin to be characterized structurally. Crystals of apo and Ca{sup 2+}-bound alpha-11 giardin diffracted to 1.1 angstroms and 2.93 angstroms, respectively. The crystal structure of selenium-substituted apo alpha-11 giardin reveals a planar array of four tandem repeats of predominantly {alpha}-helical domains, reminiscent of previously determined annexin structures, making this the highest-resolution structure of an annexin to date. The apo alpha-11 giardin structure also reveals a hydrophobic core formed between repeats I/IV and II/III, a region typically hydrophilic in other annexins. Surprisingly, the Ca{sup 2+}-bound structure contains only a single calcium ion, located in the DE loop of repeat I and coordinated differently from the two types of calcium sites observed in previous annexin structures. The apo and Ca{sup 2+}-bound alpha-11 giardin structures assume overall similar conformations; however, Ca2+-bound alpha-11 giardin crystallized in a lower-symmetry space group with four molecules in the asymmetric unit. Vesicle-binding studies suggest that alpha-11 giardin, unlike most other annexins, does not bind to vesicles composed of acidic phospholipids in a calcium-dependent manner.« less

Using molecular principal axes for structural comparison: determining the tertiary changes of a FAB antibody domain induced by antigenic binding

PubMed Central

Silverman, B David

2007-01-01

Background Comparison of different protein x-ray structures has previously been made in a number of different ways; for example, by visual examination, by differences in the locations of secondary structures, by explicit superposition of structural elements, e.g. α-carbon atom locations, or by procedures that utilize a common symmetry element or geometrical feature of the structures to be compared. Results A new approach is applied to determine the structural changes that an antibody protein domain experiences upon its interaction with an antigenic target. These changes are determined with the use of two different, however comparable, sets of principal axes that are obtained by diagonalizing the second-order tensors that yield the moments-of-geometry as well as an ellipsoidal characterization of domain shape, prior to and after interaction. Determination of these sets of axes for structural comparison requires no internal symmetry features of the domains, depending solely upon their representation in three-dimensional space. This representation may involve atomic, Cα, or residue centroid coordinates. The present analysis utilizes residue centroids. When the structural changes are minimal, the principal axes of the domains, prior to and after interaction, are essentially comparable and consequently may be used for structural comparison. When the differences of the axes cannot be neglected, but are nevertheless slight, a smaller relatively invariant substructure of the domains may be utilized for comparison. The procedure yields two distance metrics for structural comparison. First, the displacements of the residue centroids due to antigenic binding, referenced to the ellipsoidal principal axes, are noted. Second, changes in the ellipsoidal distances with respect to the non-interacting structure provide a direct measure of the spatial displacements of the residue centroids, towards either the interior or exterior of the domain. Conclusion With use of x-ray data from the protein data bank (PDB), these two metrics are shown to highlight, in a manner different from before, the structural changes that are induced in the overall domains as well as in the H3 loops of the complementarity-determining regions (CDR) upon FAB antibody binding to a truncated and to a synthetic hemagglutinin viral antigenic target. PMID:17996091

A crystal-chemical classification of borate structures with emphasis on hydrated borates

USGS Publications Warehouse

Christ, C.L.; Clark, J.R.

1977-01-01

The rules governing formation of hydrated borate polyanions that were proposed by C.L. Christ in 1960 are critically reviewed and new rules added on the basis of recent crystal structure determinations. Principles and classifications previously published by others are also critically reviewed briefly. The fundamental building blocks from which borate polyanions can be constructed are defined on the basis of the number n of boron atoms, and the fully hydrated polyanions are illustrated. Known structures are grouped accordingly, and a shorthand notation using n and symbols ?? = triangle, T = tetrahedron is introduced so that the polyanions can be easily characterized. For example, 3:??+2T describes [B3O3(OH)5]2-. Correct structural formulas are assigned borates with known structures whereas borates of unknown structure are grouped separately. ?? 1977 Springer-Verlag.

Rapid cable tension estimation using dynamic and mechanical properties

NASA Astrophysics Data System (ADS)

Martínez-Castro, Rosana E.; Jang, Shinae; Christenson, Richard E.

2016-04-01

Main tension elements are critical to the overall stability of cable-supported bridges. A dependable and rapid determination of cable tension is desired to assess the state of a cable-supported bridge and evaluate its operability. A portable smart sensor setup is presented to reduce post-processing time and deployment complexity while reliably determining cable tension using dynamic characteristics extracted from spectral analysis. A self-recording accelerometer is coupled with a single-board microcomputer that communicates wirelessly with a remote host computer. The portable smart sensing device is designed such that additional algorithms, sensors and controlling devices for various monitoring applications can be installed and operated for additional structural assessment. The tension-estimating algorithms are based on taut string theory and expand to consider bending stiffness. The successful combination of cable properties allows the use of a cable's dynamic behavior to determine tension force. The tension-estimating algorithms are experimentally validated on a through-arch steel bridge subject to ambient vibration induced by passing traffic. The tension estimation is determined in well agreement with previously determined tension values for the structure.

NMR and X-ray structural characterization and conformational aspects of fluorinated (5Z)-3-benzil-5-arylidenofuran-2(5H)-ones

NASA Astrophysics Data System (ADS)

Teixeira, R. R.; Barbosa, L. C. A.; Kabeshov, M. A.; Maltha, C. R. A.; Corrêa, R. S.; Doriguetto, A. C.

2014-10-01

Herein we describe structural insights of (5Z)-3-benzyl-5-(2-fluorobenzylidene)furan-2(5H)-one (6) and (5Z)-3-benzyl-5-(pentafluorobenzylidene)furan-2(5H)-one (7), γ-alkylidenebutenolides analogues of the natural products nostoclides. Their structures were investigated by NMR spectroscopy and X-ray crystallography. The stereochemistry of the exocyclic double bond of these fluorinated compounds was determined to be Z by NMR analysis and confirmed by X-ray data. Compounds 6 and 7 crystallized in the monoclinic crystal system P21/c group. A comparison between structural features of (6) and (7) and nostoclide derivatives previously published by us is described.

Atoms in Action: Observing Atomic Motion with Dynamic in situ X-ray Diffraction

NASA Astrophysics Data System (ADS)

Cox, Jordan Michael

Metal-organic framework (MOF) materials are rich in both structural diversity and application. These materials are comprised of metal atoms or clusters which are connected in a three-dimensional polymer-like network by bridging organic linker molecules. One of the major attractive features in MOFs is their permanent pore space which can potentially be used to adsorb or exchange foreign molecules from/with the surrounding environment. While MOFs are an active area of scientific interest, MOF materials are still relatively new, only 20 years old. As such, there is still much that needs to be understood about these materials before they can be effectively applied to widespread chemical problems like CO2 sequestration or low-pressure hydrogen fuel storage. One of the most important facets of MOF chemistry to understand in order to rationally design MOF materials with tailor-made properties is the relationship between the structural features in a MOF and the chemical and physical properties of that material. By examining in detail the atomic structure of a MOF with known properties under a variety of conditions, scientists can begin to unravel the guiding principles which govern these relationships. X-ray diffraction remains one of the most effective tools for determining the structure of a crystalline material with atomic resolution, and has been applied to the determination of MOF structures for years. Typically these experiments have been carried out using powder X-ray diffraction, but this technique lacks the high-resolution structural information found in single-crystal methods. Some studies have been reported which use specialized devices, sometimes called Environmental Control Cells, to study single crystalline MOFs under non-ambient chemical conditions in situ . However, these in situ studies are performed under static conditions. Even in cases where the ECC provides continued access to the local chemical environment during diffraction data collections, the environment is left static or data is not collected until after the material has equilibrated to its new environment. First, a unique ECC has been designed and constructed which allows continuous access to the local chemical environment of a single-crystal sample while maintaining ease of use, minimizing size, and which is easily adaptable to a wide variety of gaseous and liquid chemical stimuli. Novel methods have been developed and are herein described for utilizing this ECC and in situ X-ray diffraction methods in a dynamic manner for monitoring the structural responses of single crystals to changes in their local chemical environment. These methods provide the opportunity for the determination of changes in unit cell parameters and even complete crystal structures during adsorption, desorption, and exchange processes in MOF materials. The application of these methods to the determination of the dehydration process of a previously reported cobalt-based MOF have revealed surprising structural and dynamics data. Several new intermediate structures have been determined in this process, including one metastable species and several actively transitioning species during the dehydration process. Applying these methods to the ethanol solvation process in the same material again yielded results which were richer in structural information than the previously reported ex situ structures. A computational study of rotational potential energy surfaces in a family of photochromic MOF linkers revealed the important role rotational stereoisomers can play in maintaining light-activated functionality when these linkers are incorporated into next-generation functional MOF materials. Finally, the application of novel photocrystallography techniques were used in conjunction with spectroscopic methods to determine the nature of the anomalous behavior of a photochromic diarylethene single-crystal.

Intermolecular shielding contributions studied by modeling the 13C chemical-shift tensors of organic single crystals with plane waves

PubMed Central

Johnston, Jessica C.; Iuliucci, Robbie J.; Facelli, Julio C.; Fitzgerald, George; Mueller, Karl T.

2009-01-01

In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge-including projector augmented wave method, which uses pseudopotentials to approximate the nodal structure of the core electrons, to determine the magnetic properties of crystals by predicting the full chemical-shift tensors of all 13C nuclides in 14 organic single crystals from which experimental tensors have previously been reported. Plane-wave methods use periodic boundary conditions to incorporate the lattice structure, providing a substantial improvement for modeling the chemical shifts in hydrogen-bonded systems. Principal tensor components can now be predicted to an accuracy that approaches the typical experimental uncertainty. Moreover, methods that include the full solid-phase structure enable geometry optimizations to be performed on the input structures prior to calculation of the shielding. Improvement after optimization is noted here even when neutron diffraction data are used for determining the initial structures. After geometry optimization, the isotropic shift can be predicted to within 1 ppm. PMID:19831448

A closer look at the lower-order structure of the Personality Inventory for DSM-5: comparison with the Five-Factor Model.

PubMed

Griffin, Sarah A; Samuel, Douglas B

2014-10-01

The Personality Inventory for DSM-5 (PID-5) was developed as a measure of the maladaptive personality trait model included within Section III of the DSM-5. Although preliminary findings have suggested the PID-5 has a five-factor structure that overlaps considerably with the Five-Factor Model (FFM) at the higher order level, there has been much less attention on the specific locations of the 25 lower-order traits. Joint exploratory factor analysis of the PID-5 traits and the 30 facets of the NEO-PI-R were used to determine the lower-order structure of the PID-5. Results indicated the PID-5's domain-level structure closely resembled the FFM. We also explored the placement of several lower-order facets that have not loaded consistently in previous studies. Overall, these results indicate that the PID-5 shares a common structure with the FFM and clarify the placement of some interstitial facets. More research investigating the lower-order facets is needed to determine how they fit into the hierarchical structure and explicate their relationships to existing measures of pathological traits. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

The Adoption of Blended E-Learning Technology in Vietnam Using a Revision of the Technology Acceptance Model

ERIC Educational Resources Information Center

Tran, Khanh Ngo Nhu

2016-01-01

This study examines factors that determine the attitudes of learners toward a blended e-learning system (BELS) using data collected by questionnaire from a sample of 396 students involved in a BELS environment in Vietnam. A theoretical model is derived from previous studies and is analyzed and developed using structural equation modeling…

A Latent Variable Approach to Determining the Structure of Executive Function in Preschool Children

ERIC Educational Resources Information Center

Miller, Michael R.; Giesbrecht, Gerald F.; Muller, Ulrich; McInerney, Robert J.; Kerns, Kimberly A.

2012-01-01

The composition of executive function (EF) in preschool children was examined using confirmatory factor analysis (CFA). A sample of 129 children between 3 and 5 years of age completed a battery of EF tasks. Using performance indicators of working memory and inhibition similar to previous CFA studies with preschoolers, we replicated a unitary EF…

Physical state of interstellar atoms. [from Copernicus satellite UV data

NASA Technical Reports Server (NTRS)

York, D. G.

1974-01-01

Brief survey of the physical conditions along the lines of sight to reddened and unreddened stars, as determined from Copernicus observation of interstellar lines between 95 and 300 nm. Differences in ionization structure and density between clouds and the local intercloud medium are discussed. Some new data for beta Centauri is used to supplement the previously available data.

Analysis of the Effects of the Implementation of Cooperative Learning in Physical Education

ERIC Educational Resources Information Center

Callado, Carlos Velázquez

2012-01-01

Our research was oriented to test the effects of a structured program of cooperative learning in Physical Education classes with students in grades 5 and 6 of primary school, with and without previous experience with this methodology. In a second phase we sought to determine how students perceived the received classes for a time later. We analysed…

[[superscript 3]H]-Flunitrazepam-Labeled Benzodiazepine Binding Sites in the Hippocampal Formation in Autism: A Multiple Concentration Autoradiographic Study

ERIC Educational Resources Information Center

Guptill, Jeffrey T.; Booker, Anne B.; Gibbs, Terrell T.; Kemper, Thomas L.; Bauman, Margaret L.; Blatt, Gene J.

2007-01-01

Increasing evidence indicates that the GABAergic system in cerebellar and limbic structures is affected in autism. We extended our previous study that found reduced [[superscript 3]H] flunitrazepam-labeled benzodiazepine sites in the autistic hippocampus to determine whether this reduction was due to a decrease in binding site number (B [subscript…

Lumped mass model of a 1D metastructure for vibration suppression with no additional mass

NASA Astrophysics Data System (ADS)

Reichl, Katherine K.; Inman, Daniel J.

2017-09-01

The article examines the effectiveness of metastructures for vibration suppression from a weight standpoint. Metastructures, a metamaterial inspired concept, are structures with distributed vibration absorbers. In automotive and aerospace industries, it is critical to have low levels of vibrations while also using lightweight materials. Previous work has shown that metastructures are effective at mitigating vibrations, but do not consider the effects of mass. This work takes mass into consideration by comparing a structure with vibration absorbers to a structure of equal mass with no absorbers. These structures are modeled as one-dimensional lumped mass models, chosen for simplicity. Results compare both the steady-state and the transient responses. As a quantitative performance measure, the H2 norm, which is related to the area under the frequency response function, is calculated and compared for both the metastructure and the baseline structure. These results show that it is possible to obtain a favorable vibration response without adding additional mass to the structure. Additionally, the performance measure is utilized to optimize the geometry of the structure, determine the optimal ratio of mass in the absorber to mass of the host structure, and determine the frequencies of the absorbers. The dynamic response of this model is verified using a finite element analysis.

Structural and Histone Binding Ability Characterizations of Human PWWP Domains

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

Wu, Hong; Zeng, Hong; Lam, Robert

2013-09-25

The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members,more » implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical {beta}-barrel core, an insertion motif between the second and third {beta}-strands and a C-terminal {alpha}-helix bundle. Both the canonical {beta}-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.« less

Plasticity in interactions of fibroblast growth factor 1 (FGF1) N terminus with FGF receptors underlies promiscuity of FGF1.

PubMed

Beenken, Andrew; Eliseenkova, Anna V; Ibrahimi, Omar A; Olsen, Shaun K; Mohammadi, Moosa

2012-01-27

Tissue-specific alternative splicing in the second half of Ig-like domain 3 (D3) of fibroblast growth factor receptors 1-3 (FGFR1 to -3) generates epithelial FGFR1b-FGFR3b and mesenchymal FGFR1c-FGFR3c splice isoforms. This splicing event establishes a selectivity filter to restrict the ligand binding specificity of FGFRb and FGFRc isoforms to mesenchymally and epithelially derived fibroblast growth factors (FGFs), respectively. FGF1 is termed the "universal FGFR ligand" because it overrides this specificity barrier. To elucidate the molecular basis for FGF1 cross-reactivity with the "b" and "c" splice isoforms of FGFRs, we determined the first crystal structure of FGF1 in complex with an FGFRb isoform, FGFR2b, at 2.1 Å resolution. Comparison of the FGF1-FGFR2b structure with the three previously published FGF1-FGFRc structures reveals that plasticity in the interactions of the N-terminal region of FGF1 with FGFR D3 is the main determinant of FGF1 cross-reactivity with both isoforms of FGFRs. In support of our structural data, we demonstrate that substitution of three N-terminal residues (Gly-19, His-25, and Phe-26) of FGF2 (a ligand that does not bind FGFR2b) for the corresponding residues of FGF1 (Phe-16, Asn-22, and Tyr-23) enables the FGF2 triple mutant to bind and activate FGFR2b. These findings taken together with our previous structural data on receptor binding specificity of FGF2, FGF8, and FGF10 conclusively show that sequence divergence at the N termini of FGFs is the primary regulator of the receptor binding specificity and promiscuity of FGFs.

Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei

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

Begley, Darren W.; Hartley, Robert C.; Davies, Douglas R.

As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification ofmore » several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.« less

Is there a link between the structural impact of thoracic outlet and the development of central venous stenosis?

PubMed

Kotoda, Atsushi; Akimoto, Tetsu; Sugase, Taro; Yamamoto, Hisashi; Kusano, Eiji

2013-01-01

Central venous stenosis (CVS) is a serious complication for chronic hemodialysis (HD) patients. Previous reports of CVS have focused on prior central venous catheterization, because of the higher prevalence and potential for prevention of such an event. However, recent studies have demonstrated that CVS may also develop without a history of central venous catheterization. Although information about the etiological backgrounds regarding the development of CVS without previous central venous catheterization have gradually accumulated, the clinical impact of the chronic compression of the central venous system by the surrounding structures, which may likely determine the central venous susceptibility to CVS, remains poorly understood. This study proposes the hypothesis that the combination of chronic venous compression at the level of thoracic outlet characterized by the natural physique and elevated venous flow induced by the creation of vascular access should be evaluated as a potential factor for the development of CVS, since they may accelerate the development of venous stenosis, presumably through the stimulation of intimal hyperplasia, and thereby the subclavian venous susceptibility to CVS should be determined. Copyright © 2012 Elsevier Ltd. All rights reserved.

PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination

PubMed Central

Lee, Woonghee; Kim, Jin Hae; Westler, William M.; Markley, John L.

2011-01-01

Summary: PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY (13C-edited and/or 15N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. Availability: The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/. Contact: whlee@nmrfam.wisc.edu; markley@nmrfam.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21511715

Refined lateral energy correction functions for the KASCADE-Grande experiment based on Geant4 simulations

NASA Astrophysics Data System (ADS)

Gherghel-Lascu, A.; Apel, W. D.; Arteaga-Velázquez, J. C.; Bekk, K.; Bertaina, M.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Cantoni, E.; Chiavassa, A.; Cossavella, F.; Daumiller, K.; de Souza, V.; Di Pierro, F.; Doll, P.; Engel, R.; Engler, J.; Fuchs, B.; Fuhrmann, D.; Gils, H. J.; Glasstetter, R.; Grupen, C.; Haungs, A.; Heck, D.; Hörandel, J. R.; Huber, D.; Huege, T.; Kampert, K.-H.; Kang, D.; Klages, H. O.; Link, K.; Łuczak, P.; Mathes, H. J.; Mayer, H. J.; Milke, J.; Mitrica, B.; Morello, C.; Oehlschläger, J.; Ostapchenko, S.; Palmieri, N.; Petcu, M.; Pierog, T.; Rebel, H.; Roth, M.; Schieler, H.; Schoo, S.; Schröder, F. G.; Sima, O.; Toma, G.; Trinchero, G. C.; Ulrich, H.; Weindl, A.; Wochele, J.; Zabierowski, J.

2015-02-01

In previous studies of KASCADE-Grande data, a Monte Carlo simulation code based on the GEANT3 program has been developed to describe the energy deposited by EAS particles in the detector stations. In an attempt to decrease the simulation time and ensure compatibility with the geometry description in standard KASCADE-Grande analysis software, several structural elements have been neglected in the implementation of the Grande station geometry. To improve the agreement between experimental and simulated data, a more accurate simulation of the response of the KASCADE-Grande detector is necessary. A new simulation code has been developed based on the GEANT4 program, including a realistic geometry of the detector station with structural elements that have not been considered in previous studies. The new code is used to study the influence of a realistic detector geometry on the energy deposited in the Grande detector stations by particles from EAS events simulated by CORSIKA. Lateral Energy Correction Functions are determined and compared with previous results based on GEANT3.

Structural basis for non-competitive product inhibition in human thymidine phosphorylase: implications for drug design

PubMed Central

Omari, Kamel EL; Bronckaers, Annelies; Liekens, Sandra; Pérez-Pérez, Maria-Jésus; Balzarini, Jan; Stammers, David K.

2006-01-01

HTP (human thymidine phosphorylase), also known as PD-ECGF (platelet-derived endothelial cell growth factor) or gliostatin, has an important role in nucleoside metabolism. HTP is implicated in angiogenesis and apoptosis and therefore is a prime target for drug design, including antitumour therapies. An HTP structure in a closed conformation complexed with an inhibitor has previously been solved. Earlier kinetic studies revealed an ordered release of thymine followed by ribose phosphate and product inhibition by both ligands. We have determined the structure of HTP from crystals grown in the presence of thymidine, which, surprisingly, resulted in bound thymine with HTP in a closed dead-end com-plex. Thus thymine appears to be able to reassociate with HTP after its initial ordered release before ribose phosphate and induces the closed conformation, hence explaining the mechanism of non-competitive product inhibition. In the active site in one of the four HTP molecules within the crystal asymmetric unit, additional electron density is present. This density has not been previously seen in any pyrimidine nucleoside phosphorylase and it defines a subsite that may be exploitable in drug design. Finally, because our crystals did not require proteolysed HTP to grow, the structure reveals a loop (residues 406–415), disordered in the previous HTP structure. This loop extends across the active-site cleft and appears to stabilize the dimer interface and the closed conformation by hydrogen-bonding. The present study will assist in the design of HTP inhibitors that could lead to drugs for anti-angiogenesis as well as for the potentiation of other nucleoside drugs. PMID:16803458

Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method.

PubMed

Takeda, Mitsuhiro; Chang, Chung-ke; Ikeya, Teppei; Güntert, Peter; Chang, Yuan-hsiang; Hsu, Yen-lan; Huang, Tai-huang; Kainosho, Masatsune

2008-07-18

The C-terminal domain (CTD) of the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (NP) contains a potential RNA-binding region in its N-terminal portion and also serves as a dimerization domain by forming a homodimer with a molecular mass of 28 kDa. So far, the structure determination of the SARS-CoV NP CTD in solution has been impeded by the poor quality of NMR spectra, especially for aromatic resonances. We have recently developed the stereo-array isotope labeling (SAIL) method to overcome the size problem of NMR structure determination by utilizing a protein exclusively composed of stereo- and regio-specifically isotope-labeled amino acids. Here, we employed the SAIL method to determine the high-quality solution structure of the SARS-CoV NP CTD by NMR. The SAIL protein yielded less crowded and better resolved spectra than uniform (13)C and (15)N labeling, and enabled the homodimeric solution structure of this protein to be determined. The NMR structure is almost identical with the previously solved crystal structure, except for a disordered putative RNA-binding domain at the N-terminus. Studies of the chemical shift perturbations caused by the binding of single-stranded DNA and mutational analyses have identified the disordered region at the N-termini as the prime site for nucleic acid binding. In addition, residues in the beta-sheet region also showed significant perturbations. Mapping of the locations of these residues onto the helical model observed in the crystal revealed that these two regions are parts of the interior lining of the positively charged helical groove, supporting the hypothesis that the helical oligomer may form in solution.

Determining the 3-D structure and motion of objects using a scanning laser range sensor

NASA Technical Reports Server (NTRS)

Nandhakumar, N.; Smith, Philip W.

1993-01-01

In order for the EVAHR robot to autonomously track and grasp objects, its vision system must be able to determine the 3-D structure and motion of an object from a sequence of sensory images. This task is accomplished by the use of a laser radar range sensor which provides dense range maps of the scene. Unfortunately, the currently available laser radar range cameras use a sequential scanning approach which complicates image analysis. Although many algorithms have been developed for recognizing objects from range images, none are suited for use with single beam, scanning, time-of-flight sensors because all previous algorithms assume instantaneous acquisition of the entire image. This assumption is invalid since the EVAHR robot is equipped with a sequential scanning laser range sensor. If an object is moving while being imaged by the device, the apparent structure of the object can be significantly distorted due to the significant non-zero delay time between sampling each image pixel. If an estimate of the motion of the object can be determined, this distortion can be eliminated; but, this leads to the motion-structure paradox - most existing algorithms for 3-D motion estimation use the structure of objects to parameterize their motions. The goal of this research is to design a rigid-body motion recovery technique which overcomes this limitation. The method being developed is an iterative, linear, feature-based approach which uses the non-zero image acquisition time constraint to accurately recover the motion parameters from the distorted structure of the 3-D range maps. Once the motion parameters are determined, the structural distortion in the range images is corrected.

Solution NMR Refinement of a Metal Ion Bound Protein Using Metal Ion Inclusive Restrained Molecular Dynamics Methods

PubMed Central

Chakravorty, Dhruva K.; Wang, Bing; Lee, Chul Won; Guerra, Alfredo J.; Giedroc, David P.; Merz, Kenneth M.

2013-01-01

Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational dynamics in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies. PMID:23609042

The latent structure of alcohol misuse in young adults: Do taxometric results differ as a function of prior criminal history?

PubMed

Walters, Glenn D

2015-12-01

The purpose of this study was to determine whether the latent structure of alcohol misuse is categorical or continuous in male and female adults with and without a history of prior criminal offending. Data from 3452 (1530 male, 1922 female) 27-to-32 year old members of the National Longitudinal Study of Adolescent to Adult Health (Add Health) were subjected to taxometric analysis using three nonredundant taxometric procedures--mean above minus below a cut (MAMBAC), maximum covariance (MAXCOV), and latent mode factor analysis (L-Mode). Analyses produced results consistent with categorical latent structure in males with a previous history of criminal offending but not in males without a previous history of criminal offending or females with or without a history of criminal offending. The findings from the other groups were indeterminate for the most part (i.e., neither categorical nor continuous). The presumptive taxon was validated by testing differences in age of onset and frequency of criminal arrest and drunkenness between the putative taxon and the upper portion of the complement. As predicted, all four validation outcomes were significantly worse in the taxon group. On the basis of these results it is concluded that alcohol misuse in young adults may have features of both categorical and continuous latent structure and that the categorical aspects are more prominent in males with a history of offending behavior. Additional research is required to determine which aspects and features of alcohol misuse are categorical and which aspects and features are continuous. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.

PubMed

Razban, Rostam M; Gilson, Amy I; Durfee, Niamh; Strobelt, Hendrik; Dinkla, Kasper; Choi, Jeong-Mo; Pfister, Hanspeter; Shakhnovich, Eugene I

2018-05-08

Protein evolution spans time scales and its effects span the length of an organism. A web app named ProteomeVis is developed to provide a comprehensive view of protein evolution in the S. cerevisiae and E. coli proteomes. ProteomeVis interactively creates protein chain graphs, where edges between nodes represent structure and sequence similarities within user-defined ranges, to study the long time scale effects of protein structure evolution. The short time scale effects of protein sequence evolution are studied by sequence evolutionary rate (ER) correlation analyses with protein properties that span from the molecular to the organismal level. We demonstrate the utility and versatility of ProteomeVis by investigating the distribution of edges per node in organismal protein chain universe graphs (oPCUGs) and putative ER determinants. S. cerevisiae and E. coli oPCUGs are scale-free with scaling constants of 1.79 and 1.56, respectively. Both scaling constants can be explained by a previously reported theoretical model describing protein structure evolution (Dokholyan et al., 2002). Protein abundance most strongly correlates with ER among properties in ProteomeVis, with Spearman correlations of -0.49 (p-value<10-10) and -0.46 (p-value<10-10) for S. cerevisiae and E. coli, respectively. This result is consistent with previous reports that found protein expression to be the most important ER determinant (Zhang and Yang, 2015). ProteomeVis is freely accessible at http://proteomevis.chem.harvard.edu. Supplementary data are available at Bioinformatics. shakhnovich@chemistry.harvard.edu.

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

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

Swenson, Tami L.; Karaoz, Ulas; Swenson, Joel M.

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). For this study, we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negativelymore » correlated with the abundance of the isolate's closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.« less

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

DOE PAGES

Swenson, Tami L.; Karaoz, Ulas; Swenson, Joel M.; ...

2018-01-02

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). For this study, we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negativelymore » correlated with the abundance of the isolate's closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.« less

Structure and bioactivity of steroidal saponins isolated from the roots of Chamaelirium luteum (false unicorn).

PubMed

Challinor, Victoria L; Stuthe, Julia M U; Parsons, Peter G; Lambert, Lynette K; Lehmann, Reginald P; Kitching, William; De Voss, James J

2012-08-24

Phytochemical investigation of Chamaelirium luteum ("false unicorn") resulted in the isolation of 15 steroidal glycosides. Twelve of these (1, 2, 4-9, 11-13, and 15) are apparently unique to this species, and eight of these (6-9, 11-13, and 15) are previously unreported compounds; one (15) possesses a new steroidal aglycone. In addition, the absolute configuration of (23R,24S)-chiograsterol A (10) was defined, and its full spectroscopic characterization is reported for the first time. The structures and configurations of the saponins were determined using a combination of multistage mass spectrometry (MS(n)), 1D and 2D NMR experiments, and chemical degradation. The antiproliferative activity of nine compounds obtained in the present work, and eight related compounds generated in previous work, was compared in six human tumor cell lines, with aglycones 3 and 10 and related derivatives 16, 17, 19, and 20 all displaying significant antiproliferative activity.

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics.

PubMed

Swenson, Tami L; Karaoz, Ulas; Swenson, Joel M; Bowen, Benjamin P; Northen, Trent R

2018-01-02

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate's closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.

Classification of the Pospiviroidae based on their structural hallmarks.

PubMed

Giguère, Tamara; Perreault, Jean-Pierre

2017-01-01

The simplest known plant pathogens are the viroids. Because of their non-coding single-stranded circular RNA genome, they depend on both their sequence and their structure for both a successful infection and their replication. In the recent years, important progress in the elucidation of their structures was achieved using an adaptation of the selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) protocol in order to probe viroid structures in solution. Previously, SHAPE has been adapted to elucidate the structures of all of the members of the family Avsunviroidae, as well as those of a few members of the family Pospiviroidae. In this study, with the goal of providing an entire compendium of the secondary structures of the various viroid species, a total of thirteen new Pospiviroidae members were probed in solution using the SHAPE protocol. More specifically, the secondary structures of eleven species for which the genus was previously known were initially elucidated. At this point, considering all of the SHAPE elucidated secondary structures, a classification system for viroids in their respective genera was proposed. On the basis of the structural classification reported here, the probings of both the Grapevine latent viroid and the Dahlia latent viroid provide sound arguments for the determination of their respective genera, which appear to be Apscaviroid and Hostuviroid, respectively. More importantly, this study provides the complete repertoire of the secondary structures, mapped in solution, of all of the accepted viroid species reported thus far. In addition, a classification scheme based on structural hallmarks, an important tool for many biological studies, is proposed.

Classification of the Pospiviroidae based on their structural hallmarks

PubMed Central

Giguère, Tamara

2017-01-01

The simplest known plant pathogens are the viroids. Because of their non-coding single-stranded circular RNA genome, they depend on both their sequence and their structure for both a successful infection and their replication. In the recent years, important progress in the elucidation of their structures was achieved using an adaptation of the selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) protocol in order to probe viroid structures in solution. Previously, SHAPE has been adapted to elucidate the structures of all of the members of the family Avsunviroidae, as well as those of a few members of the family Pospiviroidae. In this study, with the goal of providing an entire compendium of the secondary structures of the various viroid species, a total of thirteen new Pospiviroidae members were probed in solution using the SHAPE protocol. More specifically, the secondary structures of eleven species for which the genus was previously known were initially elucidated. At this point, considering all of the SHAPE elucidated secondary structures, a classification system for viroids in their respective genera was proposed. On the basis of the structural classification reported here, the probings of both the Grapevine latent viroid and the Dahlia latent viroid provide sound arguments for the determination of their respective genera, which appear to be Apscaviroid and Hostuviroid, respectively. More importantly, this study provides the complete repertoire of the secondary structures, mapped in solution, of all of the accepted viroid species reported thus far. In addition, a classification scheme based on structural hallmarks, an important tool for many biological studies, is proposed. PMID:28783761

Identification and structural characterization of O-beta-ribosyl-(1"----2')-adenosine-5"-phosphate in yeast methionine initiator tRNA.

PubMed

Keith, G; Glasser, A L; Desgrès, J; Kuo, K C; Gehrke, C W

1990-10-25

We report in this paper on the complete structure determination of the modified nucleotide A*, now called Ar(p), that was previously identified in yeast methionine initiator tRNA as an isomeric form of O-ribosyl-adenosine bearing an additional phosphoryl-monoester group on its ribose2 moiety. By using the chemical procedure of periodate oxidation and subsequent beta-elimination with cyclohexylamine on mono- and dinucleotides containing Ar(p), we characterized the location of the phosphate group on the C-5" of the ribose2 moiety, and the linkage between the two riboses as a (1"----2')-glycosidic bond. Since the structural difference between phosphatase treated Ar(p) and authentic O-alpha-ribosyl-(1"----2')-adenosine from poly(ADP-Ribose) was previously assigned to an isomeric difference in the ribose2-ribose1 linkage, the (1"----2')-glycosidic bond of Ar(p) was deduced to have a beta-spatial configuration. Thus, final chemical structure for Ar(p) at the position 64 in yeast initiator tRNA(Met) has been established as O-beta-ribosyl-(1"----2')-adenosine-5"-phosphate. This nucleotide is linked by a 3',5'-phosphodiester bond to G at the position 65.

The relationship between crystal structure and methyl and t-butyl group dynamics in van der Waals organic solids

NASA Astrophysics Data System (ADS)

Beckmann, Peter A.; Paty, Carol; Allocco, Elizabeth; Herd, Maria; Kuranz, Carolyn; Rheingold, Arnold L.

2004-03-01

We report x-ray diffractometry in a single crystal of 2-t-butyl-4-methylphenol (TMP) and low-frequency solid state nuclear magnetic resonance (NMR) proton relaxometry in a polycrystalline sample of TMP. The x-ray data show TMP to have a monoclinic, P21/c, structure with eight molecules per unit cell and two crystallographically inequivalent t-butyl group (C(CH3)3) sites. The proton spin-lattice relaxation rates were measured between 90 and 310 K at NMR frequencies of 8.50, 22.5, and 53.0 MHz. The relaxometry data is fitted with two models characterizing the dynamics of the t-butyl groups and their constituent methyl groups, both of which are consistent with the determined x-ray structure. In addition to presenting results for TMP, we review previously reported x-ray diffractometry and low-frequency NMR relaxometry in two other van der Waals solids which have a simpler structure. In both cases, a unique model for the reorientational dynamics was found. Finally, we review a similar previously reported analysis in a van der Waals solid with a very complex structure in which case fitting the NMR relaxometry requires very many parameters and serves mainly as a flag for a careful x-ray diffraction study.

Experimental identification of the behaviour of and lateral forces from freely-walking pedestrians on laterally oscillating structures in a virtual reality environment.

PubMed

Bocian, Mateusz; Macdonald, John H G; Burn, Jeremy F; Redmill, David

2015-12-15

Modelling pedestrian loading on lively structures such as bridges remains a challenge. This is because pedestrians have the capacity to interact with vibrating structures which can lead to amplification of the structural response. Current design guidelines are often inaccurate and limiting as they do not sufficiently acknowledge this effect. This originates in scarcity of data on pedestrian behaviour on vibrating ground and uncertainty as to the accuracy of results from previous experimental campaigns aiming to quantify pedestrian behaviour in this case. To this end, this paper presents a novel experimental setup developed to evaluate pedestrian actions on laterally oscillating ground in the laboratory environment while avoiding the implications of artificiality and allowing for unconstrained gait. A biologically-inspired approach was adopted in its development, relying on appreciation of operational complexities of biological systems, in particular their adaptability and control requirements. In determination of pedestrian forces to the structure consideration was given to signal processing issues which have been neglected in past studies. The results from tests conducted on the setup are related to results from previous experimental investigations and outputs of the inverted pendulum pedestrian model for walking on laterally oscillating ground, which is capable of generating self-excited forces.

Genetic structure of the crown-of-thorns seastar in the Pacific Ocean, with focus on Guam

PubMed Central

Tusso, Sergio; Morcinek, Kerstin; Vogler, Catherine; Schupp, Peter J.; Caballes, Ciemon F.; Vargas, Sergio

2016-01-01

Population outbreaks of the corallivorous crown-of-thorns seastar (COTS), Acanthaster ‘planci’ L., are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared samples from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations sampled were found to be structured in three significantly differentiated groups: (1) all locations immediately around Guam, as well as Kingman Reef and Swains Island; (2) Japan, Philippines, GBR and Vanuatu; and (3) Johnston Atoll, which was significantly different from all other localities. The lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island suggests potential long-distance dispersal of COTS in the Pacific. PMID:27168979

Structural Basis for High Affinity Volatile Anesthetic Binding in a Natural 4-helix Bundle Protein

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

Liu,R.; Loll, P.; Eckenhoff, R.

2005-01-01

Physiologic sites for inhaled anesthetics are presumed to be cavities within transmembrane 4-{alpha}-helix bundles of neurotransmitter receptors, but confirmation of binding and structural detail of such sites remains elusive. To provide such detail, we screened soluble proteins containing this structural motif, and found only one that exhibited evidence of strong anesthetic binding. Ferritin is a 24-mer of 4-{alpha}-helix bundles; both halothane and isoflurane bind with K{sub A} values of {approx}10{sup 5} M{sup -1, } higher than any previously reported inhaled anesthetic-protein interaction. The crystal structures of the halothane/apoferritin and isoflurane/apoferritin complexes were determined at 1.75 Angstroms resolution, revealing a commonmore » anesthetic binding pocket within an interhelical dimerization interface. The high affinity is explained by several weak polar contacts and an optimal host/guest packing relationship. Neither the acidic protons nor ether oxygen of the anesthetics contribute to the binding interaction. Compared with unliganded apoferritin, the anesthetic produced no detectable alteration of structure or B factors. The remarkably high affinity of the anesthetic/apoferritin complex implies greater selectivity of protein sites than previously thought, and suggests that direct protein actions may underlie effects at lower than surgical levels of anesthetic, including loss of awareness.« less

Double-flow focused liquid injector for efficient serial femtosecond crystallography

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

Oberthuer, Dominik; Knoška, Juraj; Wiedorn, Max O.

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Furthermore, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improvedmore » operation and characteristics of these devices.« less

Double-flow focused liquid injector for efficient serial femtosecond crystallography

PubMed Central

Oberthuer, Dominik; Knoška, Juraj; Wiedorn, Max O.; Beyerlein, Kenneth R.; Bushnell, David A.; Kovaleva, Elena G.; Heymann, Michael; Gumprecht, Lars; Kirian, Richard A.; Barty, Anton; Mariani, Valerio; Tolstikova, Aleksandra; Adriano, Luigi; Awel, Salah; Barthelmess, Miriam; Dörner, Katerina; Xavier, P. Lourdu; Yefanov, Oleksandr; James, Daniel R.; Nelson, Garrett; Wang, Dingjie; Calvey, George; Chen, Yujie; Schmidt, Andrea; Szczepek, Michael; Frielingsdorf, Stefan; Lenz, Oliver; Snell, Edward; Robinson, Philip J.; Šarler, Božidar; Belšak, Grega; Maček, Marjan; Wilde, Fabian; Aquila, Andrew; Boutet, Sébastien; Liang, Mengning; Hunter, Mark S.; Scheerer, Patrick; Lipscomb, John D.; Weierstall, Uwe; Kornberg, Roger D.; Spence, John C. H.; Pollack, Lois; Chapman, Henry N.; Bajt, Saša

2017-01-01

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices. PMID:28300169

Double-flow focused liquid injector for efficient serial femtosecond crystallography

DOE PAGES

Oberthuer, Dominik; Knoška, Juraj; Wiedorn, Max O.; ...

2017-03-16

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Furthermore, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improvedmore » operation and characteristics of these devices.« less

Redetermination of Na(3)TaF(8).

PubMed

Langer, Vratislav; Smrcok, Lubomír; Boca, Miroslav

2010-09-01

The crystal structure of trisodium octafluoridotantalate, Na(3)TaF(8), has been redetermined using diffractometer data collected at 153 K, resulting in more accurate bond distances and angles than obtained from a previous structure determination based on film data. The structure is built from layers running along [101], which are formed by distorted [TaF(8)] antiprisms and [NaF(6)] rectangular bipyramids sharing edges and corners. The individual layers are separated by eight-coordinated Na ions. Two atoms in the asymmetric unit are in special positions: the Ta atom is on a twofold axis in Wyckoff position 4e and one of the Na ions lies on an inversion centre in Wyckoff site 4d.

Improving the seismic torsional behavior of plan-asymmetric, single-storey, concrete moment resisting buildings with fluid viscous dampers

NASA Astrophysics Data System (ADS)

Rofooei, Fayaz Rahimzadeh; Mohammadzadeh, Sahar

2016-03-01

The optimal distribution of fluid viscous dampers (FVD) in controlling the seismic response of eccentric, single-storey, moment resisting concrete structures is investigated using the previously defined center of damping constant (CDC). For this purpose, a number of structural models with different one-way stiffness and strength eccentricities are considered. Extensive nonlinear time history analyses are carried out for various arrangements of FVDs. It is shown that the arrangement of FVDs for controlling the torsional behavior due to asymmetry in the concrete structures is very dependent on the intensity of the peak ground acceleration (PGA) and the extent of the structural stiffness and strength eccentricities. The results indicate that, in the linear range of structural behavior the stiffness eccentricity es which is the main parameter in determining the location of optimal CDC, is found to be less or smaller than the optimal damping constant eccentricity e*d, i.e., |e*d| > |es|. But, in the nonlinear range of structural behavior where the strength eccentricity er is the dominant factor in determining the location of optimal CDC, |e*d| > |er|. It is also concluded that for the majority of the plan-asymmetric, concrete structures considered in this study with er ≠ 0, the optimal CDC approaches the center of mass as er decreases.

‘Pd20Sn13’ revisited: crystal structure of Pd6.69Sn4.31

PubMed Central

Klein, Wilhelm; Jin, Hanpeng; Hlukhyy, Viktor; Fässler, Thomas F.

2015-01-01

The crystal structure of the title compound was previously reported with composition ‘Pd20Sn13’ [Sarah et al. (1981 ▸). Z. Metallkd, 72, 517–520]. For the original structure model, as determined from powder X-ray data, atomic coordinates from the isostructural compound Ni13Ga3Ge6 were transferred. The present structure determination, resulting in a composition Pd6.69Sn4.31, is based on single crystal X-ray data and includes anisotropic displacement parameters for all atoms as well as standard uncertainties for the atomic coordinates, leading to higher precision and accuracy for the structure model. Single crystals of the title compound were obtained via a solid-state reaction route, starting from the elements. The crystal structure can be derived from the AlB2 type of structure after removing one eighth of the atoms at the boron positions and shifting adjacent atoms in the same layer in the direction of the voids. One atomic site is partially occupied by both elements with a Pd:Sn ratio of 0.38 (3):0.62 (3). One Sn and three Pd atoms are located on special positions with site symmetry 2. (Wyckoff letter 3a and 3b). PMID:26279872

Presentation a New Model to Measure National Power of the Countries

NASA Astrophysics Data System (ADS)

Hafeznia, Mohammad Reza; Hadi Zarghani, Seyed; Ahmadipor, Zahra; Roknoddin Eftekhari, Abdelreza

In this research, based on the assessment of previous models for the evaluation of national power, a new model is presented to measure national power; it is much better than previous models. Paying attention to all the aspects of national power (economical, social, cultural, political, military, astro-space, territorial, scientific and technological and transnational), paying attention to the usage of 87 factors, stressing the usage of new and strategically compatible variables to the current time are some of the benefits of this model. Also using the Delphi method and referring to the opinions of experts about determining the role and importance of variables affecting national power, the option of drawing out the global power structure are some the other advantages that this model has compared to previous ones.

Constraining the physical structure of the inner few 100 AU scales of deeply embedded low-mass protostars

NASA Astrophysics Data System (ADS)

Persson, M. V.; Harsono, D.; Tobin, J. J.; van Dishoeck, E. F.; Jørgensen, J. K.; Murillo, N.; Lai, S.-P.

2016-05-01

Context. The physical structure of deeply embedded low-mass protostars (Class 0) on scales of less than 300 AU is still poorly constrained. While molecular line observations demonstrate the presence of disks with Keplerian rotation toward a handful of sources, others show no hint of rotation. Determining the structure on small scales (a few 100 AU) is crucial for understanding the physical and chemical evolution from cores to disks. Aims: We determine the presence and characteristics of compact, disk-like structures in deeply embedded low-mass protostars. A related goal is investigating how the derived structure affects the determination of gas-phase molecular abundances on hot-core scales. Methods: Two models of the emission, a Gaussian disk intensity distribution and a parametrized power-law disk model, are fitted to subarcsecond resolution interferometric continuum observations of five Class 0 sources, including one source with a confirmed Keplerian disk. Prior to fitting the models to the de-projected real visibilities, the estimated envelope from an independent model and any companion sources are subtracted. For reference, a spherically symmetric single power-law envelope is fitted to the larger scale emission (~1000 AU) and investigated further for one of the sources on smaller scales. Results: The radii of the fitted disk-like structures range from ~90-170 AU, and the derived masses depend on the method. Using the Gaussian disk model results in masses of 54-556 × 10-3 M⊙, and using the power-law disk model gives 9-140 × 10-3 M⊙. While the disk radii agree with previous estimates the masses are different for some of the sources studied. Assuming a typical temperature distribution (r-0.5), the fractional amount of mass in the disk above 100 K varies from 7% to 30%. Conclusions: A thin disk model can approximate the emission and physical structure in the inner few 100 AU scales of the studied deeply embedded low-mass protostars and paves the way for analysis of a larger sample with ALMA. Kinematic data are needed to determine the presence of any Keplerian disk. Using previous observations of p-H218O, we estimate the relative gas phase water abundances relative to total warm H2 to be 6.2 × 10-5 (IRAS 2A), 0.33 × 10-5 (IRAS 4A-NW), 1.8 × 10-7 (IRAS 4B), and < 2 × 10-7 (IRAS 4A-SE), roughly an order of magnitude higher than previously inferred when both warm and cold H2 were used as reference. A spherically symmetric single power-law envelope model fails to simultaneously reproduce both the small- and large-scale emission. Based on observations carried out with the IRAM Plateau de Bure Interferometer. IRAM is supported by INSU/CNRS (France), MPG (Germany) and IGN (Spain).Continuum data for the sources are available through http://dx.doi.org/10.5281/zenodo.47642 and at CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/590/A33

Automatic Event Detection in Search for Inter-Moss Loops in IRIS Si IV Slit-Jaw Images

NASA Technical Reports Server (NTRS)

Fayock, Brian; Winebarger, Amy R.; De Pontieu, Bart

2015-01-01

The high-resolution capabilities of the Interface Region Imaging Spectrometer (IRIS) mission have allowed the exploration of the finer details of the solar magnetic structure from the chromosphere to the lower corona that have previously been unresolved. Of particular interest to us are the relatively short-lived, low-lying magnetic loops that have foot points in neighboring moss regions. These inter-moss loops have also appeared in several AIA pass bands, which are generally associated with temperatures that are at least an order of magnitude higher than that of the Si IV emission seen in the 1400 angstrom pass band of IRIS. While the emission lines seen in these pass bands can be associated with a range of temperatures, the simultaneous appearance of these loops in IRIS 1400 and AIA 171, 193, and 211 suggest that they are not in ionization equilibrium. To study these structures in detail, we have developed a series of algorithms to automatically detect signal brightening or events on a pixel-by-pixel basis and group them together as structures for each of the above data sets. These algorithms have successfully picked out all activity fitting certain adjustable criteria. The resulting groups of events are then statistically analyzed to determine which characteristics can be used to distinguish the inter-moss loops from all other structures. While a few characteristic histograms reveal that manually selected inter-moss loops lie outside the norm, a combination of several characteristics will need to be used to determine the statistical likelihood that a group of events be categorized automatically as a loop of interest. The goal of this project is to be able to automatically pick out inter-moss loops from an entire data set and calculate the characteristics that have previously been determined manually, such as length, intensity, and lifetime. We will discuss the algorithms, preliminary results, and current progress of automatic characterization.

Attenuation and source properties at the Coso Geothermal area, California

USGS Publications Warehouse

Hough, S.E.; Lees, J.M.; Monastero, F.

1999-01-01

We use a multiple-empirical Green's function method to determine source properties of small (M -0.4 to 1.3) earthquakes and P- and S-wave attenuation at the Coso Geothermal Field, California. Source properties of a previously identified set of clustered events from the Coso geothermal region are first analyzed using an empirical Green's function (EGF) method. Stress-drop values of at least 0.5-1 MPa are inferred for all of the events; in many cases, the corner frequency is outside the usable bandwidth, and the stress drop can only be constrained as being higher than 3 MPa. P- and S-wave stress-drop estimates are identical to the resolution limits of the data. These results are indistinguishable from numerous EGF studies of M 2-5 earthquakes, suggesting a similarity in rupture processes that extends to events that are both tiny and induced, providing further support for Byerlee's Law. Whole-path Q estimates for P and S waves are determined using the multiple-empirical Green's function (MEGF) method of Hough (1997), whereby spectra from clusters of colocated events at a given station are inverted for a single attenuation parameter, ??, with source parameters constrained from EGF analysis. The ?? estimates, which we infer to be resolved to within 0.01 sec or better, exhibit almost as much scatter as a function of hypocentral distance as do values from previous single-spectrum studies for which much higher uncertainties in individual ?? estimates are expected. The variability in ?? estimates determined here therefore suggests real lateral variability in Q structure. Although the ray-path coverage is too sparse to yield a complete three-dimensional attenuation tomographic image, we invert the inferred ?? value for three-dimensional structure using a damped least-squares method, and the results do reveal significant lateral variability in Q structure. The inferred attenuation variability corresponds to the heat-flow variations within the geothermal region. A central low-Q region corresponds well with the central high-heat flow region; additional detailed structure is also suggested.

The application of a shift theorem analysis technique to multipoint measurements

NASA Astrophysics Data System (ADS)

Dieckmann, M. E.; Chapman, S. C.

1999-03-01

A Fourier domain technique has been proposed previously which, in principle, quantifies the extent to which multipoint in-situ measurements can identify whether or not an observed structure is time stationary in its rest frame. Once a structure, sampled for example by four spacecraft, is shown to be quasi-stationary in its rest frame, the structure's velocity vector can be determined with respect to the sampling spacecraft. We investigate the properties of this technique, which we will refer to as a stationarity test, by applying it to two point measurements of a simulated boundary layer. The boundary layer was evolved using a PIC (particle in cell) electromagnetic code. Initial and boundary conditions were chosen such, that two cases could be considered, i.e. a spacecraft pair moving through (1) a time stationary boundary structure and (2) a boundary structure which is evolving (expanding) in time. The code also introduces noise in the simulated data time series which is uncorrelated between the two spacecraft. We demonstrate that, provided that the time series is Hanning windowed, the test is effective in determining the relative velocity between the boundary layer and spacecraft and in determining the range of frequencies over which the data can be treated as time stationary or time evolving. This work presents a first step towards understanding the effectiveness of this technique, as required in order for it to be applied to multispacecraft data.

An Improved Analysis of the Sevoflurane-Benzene Structure by Chirped Pulse Ftmw Spectroscopy

NASA Astrophysics Data System (ADS)

Seifert, Nathan A.; Perez, Cristobal; Zaleski, Daniel P.; Neill, Justin L.; Pate, Brooks H.; Lesarri, Alberto; Vallejo, Montserrat; Cocinero, Emilio J.; Castano, Fernando; Kleiner, Isabelle

2013-06-01

Recent improvements to the 2-8 GHz CP-FTMW spectrometer at University of Virginia have improved the structural and spectroscopic analysis of the sevoflurane-benzene cluster. Previously reported results, although robust, were limited to a fit of the a-type transitions of the normal species in the determination of the six-fold barrier to benzene internal rotation. Structural analysis was limited to the benzene hydrogen atom positions using benzene-d_{1}. The increased sensitivity of the new 2-8 GHz setup allows for a full internal rotation analysis of the a- and c-type transitions of the normal species, which was performed with BELGI. A fit value for V_{6} of 32.868(11) cm^{-1} is determined. Additionally, a full substitution structure of the benzene carbon atom positions was determined in natural abundance. Also, new measurements of a sevoflurane/benzene-d_{1} mixture enabled detection of 33 of the 60 possible ^{2}D / ^{13}C double isotopologues. This abundance of isotopic data, a total of 45 isotopologues, enabled a full heavy atom least-squares r_{0} structure fit for the complex, including positions for all seven fluorines in sevoflurane. N. A. Seifert, D. P. Zaleski, J. L. Neill, B. H. Pate, A. Lesarri, M. Vallejo, E. J. Cocinero, F. Castańo. 67th OSU Int. Symp. On Mol. Spectrosc., Columbus, OH, 2012, MH13.

Experimental determination of thermodynamic equilibrium in biocatalytic transamination.

PubMed

Tufvesson, Pär; Jensen, Jacob S; Kroutil, Wolfgang; Woodley, John M

2012-08-01

The equilibrium constant is a critical parameter for making rational design choices in biocatalytic transamination for the synthesis of chiral amines. However, very few reports are available in the scientific literature determining the equilibrium constant (K) for the transamination of ketones. Various methods for determining (or estimating) equilibrium have previously been suggested, both experimental as well as computational (based on group contribution methods). However, none of these were found suitable for determining the equilibrium constant for the transamination of ketones. Therefore, in this communication we suggest a simple experimental methodology which we hope will stimulate more accurate determination of thermodynamic equilibria when reporting the results of transaminase-catalyzed reactions in order to increase understanding of the relationship between substrate and product molecular structure on reaction thermodynamics. Copyright © 2012 Wiley Periodicals, Inc.

Protein Chaperones Q8ZP25_SALTY from Salmonella Typhimurium and HYAE_ECOLI from Escherichia coli Exhibit Thioredoxin-like Structures Despite Lack of Canonical Thioredoxin Active Site Sequence Motif

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

Parish, D.; Benach, J; Liu, G

2008-01-01

The structure of the 142-residue protein Q8ZP25 SALTY encoded in the genome of Salmonella typhimurium LT2 was determined independently by NMR and X-ray crystallography, and the structure of the 140-residue protein HYAE ECOLI encoded in the genome of Escherichia coli was determined by NMR. The two proteins belong to Pfam (Finn et al. 34:D247-D251, 2006) PF07449, which currently comprises 50 members, and belongs itself to the 'thioredoxin-like clan'. However, protein HYAE ECOLI and the other proteins of Pfam PF07449 do not contain the canonical Cys-X-X-Cys active site sequence motif of thioredoxin. Protein HYAE ECOLI was previously classified as a (NiFe)more » hydrogenase-1 specific chaperone interacting with the twin-arginine translocation (Tat) signal peptide. The structures presented here exhibit the expected thioredoxin-like fold and support the view that members of Pfam family PF07449 specifically interact with Tat signal peptides.« less

Methods and Piezoelectric Imbedded Sensors for Damage Detection in Composite Plates Under Ambient and Cryogenic Conditions

NASA Technical Reports Server (NTRS)

Engberg, Robert; Ooi, Teng K.

2004-01-01

New methods for structural health monitoring are being assessed, especially in high-performance, extreme environment, safety-critical applications. One such application is for composite cryogenic fuel tanks. The work presented here attempts to characterize and investigate the feasibility of using imbedded piezoelectric sensors to detect cracks and delaminations under cryogenic and ambient conditions. A variety of damage detection methods and different Sensors are employed in the different composite plate samples to aid in determining an optimal algorithm, sensor placement strategy, and type of imbedded sensor to use. Variations of frequency, impedance measurements, and pulse echoing techniques of the sensors are employed and compared. Statistical and analytic techniques are then used to determine which method is most desirable for a specific type of damage. These results are furthermore compared with previous work using externally mounted sensors. Results and optimized methods from this work can then be incorporated into a larger composite structure to validate and assess its structural health. This could prove to be important in the development and qualification of any 2" generation reusable launch vehicle using composites as a structural element.

A Unified Theory for Plants and Plant Structure

NASA Astrophysics Data System (ADS)

Wagner, Orvin E.

1998-04-01

The wave theory provides for quantization of plant structure. If one measures many spacings between plant structures it becomes apparent that certain spacings repeat from plant to plant. These spacings are associated with certain discrete frequencies associated with plant operation. When a branch grows it extend by one or more of discrete half wavelengths associated with permitted frequencies. If conditions are optimum it grows by the larger permitted half wavelengths. The angle that the branch makes with the vertical also determines the length because vertical wave velocities are in general larger than horizontal wave velocities as mentioned in the previous abstract. It also appears that cell dimensions are determined by permitted wavelengths. In conifer fiber cells it appears that there is an exact ratio between the average reciprocals of vertical lengths and horizontal reciprocal averages with a value of 1.50 in the data taken so far. Similar ratios for external structure spacings include 1.50, 1.25, 1.33, 1.66, 3.0, These ratios appear to represent ratios of vertical to horizontal velocities (Wagner 1996). See the Wagner web page.

Prediction of Water Binding to Protein Hydration Sites with a Discrete, Semiexplicit Solvent Model.

PubMed

Setny, Piotr

2015-12-08

Buried water molecules are ubiquitous in protein structures and are found at the interface of most protein-ligand complexes. Determining their distribution and thermodynamic effect is a challenging yet important task, of great of practical value for the modeling of biomolecular structures and their interactions. In this study, we present a novel method aimed at the prediction of buried water molecules in protein structures and estimation of their binding free energies. It is based on a semiexplicit, discrete solvation model, which we previously introduced in the context of small molecule hydration. The method is applicable to all macromolecular structures described by a standard all-atom force field, and predicts complete solvent distribution within a single run with modest computational cost. We demonstrate that it indicates positions of buried hydration sites, including those filled by more than one water molecule, and accurately differentiates them from sterically accessible to water but void regions. The obtained estimates of water binding free energies are in fair agreement with reference results determined with the double decoupling method.

Theoretical investigations on diamondoids (CnHm, n = 10-41): Nomenclature, structural stabilities, and gap distributions

NASA Astrophysics Data System (ADS)

Wang, Ya-Ting; Zhao, Yu-Jun; Liao, Ji-Hai; Yang, Xiao-Bao

2018-01-01

Combining the congruence check and the first-principles calculations, we have systematically investigated the structural stabilities and gap distributions of possible diamondoids (CnHm) with the carbon numbers (n) from 10 to 41. A simple method for the nomenclature is proposed, which can be used to distinguish and screen the candidates with high efficiency. Different from previous theoretical studies, the possible diamondoids can be enumerated according to our nomenclature, without any pre-determination from experiments. The structural stabilities and electronic properties have been studied by density functional based tight binding and first-principles methods, where a nearly linear correlation is found between the energy gaps obtained by these two methods. According to the formation energy of structures, we have determined the stable configurations as a function of chemical potential. The maximum and minimum energy gaps are found to be dominated by the shape of diamondoids for clusters with a given number of carbon atoms, while the gap decreases in general as the size increases due to the quantum confinement.

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.

Classification of trabeculae into three-dimensional rodlike and platelike structures via local inertial anisotropy.

PubMed

Vasilić, Branimir; Rajapakse, Chamith S; Wehrli, Felix W

2009-07-01

Trabecular bone microarchitecture is a significant determinant of the bone's mechanical properties and is thus of major clinical relevance in predicting fracture risk. The three-dimensional nature of trabecular bone is characterized by parameters describing scale, topology, and orientation of structural elements. However, none of the current methods calculates all three types of parameters simultaneously and in three dimensions. Here the authors present a method that produces a continuous classification of voxels as belonging to platelike or rodlike structures that determines their orientation and estimates their thickness. The method, dubbed local inertial anisotropy (LIA), treats the image as a distribution of mass density and the orientation of trabeculae is determined from a locally calculated tensor of inertia at each voxel. The orientation entropies of rods and plates are introduced, which can provide new information about microarchitecture not captured by existing parameters. The robustness of the method to noise corruption, resolution reduction, and image rotation is demonstrated. Further, the method is compared with established three-dimensional parameters including the structure-model index and topological surface-to-curve ratio. Finally, the method is applied to data acquired in a previous translational pilot study showing that the trabecular bone of untreated hypogonadal men is less platelike than that of their eugonadal peers.

QSAR, QSPR and QSRR in Terms of 3-D-MoRSE Descriptors for In Silico Screening of Clofibric Acid Analogues.

PubMed

Di Tullio, Maurizio; Maccallini, Cristina; Ammazzalorso, Alessandra; Giampietro, Letizia; Amoroso, Rosa; De Filippis, Barbara; Fantacuzzi, Marialuigia; Wiczling, Paweł; Kaliszan, Roman

2012-07-01

A series of 27 analogues of clofibric acid, mostly heteroarylalkanoic derivatives, have been analyzed by a novel high-throughput reversed-phase HPLC method employing combined gradient of eluent's pH and organic modifier content. The such determined hydrophobicity (lipophilicity) parameters, log kw , and acidity constants, pKa , were subjected to multiple regression analysis to get a QSRR (Quantitative StructureRetention Relationships) and a QSPR (Quantitative Structure-Property Relationships) equation, respectively, describing these pharmacokinetics-determining physicochemical parameters in terms of the calculation chemistry derived structural descriptors. The previously determined in vitro log EC50 values - transactivation activity towards PPARα (human Peroxisome Proliferator-Activated Receptor α) - have also been described in a QSAR (Quantitative StructureActivity Relationships) equation in terms of the 3-D-MoRSE descriptors (3D-Molecule Representation of Structures based on Electron diffraction descriptors). The QSAR model derived can serve for an a priori prediction of bioactivity in vitro of any designed analogue, whereas the QSRR and the QSPR models can be used to evaluate lipophilicity and acidity, respectively, of the compounds, and hence to rational guide selection of structures of proper pharmacokinetics. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source

PubMed Central

Reddy, Hemanth K.N.; Yoon, Chun Hong; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Berntsen, Peter; Bielecki, Johan; Bobkov, Sergey; Bucher, Maximilian; Carini, Gabriella A.; Carron, Sebastian; Chapman, Henry; Daurer, Benedikt; DeMirci, Hasan; Ekeberg, Tomas; Fromme, Petra; Hajdu, Janos; Hanke, Max Felix; Hart, Philip; Hogue, Brenda G.; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A.; Kurta, Ruslan P.; Larsson, Daniel S.D.; Duane Loh, N.; Maia, Filipe R.N.C.; Mancuso, Adrian P.; Mühlig, Kerstin; Munke, Anna; Nam, Daewoong; Nettelblad, Carl; Ourmazd, Abbas; Rose, Max; Schwander, Peter; Seibert, Marvin; Sellberg, Jonas A.; Song, Changyong; Spence, John C.H.; Svenda, Martin; Van der Schot, Gijs; Vartanyants, Ivan A.; Williams, Garth J.; Xavier, P. Lourdu

2017-01-01

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency. PMID:28654088

Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source

DOE PAGES

Reddy, Hemanth K. N.; Yoon, Chun Hong; Aquila, Andrew; ...

2017-06-27

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. As a result, themore » data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.« less

Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source.

PubMed

Reddy, Hemanth K N; Yoon, Chun Hong; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Berntsen, Peter; Bielecki, Johan; Bobkov, Sergey; Bucher, Maximilian; Carini, Gabriella A; Carron, Sebastian; Chapman, Henry; Daurer, Benedikt; DeMirci, Hasan; Ekeberg, Tomas; Fromme, Petra; Hajdu, Janos; Hanke, Max Felix; Hart, Philip; Hogue, Brenda G; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A; Kurta, Ruslan P; Larsson, Daniel S D; Duane Loh, N; Maia, Filipe R N C; Mancuso, Adrian P; Mühlig, Kerstin; Munke, Anna; Nam, Daewoong; Nettelblad, Carl; Ourmazd, Abbas; Rose, Max; Schwander, Peter; Seibert, Marvin; Sellberg, Jonas A; Song, Changyong; Spence, John C H; Svenda, Martin; Van der Schot, Gijs; Vartanyants, Ivan A; Williams, Garth J; Xavier, P Lourdu

2017-06-27

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65-70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.

The angular structure of ONC201, a TRAIL pathway-inducing compound, determines its potent anti-cancer activity

PubMed Central

Wagner, Jessica; Kline, Christina Leah; Pottorf, Richard S.; Nallaganchu, Bhaskara Rao; Olson, Gary L.; Dicker, David T.; Allen, Joshua E.; El-Deiry, Wafik S.

2014-01-01

We previously identified TRAIL-inducing compound 10 (TIC10), also known as NSC350625 or ONC201, from a NCI chemical library screen as a small molecule that has potent anti-tumor efficacy and a benign safety profile in preclinical cancer models. The chemical structure that was originally published by Stahle, et. al. in the patent literature was described as an imidazo[1,2-a]pyrido[4,3-d]pyrimidine derivative. The NCI and others generally accepted this as the correct structure, which was consistent with the mass spectrometry analysis outlined in the publication by Allen et. al. that first reported the molecule's anticancer properties. A recent publication demonstrated that the chemical structure of ONC201 material from the NCI is an angular [3,4-e] isomer of the originally disclosed, linear [4,3-d] structure. Here we confirm by NMR and X-ray structural analysis of the dihydrochloride salt form that the ONC201 material produced by Oncoceutics is the angular [3,4-e] structure and not the linear structure originally depicted in the patent literature and by the NCI. Similarly, in accordance with our biological evaluation, the previously disclosed anti-cancer activity is associated with the angular structure and not the linear isomer. Together these studies confirm that ONC201, produced by Oncoceutics or obtained from the NCI, possesses an angular [3,4-e] structure that represents the highly active anti-cancer compound utilized in prior preclinical studies and now entering clinical trials in advanced cancers. PMID:25587031

The angular structure of ONC201, a TRAIL pathway-inducing compound, determines its potent anti-cancer activity.

PubMed

Wagner, Jessica; Kline, Christina Leah; Pottorf, Richard S; Nallaganchu, Bhaskara Rao; Olson, Gary L; Dicker, David T; Allen, Joshua E; El-Deiry, Wafik S

2014-12-30

We previously identified TRAIL-inducing compound 10 (TIC10), also known as NSC350625 or ONC201, from a NCI chemical library screen as a small molecule that has potent anti-tumor efficacy and a benign safety profile in preclinical cancer models. The chemical structure that was originally published by Stahle, et. al. in the patent literature was described as an imidazo[1,2-a]pyrido[4,3-d]pyrimidine derivative. The NCI and others generally accepted this as the correct structure, which was consistent with the mass spectrometry analysis outlined in the publication by Allen et. al. that first reported the molecule's anticancer properties. A recent publication demonstrated that the chemical structure of ONC201 material from the NCI is an angular [3,4-e] isomer of the originally disclosed, linear [4,3-d] structure. Here we confirm by NMR and X-ray structural analysis of the dihydrochloride salt form that the ONC201 material produced by Oncoceutics is the angular [3,4-e] structure and not the linear structure originally depicted in the patent literature and by the NCI. Similarly, in accordance with our biological evaluation, the previously disclosed anti-cancer activity is associated with the angular structure and not the linear isomer. Together these studies confirm that ONC201, produced by Oncoceutics or obtained from the NCI, possesses an angular [3,4-e] structure that represents the highly active anti-cancer compound utilized in prior preclinical studies and now entering clinical trials in advanced cancers.

Looking for Structure: Is the Two-Word Stage of Language Development in Apes and Human Children the Same or Different?

ERIC Educational Resources Information Center

Patkowski, Mark

2014-01-01

Previously published corpora of two-word utterances by three chimpanzees and three human children were compared to determine whether, as has been claimed, apes possess the same basic syntactic and semantic capacities as 2-year old children. Some similarities were observed in the type of semantic relations expressed by the two groups; however,…

How to Increase PhD Completion Rates? An Impact Evaluation of Two Reforms in a Selective Graduate School, 1976-2012

ERIC Educational Resources Information Center

Geven, Koen; Skopek, Jan; Triventi, Moris

2018-01-01

Graduate and doctoral schools around the world struggle to shorten the long time to degree and to prevent high dropout rates. While most of previous research studied individual determinants of PhD completion, we analyze the impact of two structural reforms of the doctoral program on thesis completion at a selective European graduate school.…

Determination of Physical Properties of Ionic Liquids Using Molecular Simulations

DTIC Science & Technology

2010-08-20

That is, most groups rely on relatively short (100-500 ps) simulations and evaluate the viscosity via conventional Green - Kubo integration . In this...and can contribute to higher than expected viscosities . The liquid structure of the energetic ionic liquid 2-hydroxyethylhydrizinium nitrate was...claimed previously that neglect of polarizability leads to inaccuracies in the computed transport properties of ionic liquids such as viscosities

Collaborative Partner or Social Tool? New Evidence for Young Children's Understanding of Joint Intentions in Collaborative Activities

ERIC Educational Resources Information Center

Warneken, Felix; Grafenhain, Maria; Tomasello, Michael

2012-01-01

Some children's social activities are structured by joint goals. In previous research, the criterion used to determine this was relatively weak: if the partner stopped interacting, did the child attempt to re-engage her? But re-engagement attempts could easily result from the child simply realizing that she needs the partner to reach her own goal…

Analysis of stress concentration at holes in components made of 2195 aluminum-lithium

NASA Astrophysics Data System (ADS)

Ahmed, R.

1995-05-01

Because the 2195 aluminum-lithium of the super lightweight external tank (SLWT ET) has a lower toughness than the 2219 aluminum used in previous ET's, careful attention must be paid to stress concentration in the SLWT ET. This report details the initial analysis performed by NASA to determine the material properties required to ensure structural integrity in these critical areas.

Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea

PubMed Central

Toffano-Nioche, Claire; Gautheret, Daniel; Leclerc, Fabrice

2015-01-01

A structural and functional classification of H/ACA and H/ACA-like motifs is obtained from the analysis of the H/ACA guide RNAs which have been identified previously in the genomes of Euryarchaea (Pyrococcus) and Crenarchaea (Pyrobaculum). A unified structure/function model is proposed based on the common structural determinants shared by H/ACA and H/ACA-like motifs in both Euryarchaea and Crenarchaea. Using a computational approach, structural and energetic rules for the guide:target RNA-RNA interactions are derived from structural and functional data on the H/ACA RNP particles. H/ACA(-like) motifs found in Pyrococcus are evaluated through the classification and their biological relevance is discussed. Extra-ribosomal targets found in both Pyrococcus and Pyrobaculum might support the hypothesis of a gene regulation mediated by H/ACA(-like) guide RNAs in archaea. PMID:26240384

Unexpected Ground-State Structure and Mechanical Properties of Ir₂Zr Intermetallic Compound.

PubMed

Zhang, Meiguang; Cao, Rui; Zhao, Meijie; Du, Juan; Cheng, Ke

2018-01-10

Using an unbiased structure searching method, a new orthorhombic Cmmm structure consisting of ZrIr 12 polyhedron building blocks is predicted to be the thermodynamic ground-state of stoichiometric intermetallic Ir₂Zr in Ir-Zr systems. The formation enthalpy of the Cmmm structure is considerably lower than that of the previously synthesized Cu₂Mg-type phase, by ~107 meV/atom, as demonstrated by the calculation of formation enthalpy. Meanwhile, the phonon dispersion calculations further confirmed the dynamical stability of Cmmm phase under ambient conditions. The mechanical properties, including elastic stability, rigidity, and incompressibility, as well as the elastic anisotropy of Cmmm -Ir₂Zr intermetallic, have thus been fully determined. It is found that the predicted Cmmm phase exhibits nearly elastic isotropic and great resistance to shear deformations within the (100) crystal plane. Evidence of atomic bonding related to the structural stability for Ir₂Zr were manifested by calculations of the electronic structures.

Paired β-sheet structure of an Aβ(1-40) amyloid fibril revealed by electron microscopy

PubMed Central

Sachse, Carsten; Fändrich, Marcus; Grigorieff, Nikolaus

2008-01-01

Alzheimer's disease is a neurodegenerative disorder that is characterized by the cerebral deposition of amyloid fibrils formed by Aβ peptide. Despite their prevalence in Alzheimer's and other neurodegenerative diseases, important details of the structure of amyloid fibrils remain unknown. Here, we present a three-dimensional structure of a mature amyloid fibril formed by Aβ(1-40) peptide, determined by electron cryomicroscopy at ≈8-Å resolution. The fibril consists of two protofilaments, each containing ≈5-nm-long regions of β-sheet structure. A local twofold symmetry within each region suggests that pairs of β-sheets are formed from equivalent parts of two Aβ(1-40) peptides contained in each protofilament. The pairing occurs via tightly packed interfaces, reminiscent of recently reported steric zipper structures. However, unlike these previous structures, the β-sheet pairing is observed within an amyloid fibril and includes significantly longer amino acid sequences. PMID:18483195

Controlled Detonation Dynamics in Additively Manufactured High Explosives

NASA Astrophysics Data System (ADS)

Schmalzer, Andrew; Tappan, Bryce; Bowden, Patrick; Manner, Virginia; Clements, Brad; Menikoff, Ralph; Ionita, Axinte; Branch, Brittany; Dattelbaum, Dana; Espy, Michelle; Patterson, Brian; Wu, Ruilian; Mueller, Alexander

2017-06-01

The effect of structure in explosives has long been a subject of interest to explosives engineers and scientists. Through structure, detonation dynamics in explosives can be manipulated, introducing a new level of safety and directed performance into these previously difficult to control materials. New advances in additive manufacturing (AM) allow the deliberate introduction of exact internal structures at dimensions approaching the mesoscale of these energetic materials. We show through simulation and experiment that this structure can be used to control detonation behavior by manipulating complex shockwave interactions. We use high-speed video and shorting mag-wires to determine the detonation velocity in AM generated explosive structures, demonstrating, for the first time, a method of controlling the directional propagation of reactive flow through the controlled introduction of structure within a high explosive. With ongoing improvement in the AM methods available coupled with guidance through modeling and simulations, more complex interactions are being explored. LANL LDRD Office.

Deformable complex network for refining low-resolution X-ray structures

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

Zhang, Chong; Wang, Qinghua; Ma, Jianpeng, E-mail: jpma@bcm.edu

2015-10-27

A new refinement algorithm called the deformable complex network that combines a novel angular network-based restraint with a deformable elastic network model in the target function has been developed to aid in structural refinement in macromolecular X-ray crystallography. In macromolecular X-ray crystallography, building more accurate atomic models based on lower resolution experimental diffraction data remains a great challenge. Previous studies have used a deformable elastic network (DEN) model to aid in low-resolution structural refinement. In this study, the development of a new refinement algorithm called the deformable complex network (DCN) is reported that combines a novel angular network-based restraint withmore » the DEN model in the target function. Testing of DCN on a wide range of low-resolution structures demonstrated that it constantly leads to significantly improved structural models as judged by multiple refinement criteria, thus representing a new effective refinement tool for low-resolution structural determination.« less

Structural and sequence features of two residue turns in beta-hairpins.

PubMed

Madan, Bharat; Seo, Sung Yong; Lee, Sun-Gu

2014-09-01

Beta-turns in beta-hairpins have been implicated as important sites in protein folding. In particular, two residue β-turns, the most abundant connecting elements in beta-hairpins, have been a major target for engineering protein stability and folding. In this study, we attempted to investigate and update the structural and sequence properties of two residue turns in beta-hairpins with a large data set. For this, 3977 beta-turns were extracted from 2394 nonhomologous protein chains and analyzed. First, the distribution, dihedral angles and twists of two residue turn types were determined, and compared with previous data. The trend of turn type occurrence and most structural features of the turn types were similar to previous results, but for the first time Type II turns in beta-hairpins were identified. Second, sequence motifs for the turn types were devised based on amino acid positional potentials of two-residue turns, and their distributions were examined. From this study, we could identify code-like sequence motifs for the two residue beta-turn types. Finally, structural and sequence properties of beta-strands in the beta-hairpins were analyzed, which revealed that the beta-strands showed no specific sequence and structural patterns for turn types. The analytical results in this study are expected to be a reference in the engineering or design of beta-hairpin turn structures and sequences. © 2014 Wiley Periodicals, Inc.

Crystal Structures of Fatty Acid Amide Hydrolase Bound to the Carbamate Inhibitor URB597: Discovery of a Deacylating Water Molecule and Insight into Enzyme Inactivation

PubMed Central

Mileni, Mauro; Kamtekar, Satwik; Wood, David C.; Benson, Timothy E.; Cravatt, Benjamin F.; Stevens, Raymond C.

2010-01-01

The endocannabinoid system regulates a wide range of physiological processes including pain, inflammation, and cognitive/emotional states. URB597 is one of the best characterized covalent inhibitors of the endocannabinoid-degrading enzyme fatty acid amide hydrolase (FAAH). Here, we report the structure of the FAAH-URB597 complex at 2.3 Å resolution. The structure provides insights into mechanistic details of enzyme inactivation and experimental evidence of a previously uncharacterized active site water molecule that likely is involved in substrate deacylation. This water molecule is part of an extensive hydrogen-bonding network, and is coordinated indirectly to residues lining the cytosolic port of the enzyme. In order to corroborate our hypothesis concerning the role of this water molecule in FAAH’s catalytic mechanism, we determined the structure of FAAH conjugated to a urea-based inhibitor, PF-3845, to a higher resolution (2.4 Å) than previously reported. The higher resolution structure confirms the presence of the water molecule in a virtually identical location in the active site. Examination of the structures of serine hydrolases that are non-homologous to FAAH, such as elastase, trypsin, or chymotrypsin, shows a similarly positioned hydrolytic water molecule and suggest a functional convergence between the amidase signature enzymes and serine proteases. PMID:20493882

Crystal structure of fatty acid amide hydrolase bound to the carbamate inhibitor URB597: discovery of a deacylating water molecule and insight into enzyme inactivation.

PubMed

Mileni, Mauro; Kamtekar, Satwik; Wood, David C; Benson, Timothy E; Cravatt, Benjamin F; Stevens, Raymond C

2010-07-23

The endocannabinoid system regulates a wide range of physiological processes including pain, inflammation, and cognitive/emotional states. URB597 is one of the best characterized covalent inhibitors of the endocannabinoid-degrading enzyme fatty acid amide hydrolase (FAAH). Here, we report the structure of the FAAH-URB597 complex at 2.3 A resolution. The structure provides insights into mechanistic details of enzyme inactivation and experimental evidence of a previously uncharacterized active site water molecule that likely is involved in substrate deacylation. This water molecule is part of an extensive hydrogen-bonding network and is coordinated indirectly to residues lining the cytosolic port of the enzyme. In order to corroborate our hypothesis concerning the role of this water molecule in FAAH's catalytic mechanism, we determined the structure of FAAH conjugated to a urea-based inhibitor, PF-3845, to a higher resolution (2.4 A) than previously reported. The higher-resolution structure confirms the presence of the water molecule in a virtually identical location in the active site. Examination of the structures of serine hydrolases that are non-homologous to FAAH, such as elastase, trypsin, or chymotrypsin, shows a similarly positioned hydrolytic water molecule and suggests a functional convergence between the amidase signature enzymes and serine proteases. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Aboriginal population prospects.

PubMed

Gray, A; Tesfaghiorghis, H

1993-11-01

The authors examine data from the 1986 and 1991 Australian censuses to assess discrepancies between the census data and past projections of the size and structure of the Aboriginal population. They also "comment on ways in which determinants of Aboriginal population change are diverging from the parameters used for previous projections. We pay particular attention to mortality prospects.... We note the evidence for under-enumeration of the Aboriginal population in particular age groups in the 1991 Census as in previous censuses, and estimate the size of adjustments necessary to correct for some, but not all, of these deficiencies. The analysis shows that Aboriginal fertility increased in the second half of the 1980s." excerpt

Determination of the Basin Structure Beneath European Side of Istanbul

NASA Astrophysics Data System (ADS)

Karabulut, Savas; Cengiz Cinku, Mulla; Thomas, Michael; Lamontagne, Maurice

2016-04-01

Istanbul (near North Anatolian Fault Zone:NAFZ, Turkey) is located in northern part of Sea of Marmara, an area that has been influenced by possible Marmara Earthquakes. The general geology of Istanbul divided into two stratigraphic unit such as sedimentary (from Oligocene to Quaternary Deposits) and bedrock (Paleozoic and Eocene). The bedrock units consists of sand stone, clay stone to Paleozoic age and limestone to Eocene age and sedimentary unit consist of sand, clay, mil and gravel from Oligocene to Quaternary age. Earthquake disaster mitigation studies divided into two important phases, too. Firstly, earthquake, soil and engineering structure problems identify for investigation area, later on strategic emergency plan can prepare for these problems. Soil amplification play important role the disaster mitigation and the site effect analysis and basin structure is also a key parameter for determining of site effect. Some geophysical, geological and geotechnical measurements are requeired to defined this relationship. Istanbul Megacity has been waiting possible Marmara Earthquake and their related results. In order to defined to possible damage potential related to site effect, gravity measurements carried out for determining to geological structure, basin geometry and faults in Istanbul. Gravity data were collected at 640 sites by using a Scientrex CG-5 Autogravity meter Standard corrections applied to the gravity data include those for instrumental drift, Earth tides and latitude, and the free-air and Bouguer corrections. The corrected gravity data were imported into a Geosoft database to create a grid and map of the Bouguer gravity anomaly (grid cell size of 200 m). As a previously results, we determined some lineminants, faults and basins beneath Istanbul City. Especially, orientation of faults were NW-SE direction and some basin structures determined on between Buyukcekmece and Kucukcekmece Lake.

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

N,N-diethyldithiocarbamate promotes oxidative stress prior to myelin structural changes and increases myelin copper content

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

Viquez, Olga M.; Lai, Barry; Ahn, Jae Hee

2009-08-15

Dithiocarbamates are a commercially important class of compounds that can produce peripheral neuropathy in humans and experimental animals. Previous studies have supported a requirement for copper accumulation and enhanced lipid peroxidation in dithiocarbamate-mediated myelinopathy. The study presented here extends previous investigations in two areas. Firstly, although total copper levels have been shown to increase within the nerve it has not been determined whether copper is increased within the myelin compartment, the primary site of lesion development. Therefore, the distribution of copper in sciatic nerve was characterized using synchrotron X-ray fluorescence microscopy to determine whether the neurotoxic dithiocarbamate, N,N-diethyldithiocarbamate, increases coppermore » levels in myelin. Secondly, because lipid peroxidation is an ongoing process in normal nerve and the levels of lipid peroxidation products produced by dithiocarbamate exposure demonstrated an unusual cumulative dose response in previous studies the biological impact of dithiocarbamate-mediated lipid peroxidation was evaluated. Experiments were performed to determine whether dithiocarbamate-mediated lipid peroxidation products elicit an antioxidant response through measuring the protein expression levels of three enzymes, superoxide dismutase 1, heme oxygenase 1, and glutathione transferase {alpha}, that are linked to the antioxidant response element promoter. To establish the potential of oxidative injury to contribute to myelin injury the temporal relationship of the antioxidant response to myelin injury was determined. Myelin structure in peripheral nerve was assessed using multi-exponential transverse relaxation measurements (MET{sub 2}) as a function of exposure duration, and the temporal relationship of protein expression changes relative to the onset of changes in myelin integrity were determined. Initial assessments were also performed to explore the potential contribution of dithiocarbamate-mediated inhibition of proteasome function and inhibition of cuproenzyme activity to neurotoxicity, and also to assess the potential of dithiocarbamates to promote oxidative stress and injury within the central nervous system. These evaluations were performed using an established model for dithiocarbamate-mediated demyelination in the rat utilizing sciatic nerve, spinal cord and brain samples obtained from rats exposed to N,N-diethyldithiocarbamate (DEDC) by intra-abdominal pumps for periods of 2, 4, and 8 weeks and from non exposed controls. The data supported the ability of DEDC to increase copper within myelin and to enhance oxidative stress prior to structural changes detectable by MET{sub 2}. Evidence was also obtained that the excess copper produced by DEDC in the central nervous system is redox active and promotes oxidative injury.« less

Disseminins and Spiciferone Analogues: Polyketide-Derived Metabolites from a Fungicolous Isolate of Pestalotiopsis disseminata.

PubMed

Hwang, In Hyun; Swenson, Dale C; Gloer, James B; Wicklow, Donald T

2016-03-25

Seven new polyketide metabolites (disseminins A-E, 1-5, and spiciferones D and E, 7 and 8) were obtained from cultures of a fungicolous isolate of Pestalotiopsis disseminata (NRRL 62562), together with a related compound (6) previously known only as a semisynthetic product. Structures were determined mainly by analysis of HRMS and NMR data. Biogenetically related compounds 1 and 2 possess uncommon bis-tetrahydrofuran and dioxabicyclo[3.2.1]octane ring systems, respectively. X-ray crystallographic analysis of the p-bromobenzoate derivative of 1 confirmed the structure and enabled assignment of its absolute configuration.

Transformations of the dislocation structure of nickel single crystals

NASA Astrophysics Data System (ADS)

Alfyorova, E. A.; Lychagin, D. V.; Lychagina, L. L.; Tsvetkov, N. A.

2017-12-01

A relationship between different-scale deformations of crystals has not been established yet. In order to solve this task, we investigate the development of a deformation relief and dislocation structure in nickel single crystals after deformation. The stress tensor, crystallography, and geometry of specimens affect the organization of some shear along corresponding systems of sliding. The organization of shear shows some features of self-organization. It is associated with the self-organization in the dislocation subsystem analyzed previously. The effectiveness of reducing external and internal stresses determines patterns of deformation processes at different scale levels.

UO(2) Oxidative Corrosion by Nonclassical Diffusion.

PubMed

Stubbs, Joanne E; Chaka, Anne M; Ilton, Eugene S; Biwer, Craig A; Engelhard, Mark H; Bargar, John R; Eng, Peter J

2015-06-19

Using x-ray scattering, spectroscopy, and density-functional theory, we determine the structure of the oxidation front when a UO(2) (111) surface is exposed to oxygen at ambient conditions. In contrast to classical diffusion and previously reported bulk UO(2+x) structures, we find oxygen interstitials order into a nanoscale superlattice with three-layer periodicity and uranium in three oxidation states: IV, V, and VI. This oscillatory diffusion profile is driven by the nature of the electron transfer process, and has implications for understanding the initial stages of oxidative corrosion in materials at the atomistic level.

Structure of Aqueous Trehalose Solution by Neutron Diffraction and Structural Modeling.

PubMed

Olsson, Christoffer; Jansson, Helén; Youngs, Tristan; Swenson, Jan

2016-12-15

The molecular structure of an aqueous solution of the disaccharide trehalose (C 12 H 22 O 11 ) has been studied by neutron diffraction and empirical potential structure refinement modeling. Six different isotope compositions with 33 wt % trehalose (corresponding to 38 water molecules per trehalose molecule) were measured to ensure that water-water, trehalose-water, and trehalose-trehalose correlations were accurately determined. In fact, this is the first neutron diffraction study of an aqueous trehalose solution in which also the nonexchangeable hydrogen atoms in trehalose are deuterated. With this approach, it was possible to determine that (1) there is a substantial hydrogen bonding between trehalose and water (∼11 hydrogen bonds per trehalose molecule), which is in contrast to previous neutron diffraction studies, and (2) there is no tendency of clustering of trehalose, in contrast to what is generally observed by molecular dynamics simulations and experimentally found for other disaccharides. Thus, the results give the structural picture that trehalose prefers to interact with water and participate in a hydrogen-bonded network. This strong network character of the solution might be one of the key reasons for its extraordinary stabilization effect on biological materials.

Construction patterns of birds' nests provide insight into nest-building behaviours.

PubMed

Biddle, Lucia; Goodman, Adrian M; Deeming, D Charles

2017-01-01

Previous studies have suggested that birds and mammals select materials needed for nest building based on their thermal or structural properties, although the amounts or properties of the materials used have been recorded for only a very small number of species. Some of the behaviours underlying the construction of nests can be indirectly determined by careful deconstruction of the structure and measurement of the biomechanical properties of the materials used. Here we examined this idea in an investigation of Bullfinch ( Pyrrhula pyrrhula ) nests as a model for open-nesting songbird species that construct a "twig" nest, and tested the hypothesis that materials in different parts of nests serve different functions. The quantities of materials present in the nest base, sides and cup were recorded before structural analysis. Structural analysis showed that the base of the outer nests were composed of significantly thicker, stronger and more rigid materials compared to the side walls, which in turn were significantly thicker, stronger and more rigid than materials used in the cup. These results suggest that the placement of particular materials in nests may not be random, but further work is required to determine if the final structure of a nest accurately reflects the construction process.

Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data

DOE PAGES

Ginn, Helen M.; Messerschmidt, Marc; Ji, Xiaoyun; ...

2015-03-09

The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and proteinmore » core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis.« less

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.

An atomic model of brome mosaic virus using direct electron detection and real-space optimization.

PubMed

Wang, Zhao; Hryc, Corey F; Bammes, Benjamin; Afonine, Pavel V; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L; Kao, Cheng; Ludtke, Steven J; Schmid, Michael F; Adams, Paul D; Chiu, Wah

2014-09-04

Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.

Mapping transiently formed and sparsely populated conformations on a complex energy landscape

PubMed Central

Wang, Yong; Papaleo, Elena; Lindorff-Larsen, Kresten

2016-01-01

Determining the structures, kinetics, thermodynamics and mechanisms that underlie conformational exchange processes in proteins remains extremely difficult. Only in favourable cases is it possible to provide atomic-level descriptions of sparsely populated and transiently formed alternative conformations. Here we benchmark the ability of enhanced-sampling molecular dynamics simulations to determine the free energy landscape of the L99A cavity mutant of T4 lysozyme. We find that the simulations capture key properties previously measured by NMR relaxation dispersion methods including the structure of a minor conformation, the kinetics and thermodynamics of conformational exchange, and the effect of mutations. We discover a new tunnel that involves the transient exposure towards the solvent of an internal cavity, and show it to be relevant for ligand escape. Together, our results provide a comprehensive view of the structural landscape of a protein, and point forward to studies of conformational exchange in systems that are less characterized experimentally. DOI: http://dx.doi.org/10.7554/eLife.17505.001 PMID:27552057

Accommodation of structural rearrangements in the huntingtin-interacting protein 1 coiled-coil domain

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

Wilbur, Jeremy D., E-mail: jwilbur@msg.ucsf.edu; Hwang, Peter K.; Brodsky, Frances M.

2010-03-01

Variable packing interaction related to the conformational flexibility within the huntingtin-interacting protein 1 coiled coil domain. Huntingtin-interacting protein 1 (HIP1) is an important link between the actin cytoskeleton and clathrin-mediated endocytosis machinery. HIP1 has also been implicated in the pathogenesis of Huntington’s disease. The binding of HIP1 to actin is regulated through an interaction with clathrin light chain. Clathrin light chain binds to a flexible coiled-coil domain in HIP1 and induces a compact state that is refractory to actin binding. To understand the mechanism of this conformational regulation, a high-resolution crystal structure of a stable fragment from the HIP1 coiled-coilmore » domain was determined. The flexibility of the HIP1 coiled-coil region was evident from its variation from a previously determined structure of a similar region. A hydrogen-bond network and changes in coiled-coil monomer interaction suggest that the HIP1 coiled-coil domain is uniquely suited to allow conformational flexibility.« less

An examination of the validity of the Academic Motivation Scale with a United States business student sample.

PubMed

Smith, Kenneth J; Davy, Jeanette A; Rosenberg, Donald L

2010-04-01

This study examined alternative seven-, five-, and three-factor structures for the Academic Motivation Scale, with data from a large convenience sample of 2,078 students matriculating in various business courses at three AACSB-accredited regional comprehensive universities. In addition, the invariance of the scale's factor structure between male and female students and between undergraduate and Master's of Business Administration students was investigated. Finally, the internal consistency of the items loading on each of the seven AMS subscales was assessed as well as whether the correlations among the subscales supported a continuum of self-determination. Results for the full sample as well as the targeted subpopulations supported the seven factor configuration of the scale with adequate model fit achieved for all but the MBA student group. The data also generated acceptable internal consistency statistics for all of the subscales. However, in line with a number of previous studies, the correlations between subscales failed to fully support the scale's simplex structure as proposed by self-determination theory.

Molecular assembly of Clostridium botulinum progenitor M complex of type E

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

Eswaramoorthy, Subramaniam; Sun, Jingchuan; Li, Huilin

2015-12-07

Clostridium botulinum neurotoxin (BoNT) is released as a progenitor complex, in association with a non-toxic-non-hemagglutinin protein (NTNH) and other associated proteins. We have determined the crystal structure of M type Progenitor complex of botulinum neurotoxin E [PTC-E(M)], a heterodimer of BoNT and NTNH. The crystal structure reveals that the complex exists as a tight, interlocked heterodimer of BoNT and NTNH. The crystal structure explains the mechanism of molecular assembly of the complex and reveals several acidic clusters at the interface responsible for association at low acidic pH and disassociation at basic/neutral pH. Furthermore, the similarity of the general architecture betweenmore » the PTC-E(M) and the previously determined PTC-A(M) strongly suggests that the progenitor M complexes of all botulinum serotypes may have similar molecular arrangement, although the neurotoxins apparently can take very different conformation when they are released from the M complex.« less

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

PubMed Central

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; Stellato, Francesco; Chiu, Elaine; Yeh, Shin-Mei; Aquila, Andrew; Basu, Shibom; Bean, Richard; Beyerlein, Kenneth R.; Botha, Sabine; Boutet, Sébastien; DePonte, Daniel P.; Doak, R. Bruce; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; James, Daniel R.; Kupitz, Christopher; Lomb, Lukas; Messerschmidt, Marc; Nass, Karol; Rendek, Kimberly; Shoeman, Robert L.; Wang, Dingjie; Weierstall, Uwe; White, Thomas A.; Williams, Garth J.; Zatsepin, Nadia A.; Fromme, Petra; Spence, John C. H.; Goldie, Kenneth N.; Jehle, Johannes A.; Metcalf, Peter; Barty, Anton

2017-01-01

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach. PMID:28202732

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

DOE PAGES

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; ...

2017-02-15

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam ismore » often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Furthermore, our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.« less

3D temporal subtraction on multislice CT images using nonlinear warping technique

NASA Astrophysics Data System (ADS)

Ishida, Takayuki; Katsuragawa, Shigehiko; Kawashita, Ikuo; Kim, Hyounseop; Itai, Yoshinori; Awai, Kazuo; Li, Qiang; Doi, Kunio

2007-03-01

The detection of very subtle lesions and/or lesions overlapped with vessels on CT images is a time consuming and difficult task for radiologists. In this study, we have developed a 3D temporal subtraction method to enhance interval changes between previous and current multislice CT images based on a nonlinear image warping technique. Our method provides a subtraction CT image which is obtained by subtraction of a previous CT image from a current CT image. Reduction of misregistration artifacts is important in the temporal subtraction method. Therefore, our computerized method includes global and local image matching techniques for accurate registration of current and previous CT images. For global image matching, we selected the corresponding previous section image for each current section image by using 2D cross-correlation between a blurred low-resolution current CT image and a blurred previous CT image. For local image matching, we applied the 3D template matching technique with translation and rotation of volumes of interests (VOIs) which were selected in the current and the previous CT images. The local shift vector for each VOI pair was determined when the cross-correlation value became the maximum in the 3D template matching. The local shift vectors at all voxels were determined by interpolation of shift vectors of VOIs, and then the previous CT image was nonlinearly warped according to the shift vector for each voxel. Finally, the warped previous CT image was subtracted from the current CT image. The 3D temporal subtraction method was applied to 19 clinical cases. The normal background structures such as vessels, ribs, and heart were removed without large misregistration artifacts. Thus, interval changes due to lung diseases were clearly enhanced as white shadows on subtraction CT images.

Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase

PubMed Central

Kakar, Smita; Fang, Xianyang; Lubkowska, Lucyna; Zhou, Yan Ning; Shaw, Gary X.; Wang, Yun-Xing; Jin, Ding Jun; Kashlev, Mikhail; Ji, Xinhua

2015-01-01

Members of the Swi2/Snf2 (switch/sucrose non-fermentable) family depend on their ATPase activity to mobilize nucleic acid-protein complexes for gene expression. In bacteria, RapA is an RNA polymerase (RNAP)-associated Swi2/Snf2 protein that mediates RNAP recycling during transcription. It is known that the ATPase activity of RapA is stimulated by its interaction with RNAP. It is not known, however, how the RapA-RNAP interaction activates the enzyme. Previously, we determined the crystal structure of RapA. The structure revealed the dynamic nature of its N-terminal domain (Ntd), which prompted us to elucidate the solution structure and activity of both the full-length protein and its Ntd-truncated mutant (RapAΔN). Here, we report the ATPase activity of RapA and RapAΔN in the absence or presence of RNAP and the solution structures of RapA and RapAΔN either ligand-free or in complex with RNAP. Determined by small-angle x-ray scattering, the solution structures reveal a new conformation of RapA, define the binding mode and binding site of RapA on RNAP, and show that the binding sites of RapA and σ70 on the surface of RNAP largely overlap. We conclude that the ATPase activity of RapA is inhibited by its Ntd but stimulated by RNAP in an allosteric fashion and that the conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. These and previous findings outline the functional cycle of RapA, which increases our understanding of the mechanism and regulation of Swi2/Snf2 proteins in general and of RapA in particular. The new structural information also leads to a hypothetical model of RapA in complex with RNAP immobilized during transcription. PMID:26272746

Changes in habitat complexity negatively affect diverse gastropod assemblages in coralline algal turf.

PubMed

Kelaher, B P

2003-05-01

The physical structure of a habitat generally has a strong influence on the diversity and abundance of associated organisms. I investigated the role of coralline algal turf structure in determining spatial variation of gastropod assemblages at different tidal heights of a rocky shore near Sydney, Australia. The structural characteristics of algal turf tested were frond density (or structural complexity) and frond length (the vertical scale over which structural complexity was measured). This definition of structural complexity assumes that complexity of the habitat increases with increasing frond density. While frond length was unrelated to gastropod community structure, I found significant correlations between density of fronds and multivariate and univariate measures of gastropod assemblages, indicating the importance of structural complexity. In contrast to previous studies, here there were negative relationships between the density of fronds and the richness and abundance of gastropods. Artificial habitat mimics were used to manipulate the density of fronds to test the hypothesis that increasing algal structural complexity decreases the richness and abundance of gastropods. As predicted, there were significantly more species of gastropods in loosely packed than in tightly packed turf at both low- and mid-shore levels. Despite large differences between gastropod assemblages at different tidal heights, the direction and magnitude of these negative effects were similar at low- and mid-shore levels and, therefore, relatively independent of local environmental conditions. These novel results extend our previous understanding of the ecological effects of habitat structure because they demonstrate possible limitations of commonly used definitions of structural complexity, as well as distinct upper thresholds in the relationship between structural complexity and faunal species richness.

Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach

PubMed Central

Zapién-Campos, Román; Olmedo-Álvarez, Gabriela; Santillán, Moisés

2015-01-01

Most of the studies in Ecology have been devoted to analyzing the effects the environment has on individuals, populations, and communities, thus neglecting the effects of biotic interactions on the system dynamics. In the present work we study the structure of bacterial communities in the oligotrophic shallow water system of Churince, Cuatro Cienegas, Mexico. Since the physicochemical conditions of this water system are homogeneous and quite stable in time, it is an excellent candidate to study how biotic factors influence the structure of bacterial communities. In a previous study, the binary antagonistic interactions of 78 bacterial strains, isolated from Churince, were experimentally determined. We employ these data to develop a computer algorithm to simulate growth experiments in a cellular grid representing the pond. Remarkably, in our model, the dynamics of all the simulated bacterial populations is determined solely by antagonistic interactions. Our results indicate that all bacterial strains (even those that are antagonized by many other bacteria) survive in the long term, and that the underlying mechanism is the formation of bacterial community patches. Patches corresponding to less antagonistic and highly susceptible strains are consistently isolated from the highly-antagonistic bacterial colonies by patches of neutral strains. These results concur with the observed features of the bacterial community structure previously reported. Finally, we study how our findings depend on factors like initial population size, differential population growth rates, homogeneous population death rates, and enhanced bacterial diffusion. PMID:26052318

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.

Modeling of transmission line exposure to direct lightning strokes

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

Rizk, F.A.M.

1990-10-01

The paper introduces a new model for assessing the exposure of free-standing structures and horizontal conductors above flat ground to direct lightning strokes. The starting point of this work is a recently developed criterion for positive leader inception, modified to account for positive leaders initiated under the influence of a negative descending lightning stroke. Subsequent propagation of the positive leader is analyzed to define the point of encounter of the two leaders which determines the attractive radius of a structure or the attractive lateral distance of a conductor. These parameters are investigated for a wide range of heights and return-strokemore » currents. A method for analyzing shielding failure and determining the critical shielding angle is also described. The predictions of the model are compared with field observations and previously developed models.« less

Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage $${\\Phi}$$6 Major Capsid Protein

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

Nemecek, Daniel; Plevka, Pavel; Boura, Evzen

2013-11-29

Bacteriophagemore » $${\\Phi}$$6 is a double-stranded RNA virus that has been extensively studied as a model organism. In this paper we describe structure determination of $${\\Phi}$$6 major capsid protein P1. The protein crystallized in base centered orthorhombic space group C2221. Matthews’s coefficient indicated that the crystals contain from four to seven P1 subunits in the crystallographic asymmetric unit. The self-rotation function had shown presence of fivefold axes of non-crystallographic symmetry in the crystals. Thus, electron density map corresponding to a P1 pentamer was excised from a previously determined cryoEM reconstruction of the $${\\Phi}$$6 procapsid at 7 Å resolution and used as a model for molecular replacement. The phases for reflections at higher than 7 Å resolution were obtained by phase extension employing the fivefold non-crystallographic symmetry present in the crystal. Lastly, the averaged 3.6 Å-resolution electron density map was of sufficient quality to allow model building.« less

Surface determination through atomically resolved secondary-electron imaging

PubMed Central

Ciston, J.; Brown, H. G.; D'Alfonso, A. J.; Koirala, P.; Ophus, C.; Lin, Y.; Suzuki, Y.; Inada, H.; Zhu, Y.; Allen, L. J.; Marks, L. D.

2015-01-01

Unique determination of the atomic structure of technologically relevant surfaces is often limited by both a need for homogeneous crystals and ambiguity of registration between the surface and bulk. Atomically resolved secondary-electron imaging is extremely sensitive to this registration and is compatible with faceted nanomaterials, but has not been previously utilized for surface structure determination. Here we report a detailed experimental atomic-resolution secondary-electron microscopy analysis of the c(6 × 2) reconstruction on strontium titanate (001) coupled with careful simulation of secondary-electron images, density functional theory calculations and surface monolayer-sensitive aberration-corrected plan-view high-resolution transmission electron microscopy. Our work reveals several unexpected findings, including an amended registry of the surface on the bulk and strontium atoms with unusual seven-fold coordination within a typically high surface coverage of square pyramidal TiO5 units. Dielectric screening is found to play a critical role in attenuating secondary-electron generation processes from valence orbitals. PMID:26082275

Surface determination through atomically resolved secondary-electron imaging

DOE PAGES

Ciston, J.; Brown, H. G.; D’Alfonso, A. J.; ...

2015-06-17

We report that unique determination of the atomic structure of technologically relevant surfaces is often limited by both a need for homogeneous crystals and ambiguity of registration between the surface and bulk. Atomically resolved secondary-electron imaging is extremely sensitive to this registration and is compatible with faceted nanomaterials, but has not been previously utilized for surface structure determination. Here we show a detailed experimental atomic-resolution secondary-electron microscopy analysis of the c(6 x 2) reconstruction on strontium titanate (001) coupled with careful simulation of secondary-electron images, density functional theory calculations and surface monolayer-sensitive aberration-corrected plan-view high-resolution transmission electron microscopy. Our workmore » reveals several unexpected findings, including an amended registry of the surface on the bulk and strontium atoms with unusual seven-fold coordination within a typically high surface coverage of square pyramidal TiO 5 units. Lastly, dielectric screening is found to play a critical role in attenuating secondary-electron generation processes from valence orbitals.« less

Environmental and plant community determinants of species loss following nitrogen enrichment

USGS Publications Warehouse

Clark, C.M.; Cleland, E.E.; Collins, S.L.; Fargione, J.E.; Gough, L.; Gross, K.L.; Pennings, S.C.; Suding, K.N.; Grace, J.B.

2007-01-01

Global energy use and food production have increased nitrogen inputs to ecosystems worldwide, impacting plant community diversity, composition, and function. Previous studies show considerable variation across terrestrial herbaceous ecosystems in the magnitude of species loss following nitrogen (N) enrichment. What controls this variation remains unknown. We present results from 23 N-addition experiments across North America, representing a range of climatic, soil and plant community properties, to determine conditions that lead to greater diversity decline. Species loss in these communities ranged from 0 to 65% of control richness. Using hierarchical structural equation modelling, we found greater species loss in communities with a lower soil cation exchange capacity, colder regional temperature, and larger production increase following N addition, independent of initial species richness, plant productivity, and the relative abundance of most plant functional groups. Our results indicate sensitivity to N addition is co-determined by environmental conditions and production responsiveness, which overwhelm the effects of initial community structure and composition. ?? 2007 Blackwell Publishing Ltd/CNRS.

Structural variant of the intergenic internal ribosome entry site elements in dicistroviruses and computational search for their counterparts

PubMed Central

HATAKEYAMA, YOSHINORI; SHIBUYA, NORIHIRO; NISHIYAMA, TAKASHI; NAKASHIMA, NOBUHIKO

2004-01-01

The intergenic region (IGR) located upstream of the capsid protein gene in dicistroviruses contains an internal ribosome entry site (IRES). Translation initiation mediated by the IRES does not require initiator methionine tRNA. Comparison of the IGRs among dicistroviruses suggested that Taura syndrome virus (TSV) and acute bee paralysis virus have an extra side stem loop in the predicted IRES. We examined whether the side stem is responsible for translation activity mediated by the IGR using constructs with compensatory mutations. In vitro translation analysis showed that TSV has an IGR-IRES that is structurally distinct from those previously described. Because IGR-IRES elements determine the translation initiation site by virtue of their own tertiary structure formation, the discovery of this initiation mechanism suggests the possibility that eukaryotic mRNAs might have more extensive coding regions than previously predicted. To test this hypothesis, we searched full-length cDNA databases and whole genome sequences of eukaryotes using the pattern matching program, Scan For Matches, with parameters that can extract sequences containing secondary structure elements resembling those of IGR-IRES. Our search yielded several sequences, but their predicted secondary structures were suggested to be unstable in comparison to those of dicistroviruses. These results suggest that RNAs structurally similar to dicistroviruses are not common. If some eukaryotic mRNAs are translated independently of an initiator methionine tRNA, their structures are likely to be significantly distinct from those of dicistroviruses. PMID:15100433

Structural Studies on Cytosolic Domain of Magnesium Transporter MgtE from Enterococcus faecalis

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

Ragumani, S.; Sauder, J; Burley, S

2009-01-01

Magnesium (Mg{sup 2+}) is an essential element for growth and maintenance of living cells. It acts as a cofactor for many enzymes and is also essential for stability of the plasma membrane. There are two distinct classes of magnesium transporters identified in bacteria that convey Mg{sup 2+} from periplasm to cytoplasm [ATPase-dependent (MgtA and MgtB) and constitutively active (CorA and MgtE)]. Previously published work on Mg{sup 2+} transporters yielded structures of full length MgtE from Thermus thermophilus, determined at 3.5 {angstrom} resolution, and its cytoplasmic domain with and without bond Mg{sup 2+} determined at 2.3 and 3.9 {angstrom} resolution, respectively.more » Here, they report the crystal structure of the Mg{sup 2+} bound form of the cytosolic portion of MgtE (residues 6-262) from Enterococcus faecalis at 2.2 {angstrom} resolution. The present structure and magnesium bound cytosolic domain structure from T. thermophilus (PDB ID: 2YVY) are structurally similar. Three magnesium binding sites are common to both MgtE full length and the present structure. Their work revealed an additional Mg{sup 2+} binding site in the E. faecalis structure. In this report, they discuss the functional significance of Mg{sup 2+} binding sites in the cytosolic domains of MgtE transporters.« less

Characterization of a mammalian Golgi-localized protein complex, COG, that is required for normal Golgi morphology and function

PubMed Central

Ungar, Daniel; Oka, Toshihiko; Brittle, Elizabeth E.; Vasile, Eliza; Lupashin, Vladimir V.; Chatterton, Jon E.; Heuser, John E.; Krieger, Monty; Waters, M. Gerard

2002-01-01

Multiprotein complexes are key determinants of Golgi apparatus structure and its capacity for intracellular transport and glycoprotein modification. Three complexes that have previously been partially characterized include (a) the Golgi transport complex (GTC), identified in an in vitro membrane transport assay, (b) the ldlCp complex, identified in analyses of CHO cell mutants with defects in Golgi-associated glycosylation reactions, and (c) the mammalian Sec34 complex, identified by homology to yeast Sec34p, implicated in vesicular transport. We show that these three complexes are identical and rename them the conserved oligomeric Golgi (COG) complex. The COG complex comprises four previously characterized proteins (Cog1/ldlBp, Cog2/ldlCp, Cog3/Sec34, and Cog5/GTC-90), three homologues of yeast Sec34/35 complex subunits (Cog4, -6, and -8), and a previously unidentified Golgi-associated protein (Cog7). EM of ldlB and ldlC mutants established that COG is required for normal Golgi morphology. “Deep etch” EM of purified COG revealed an ∼37-nm-long structure comprised of two similarly sized globular domains connected by smaller extensions. Consideration of biochemical and genetic data for mammalian COG and its yeast homologue suggests a model for the subunit distribution within this complex, which plays critical roles in Golgi structure and function. PMID:11980916

Mapping the Binding Interface of VEGF and a Monoclonal Antibody Fab-1 Fragment with Fast Photochemical Oxidation of Proteins (FPOP) and Mass Spectrometry

NASA Astrophysics Data System (ADS)

Zhang, Ying; Wecksler, Aaron T.; Molina, Patricia; Deperalta, Galahad; Gross, Michael L.

2017-05-01

We previously analyzed the Fab-1:VEGF (vascular endothelial growth factor) system described in this work, with both native top-down mass spectrometry and bottom-up mass spectrometry (carboxyl-group or GEE footprinting) techniques. This work continues bottom-up mass spectrometry analysis using a fast photochemical oxidation of proteins (FPOP) platform to map the solution binding interface of VEGF and a fragment antigen binding region of an antibody (Fab-1). In this study, we use FPOP to compare the changes in solvent accessibility by quantitating the extent of oxidative modification in the unbound versus bound states. Determining the changes in solvent accessibility enables the inference of the protein binding sites (epitope and paratopes) and a comparison to the previously published Fab-1:VEGF crystal structure, adding to the top-down and bottom-up data. Using this method, we investigated peptide-level and residue-level changes in solvent accessibility between the unbound proteins and bound complex. Mapping these data onto the Fab-1:VEGF crystal structure enabled successful characterization of both the binding region and regions of remote conformation changes. These data, coupled with our previous higher order structure (HOS) studies, demonstrate the value of a comprehensive toolbox of methods for identifying the putative epitopes and paratopes for biotherapeutic antibodies.

In-situ crystal structure determination of seifertite SiO 2 at 129 GPa: Studying a minor phase near Earth’s core–mantle boundary

DOE PAGES

Zhang, Li; Popov, Dmitry; Meng, Yue; ...

2016-01-01

Seifertite SiO₂ likely exists as a minor phase near the core–mantle boundary. By simulating the pressure and temperature conditions near the core–mantle boundary, seifertite was synthesized as a minor phase in a coarse-grained, polycrystalline sample coexisting with the (Mg,Fe)SiO₃ post-perovskite (pPv) phase at 129 GPa and 2500 K. Here we report the first in situ single-crystal structure determination and refinement of seifertite at high pressure and after a temperature quench from laser heating. We improved the data coverage of a minor phase from a diamond-anvil cell (DAC) by merging single-crystal data of seifertite from six selected grains that had differentmore » orientations. Observed systematic absences of reflections from the six individual grains allowed only one space group: Pbcn. The refined results of seifertite are in good agreement with the predictions from previous first-principles calculations at high pressure. This approach provides a method for structure determination of a minor phase in a mineral assemblage synthesized under P-T conditions representative of the deep Earth.« less

In-situ crystal structure determination of seifertite SiO 2 at 129 GPa: Studying a minor phase near Earth’s core–mantle boundary

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

Zhang, Li; Popov, Dmitry; Meng, Yue

Seifertite SiO₂ likely exists as a minor phase near the core–mantle boundary. By simulating the pressure and temperature conditions near the core–mantle boundary, seifertite was synthesized as a minor phase in a coarse-grained, polycrystalline sample coexisting with the (Mg,Fe)SiO₃ post-perovskite (pPv) phase at 129 GPa and 2500 K. Here we report the first in situ single-crystal structure determination and refinement of seifertite at high pressure and after a temperature quench from laser heating. We improved the data coverage of a minor phase from a diamond-anvil cell (DAC) by merging single-crystal data of seifertite from six selected grains that had differentmore » orientations. Observed systematic absences of reflections from the six individual grains allowed only one space group: Pbcn. The refined results of seifertite are in good agreement with the predictions from previous first-principles calculations at high pressure. This approach provides a method for structure determination of a minor phase in a mineral assemblage synthesized under P-T conditions representative of the deep Earth.« less

Multiple-step preparation and physicochemical characterization of crystalline α-germanium hydrogenphosphate

NASA Astrophysics Data System (ADS)

Romano, Ricardo; Ruiz, Ana I.; Alves, Oswaldo L.

2004-04-01

The reaction between germanium oxide and phosphoric acid has previously been described and led to impure germanium hydrogenphosphate samples with low crystallinity. A new multiple-step route involving the same reaction under refluxing and soft hydrothermal conditions is described for the preparation of pure and crystalline α-GeP. The physicochemical characterization of the samples allows accompaniment of the reaction evolution as well as determining short- and long-range structural organization. The phase purity of the α-GeP sample was confirmed by applying Rietveld's profile analysis, which also determined the cell parameters of its crystals.

Cyclodepsipeptides, sesquiterpenoids, and other cytotoxic metabolites from the filamentous fungus Trichothecium sp. (MSX 51320).

PubMed

Sy-Cordero, Arlene A; Graf, Tyler N; Adcock, Audrey F; Kroll, David J; Shen, Qi; Swanson, Steven M; Wani, Mansukh C; Pearce, Cedric J; Oberlies, Nicholas H

2011-10-28

Two new cyclodepsipeptides (1 and 2), two new sesquiterpenoids (3 and 4), and the known compounds guangomide A (5), roseotoxin S, and three simple trichothecenes were isolated from the cytotoxic organic extract of a terrestrial filamentous fungus, Trichothecium sp. The structures were determined using NMR spectroscopy and mass spectrometry. Absolute configurations of the cyclodepsipeptides were established by employing chiral HPLC, while the relative configurations of 3 and 4 were determined via NOESY data. The isolation of guangomide A was of particular interest, since it was reported previously from a marine-derived fungus.

Phase relations in the Fe-FeSi system at high pressures and temperatures

NASA Astrophysics Data System (ADS)

Fischer, Rebecca A.; Campbell, Andrew J.; Reaman, Daniel M.; Miller, Noah A.; Heinz, Dion L.; Dera, Przymyslaw; Prakapenka, Vitali B.

2013-07-01

The Earth's core is comprised mostly of iron and nickel, but it also contains several weight percent of one or more unknown light elements, which may include silicon. Therefore it is important to understand the high pressure, high temperature properties and behavior of alloys in the Fe-FeSi system, such as their phase diagrams. We determined melting temperatures and subsolidus phase relations of Fe-9 wt% Si and stoichiometric FeSi using synchrotron X-ray diffraction at high pressures and temperatures, up to ~200 GPa and ~145 GPa, respectively. Combining this data with that of previous studies, we generated phase diagrams in pressure-temperature, temperature-composition, and pressure-composition space. We find the B2 crystal structure in Fe-9Si where previous studies reported the less ordered bcc structure, and a shallower slope for the hcp+B2 to fcc+B2 boundary than previously reported. In stoichiometric FeSi, we report a wide B2+B20 two-phase field, with complete conversion to the B2 structure at ~42 GPa. The minimum temperature of an Fe-Si outer core is 4380 K, based on the eutectic melting point of Fe-9Si, and silicon is shown to be less efficient at depressing the melting point of iron at core conditions than oxygen or sulfur. At the highest pressures reached, only the hcp and B2 structures are seen in the Fe-FeSi system. We predict that alloys containing more than ~4-8 wt% silicon will convert to an hcp+B2 mixture and later to the hcp structure with increasing pressure, and that an iron-silicon alloy in the Earth's inner core would most likely be a mixture of hcp and B2 phases.

Phase relations in the Fe-FeSi system at high pressures and temperatures

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

Fischer, Rebecca A.; Campbell, Andrew J.; Reaman, Daniel M.

2016-07-29

The Earth's core is comprised mostly of iron and nickel, but it also contains several weight percent of one or more unknown light elements, which may include silicon. Therefore it is important to understand the high pressure, high temperature properties and behavior of alloys in the Fe–FeSi system, such as their phase diagrams. We determined melting temperatures and subsolidus phase relations of Fe–9 wt% Si and stoichiometric FeSi using synchrotron X-ray diffraction at high pressures and temperatures, up to ~200 GPa and ~145 GPa, respectively. Combining this data with that of previous studies, we generated phase diagrams in pressure–temperature, temperature–composition,more » and pressure–composition space. We find the B2 crystal structure in Fe–9Si where previous studies reported the less ordered bcc structure, and a shallower slope for the hcp+B2 to fcc+B2 boundary than previously reported. In stoichiometric FeSi, we report a wide B2+B20 two-phase field, with complete conversion to the B2 structure at ~42 GPa. The minimum temperature of an Fe–Si outer core is 4380 K, based on the eutectic melting point of Fe–9Si, and silicon is shown to be less efficient at depressing the melting point of iron at core conditions than oxygen or sulfur. At the highest pressures reached, only the hcp and B2 structures are seen in the Fe–FeSi system. We predict that alloys containing more than ~4–8 wt% silicon will convert to an hcp+B2 mixture and later to the hcp structure with increasing pressure, and that an iron–silicon alloy in the Earth's inner core would most likely be a mixture of hcp and B2 phases.« less

The influence of climatic niche preferences on the population genetic structure of a mistletoe species complex.

PubMed

Ramírez-Barahona, Santiago; González, Clementina; González-Rodríguez, Antonio; Ornelas, Juan Francisco

2017-06-01

The prevalent view on genetic structuring in parasitic plants is that host-race formation is caused by varying degrees of host specificity. However, the relative importance of ecological niche divergence and host specificity to population differentiation remains poorly understood. We evaluated the factors associated with population differentiation in mistletoes of the Psittacanthus schiedeanus complex (Loranthaceae) in Mexico. We used genetic data from chloroplast sequences and nuclear microsatellites to study population genetic structure and tested its association with host preferences and climatic niche variables. Pairwise genetic differentiation was associated with environmental and host preferences, independent of geography. However, environmental predictors appeared to be more important than host preferences to explain genetic structure, supporting the hypothesis that the occurrence of the parasite is largely determined by its own climatic niche and, to a lesser degree, by host specificity. Genetic structure is significant within this mistletoe species complex, but the processes associated with this structure appear to be more complex than previously thought. Although host specificity was not supported as the major determinant of population differentiation, we consider this to be part of a more comprehensive ecological model of mistletoe host-race formation that incorporates the effects of climatic niche evolution. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Direct observation of the ferroelectric polarization in the layered perovskite Bi{sub 4}Ti{sub 3}O{sub 12}

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

Urushihara, Daisuke; Asaka, Toru, E-mail: asaka.toru@nitech.ac.jp; Frontier Research Institute for Materials Science, Nagoya Institute of Technology, Nagoya 466-8555

We investigated the crystal structure and ferroelectric domains of Bi{sub 4}Ti{sub 3}O{sub 12} (BTO) by means of transmission electron microscopy (TEM) and single-crystal X-ray diffractometry. From the extinction rule, we determined that the space group in the ferroelectric phase of BTO is P1a1 rather than B2cb and B1a1 which have been proposed previously. We successfully refined the crystal structure based on the space group P1a1. The 180° and 90° ferroelectric domain structures were observed by the [001]-zone dark-field TEM imaging. In the 180° domain structure, we determined that one component of the polarization vector is parallel to the a-axis. Anmore » annular bright-field scanning transmission electron microscopy (ABF-STEM) was performed for the direct observation of the crystal structures. The ABF-STEM images displayed the contrasts with respect to every atomic position in spite of the highly distorted structure of BTO. We could evaluate the tilting and distortion of the [TiO{sub 6}] octahedra relatively. Therefore, we directly observed the ferroelectric displacements of Bi and Ti ions.« less

Structure of the human transcobalamin beta domain in four distinct states

PubMed Central

Bloch, Joël S.; Ruetz, Markus; Kräutler, Bernhard

2017-01-01

Vitamin B12 (cyanocobalamin, CNCbl) is an essential cofactor-precursor for two biochemical reactions in humans. When ingested, cobalamins (Cbl) are transported via a multistep transport system into the bloodstream, where the soluble protein transcobalamin (TC) binds Cbl and the complex is taken up into the cells via receptor mediated endocytosis. Crystal structures of TC in complex with CNCbl have been solved previously. However, the initial steps of holo-TC assembly have remained elusive. Here, we present four crystal structures of the beta domain of human TC (TC-beta) in different substrate-bound states. These include the apo and CNCbl-bound states, providing insight into the early steps of holo-TC assembly. We found that in vitro assembly of TC-alpha and TC-beta to a complex was Cbl-dependent. We also determined the structure of TC-beta in complex with cobinamide (Cbi), an alternative substrate, shedding light on the specificity of TC. We finally determined the structure of TC-beta in complex with an inhibitory antivitamin B12 (anti-B12). We used this structure to model the binding of anti-B12 into full-length holo-TC and could rule out that the inhibitory function of anti-B12 was based on an inability to form a functional complex with TC. PMID:28910388

Structural Health Monitoring of Composite Plates Under Ambient and Cryogenic Conditions

NASA Technical Reports Server (NTRS)

Engberg, Robert C.

2005-01-01

Methods for structural health monitoring are now being assessed, especially in high-performance, extreme environment, safety-critical applications. One such application is for composite cryogenic fuel tanks. The work presented here attempts to characterize and investigate the feasibility of using imbedded piezoelectric sensors to detect cracks and delaminations under cryogenic and ambient conditions. Different types of excitation and response signals and different sensors are employed in composite plate samples to aid in determining an optimal algorithm, sensor placement strategy, and type of imbedded sensor to use. Variations of frequency and high frequency chirps of the sensors are employed and compared. Statistical and analytic techniques are then used to determine which method is most desirable for a specific type of damage and operating environment. These results are furthermore compared with previous work using externally mounted sensors. More work is needed to accurately account for changes in temperature seen in these environments and be statistically significant. Sensor development and placement strategy are other areas of further work to make structural health monitoring more robust. Results from this and other work might then be incorporated into a larger composite structure to validate and assess its structural health. This could prove to be important in the development and qualification of any 2nd generation reusable launch vehicle using composites as a structural element.

Rapid determination of the isomeric truxillines in illicit cocaine via capillary gas chromatography/flame ionization detection and their use and implication in the determination of cocaine origin and trafficking routes.

PubMed

Mallette, Jennifer R; Casale, John F

2014-10-17

The isomeric truxillines are a group of minor alkaloids present in all illicit cocaine samples. The relative amount of truxillines in cocaine is indicative of the variety of coca used for cocaine processing, and thus, is useful in source determination. Previously, the determination of isomeric truxillines in cocaine was performed with a gas chromatography/electron capture detection method. However, due to the tedious sample preparation as well as the expense and maintenance required of electron capture detectors, the protocol was converted to a gas chromatography/flame-ionization detection method. Ten truxilline isomers (alpha-, beta-, delta-, epsilon-, gamma-, omega, zeta-, peri-, neo-, and epi-) were quantified relative to a structurally related internal standard, 4',4″-dimethyl-α-truxillic acid dimethyl ester. The method was shown to have a linear response from 0.001 to 1.00 mg/mL and a lower detection limit of 0.001 mg/mL. In this method, the truxillines are directly reduced with lithium aluminum hydride and then acylated with heptafluorobutyric anhydride prior to analysis. The analysis of more than 100 cocaine hydrochloride samples is presented and compared to data obtained by the previous methodology. Authentic cocaine samples obtained from the source countries of Colombia, Bolivia, and Peru were also analyzed, and comparative data on more than 23,000 samples analyzed over the past 10 years with the previous methodology is presented. Published by Elsevier B.V.

Structure of Human Pancreatic Lipase-Related Protein 2 with the Lid in an Open Conformation

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

Eydoux, Cecilia; Spinelli, Silvia; Davis, Tara L.

2008-10-02

Access to the active site of pancreatic lipase (PL) is controlled by a surface loop, the lid, which normally undergoes conformational changes only upon addition of lipids or amphiphiles. Structures of PL with their lids in the open and functional conformation have required cocrystallization with amphiphiles. Here we report two crystal structures of wild-type and unglycosylated human pancreatic lipase-related protein 2 (HPLRP2) with the lid in an open conformation in the absence of amphiphiles. These structures solved independently are strikingly similar, with some residues of the lid being poorly defined in the electron-density map. The open conformation of the lidmore » is however different from that previously observed in classical liganded PL, suggesting different kinetic properties for HPLRP2. Here we show that the HPLRP2 is directly inhibited by E600, does not present interfacial activation, and acts preferentially on substrates forming monomers or small aggregates (micelles) dispersed in solution like monoglycerides, phospholipids and galactolipids, whereas classical PL displays reverse properties and a high specificity for unsoluble substrates like triglycerides and diglycerides forming oil-in-water interfaces. These biochemical properties imply that the lid of HPLRP2 is likely to spontaneously adopt in solution the open conformation observed in the crystal structure. This open conformation generates a large cavity capable of accommodating the digalactose polar head of galactolipids, similar to that previously observed in the active site of the guinea pig PLRP2, but absent from the classical PL. Most of the structural and kinetic properties of HPLRP2 were found to be different from those of rat PLRP2, the structure of which was previously obtained with the lid in a closed conformation. Our findings illustrate the essential role of the lid in determining the substrate specificity and the mechanism of action of lipases.« less

Structure of human pancreatic lipase-related protein 2 with the lid in an open conformation.

PubMed

Eydoux, Cécilia; Spinelli, Silvia; Davis, Tara L; Walker, John R; Seitova, Alma; Dhe-Paganon, Sirano; De Caro, Alain; Cambillau, Christian; Carrière, Frédéric

2008-09-09

Access to the active site of pancreatic lipase (PL) is controlled by a surface loop, the lid, which normally undergoes conformational changes only upon addition of lipids or amphiphiles. Structures of PL with their lids in the open and functional conformation have required cocrystallization with amphiphiles. Here we report two crystal structures of wild-type and unglycosylated human pancreatic lipase-related protein 2 (HPLRP2) with the lid in an open conformation in the absence of amphiphiles. These structures solved independently are strikingly similar, with some residues of the lid being poorly defined in the electron-density map. The open conformation of the lid is however different from that previously observed in classical liganded PL, suggesting different kinetic properties for HPLRP2. Here we show that the HPLRP2 is directly inhibited by E600, does not present interfacial activation, and acts preferentially on substrates forming monomers or small aggregates (micelles) dispersed in solution like monoglycerides, phospholipids and galactolipids, whereas classical PL displays reverse properties and a high specificity for unsoluble substrates like triglycerides and diglycerides forming oil-in-water interfaces. These biochemical properties imply that the lid of HPLRP2 is likely to spontaneously adopt in solution the open conformation observed in the crystal structure. This open conformation generates a large cavity capable of accommodating the digalactose polar head of galactolipids, similar to that previously observed in the active site of the guinea pig PLRP2, but absent from the classical PL. Most of the structural and kinetic properties of HPLRP2 were found to be different from those of rat PLRP2, the structure of which was previously obtained with the lid in a closed conformation. Our findings illustrate the essential role of the lid in determining the substrate specificity and the mechanism of action of lipases.

Structural identifiability of cyclic graphical models of biological networks with latent variables.

PubMed

Wang, Yulin; Lu, Na; Miao, Hongyu

2016-06-13

Graphical models have long been used to describe biological networks for a variety of important tasks such as the determination of key biological parameters, and the structure of graphical model ultimately determines whether such unknown parameters can be unambiguously obtained from experimental observations (i.e., the identifiability problem). Limited by resources or technical capacities, complex biological networks are usually partially observed in experiment, which thus introduces latent variables into the corresponding graphical models. A number of previous studies have tackled the parameter identifiability problem for graphical models such as linear structural equation models (SEMs) with or without latent variables. However, the limited resolution and efficiency of existing approaches necessarily calls for further development of novel structural identifiability analysis algorithms. An efficient structural identifiability analysis algorithm is developed in this study for a broad range of network structures. The proposed method adopts the Wright's path coefficient method to generate identifiability equations in forms of symbolic polynomials, and then converts these symbolic equations to binary matrices (called identifiability matrix). Several matrix operations are introduced for identifiability matrix reduction with system equivalency maintained. Based on the reduced identifiability matrices, the structural identifiability of each parameter is determined. A number of benchmark models are used to verify the validity of the proposed approach. Finally, the network module for influenza A virus replication is employed as a real example to illustrate the application of the proposed approach in practice. The proposed approach can deal with cyclic networks with latent variables. The key advantage is that it intentionally avoids symbolic computation and is thus highly efficient. Also, this method is capable of determining the identifiability of each single parameter and is thus of higher resolution in comparison with many existing approaches. Overall, this study provides a basis for systematic examination and refinement of graphical models of biological networks from the identifiability point of view, and it has a significant potential to be extended to more complex network structures or high-dimensional systems.

N-Alkyl Urea Hydroxamic Acids as a New Class of Peptide Deformylase Inhibitors with Antibacterial Activity

PubMed Central

Hackbarth, Corinne J.; Chen, Dawn Z.; Lewis, Jason G.; Clark, Kirk; Mangold, James B.; Cramer, Jeffrey A.; Margolis, Peter S.; Wang, Wen; Koehn, Jim; Wu, Charlotte; Lopez, S.; Withers III, George; Gu, Helen; Dunn, Elina; Kulathila, R.; Pan, Shi-Hao; Porter, Wilma L.; Jacobs, Jeff; Trias, Joaquim; Patel, Dinesh V.; Weidmann, Beat; White, Richard J.; Yuan, Zhengyu

2002-01-01

Peptide deformylase (PDF) is a prokaryotic metalloenzyme that is essential for bacterial growth and is a new target for the development of antibacterial agents. All previously reported PDF inhibitors with sufficient antibacterial activity share the structural feature of a 2-substituted alkanoyl at the P1′ site. Using a combination of iterative parallel synthesis and traditional medicinal chemistry, we have identified a new class of PDF inhibitors with N-alkyl urea at the P1′ site. Compounds with MICs of ≤4 μg/ml against gram-positive and gram-negative pathogens, including Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae, have been identified. The concentrations needed to inhibit 50% of enzyme activity (IC50s) for Escherichia coli Ni-PDF were ≤0.1 μM, demonstrating the specificity of the inhibitors. In addition, these compounds were very selective for PDF, with IC50s of consistently >200 μM for matrilysin and other mammalian metalloproteases. Structure-activity relationship analysis identified preferred substitutions resulting in improved potency and decreased cytotoxity. One of the compounds (VRC4307) was cocrystallized with PDF, and the enzyme-inhibitor structure was determined at a resolution of 1.7 Å. This structural information indicated that the urea compounds adopt a binding position similar to that previously determined for succinate hydroxamates. Two compounds, VRC4232 and VRC4307, displayed in vivo efficacy in a mouse protection assay, with 50% protective doses of 30.8 and 17.9 mg/kg of body weight, respectively. These N-alkyl urea hydroxamic acids provide a starting point for identifying new PDF inhibitors that can serve as antimicrobial agents. PMID:12183225

Radio-continuum survey of the Coma/A1367 supercluster. IV - 1.4 GHz observations of CGCG galaxies

NASA Astrophysics Data System (ADS)

del Castillo, E.; Gavazzi, G.; Jaffe, W.

1988-05-01

1.4 GHz radio-continuum observations of 148 CGCG galaxies in the Coma supercluster region were obtained with the VLA in C array configuration. Comparison with previous measurements at 0.6 GHz leads to an average spectral index >α< = 0.8. The structures of 29 galaxies in this region determined with high-resolution VLA (A array) observations are presented.

Mean field approximation for biased diffusion on Japanese inter-firm trading network.

PubMed

Watanabe, Hayafumi

2014-01-01

By analysing the financial data of firms across Japan, a nonlinear power law with an exponent of 1.3 was observed between the number of business partners (i.e. the degree of the inter-firm trading network) and sales. In a previous study using numerical simulations, we found that this scaling can be explained by both the money-transport model, where a firm (i.e. customer) distributes money to its out-edges (suppliers) in proportion to the in-degree of destinations, and by the correlations among the Japanese inter-firm trading network. However, in this previous study, we could not specifically identify what types of structure properties (or correlations) of the network determine the 1.3 exponent. In the present study, we more clearly elucidate the relationship between this nonlinear scaling and the network structure by applying mean-field approximation of the diffusion in a complex network to this money-transport model. Using theoretical analysis, we obtained the mean-field solution of the model and found that, in the case of the Japanese firms, the scaling exponent of 1.3 can be determined from the power law of the average degree of the nearest neighbours of the network with an exponent of -0.7.

RNA Thermodynamic Structural Entropy

PubMed Central

Garcia-Martin, Juan Antonio; Clote, Peter

2015-01-01

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner’99 and Turner’04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs. PMID:26555444

RNA Thermodynamic Structural Entropy.

PubMed

Garcia-Martin, Juan Antonio; Clote, Peter

2015-01-01

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs.

Effects of experimentally measured pressure oscillations on the vibration of a solid rocket motor

NASA Technical Reports Server (NTRS)

Schoenster, J. A.; Pierce, H. B.

1972-01-01

Results are presented of firing a Nike rocket against a backstop for the purpose of obtaining pressure fluctuations in the rocket case and determining their relationship to structural vibrations of the case. Special care was required to obtain these pressure fluctuations because of the much higher static pressure generated in the rocket. Very small pressure fluctuations within the rocket case can cause significant vibration levels. A previously observed high frequency was shown to decrease with time before completely disappearing at about 1 second of burning time. The vibration of the case itself is probably related to the longitudinal structural modes at frequencies below 500 Hz and is dependent on local structural conditions at frequencies above this value.

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

PubMed Central

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

2006-01-01

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

How Life History Can Sway the Fixation Probability of Mutants

PubMed Central

Li, Xiang-Yi; Kurokawa, Shun; Giaimo, Stefano; Traulsen, Arne

2016-01-01

In this work, we study the effects of demographic structure on evolutionary dynamics when selection acts on reproduction, survival, or both. In contrast to the previously discovered pattern that the fixation probability of a neutral mutant decreases while the population becomes younger, we show that a mutant with a constant selective advantage may have a maximum or a minimum of the fixation probability in populations with an intermediate fraction of young individuals. This highlights the importance of life history and demographic structure in studying evolutionary dynamics. We also illustrate the fundamental differences between selection on reproduction and selection on survival when age structure is present. In addition, we evaluate the relative importance of size and structure of the population in determining the fixation probability of the mutant. Our work lays the foundation for also studying density- and frequency-dependent effects in populations when demographic structures cannot be neglected. PMID:27129737

Analysis of the local structure around Cr3+ centers in perovskite KMgF3 using both ab initio (DFT) and semi-empirical (SPM) calculations

NASA Astrophysics Data System (ADS)

Emül, Y.; Erbahar, D.; Açıkgöz, M.

2014-11-01

The local structure around Cr3+ centers in perovskite KMgF3 crystal have been investigated through the applications of both an ab-initio, density functional theory (DFT), and a semi empirical, superposition model (SPM), analyses. A supercell approach is used for DFT calculations. All the tetragonal (Cr3+-VMg and Cr3+-Li+), trigonal (Cr3+-VK), and CrF5O cluster centers have been considered with various structural models based on the previously suggested experimental inferences. The significant structural changes around the Cr3+ centers induced by Mg2+ or K+ vacancies and the Li substitution at those vacancy sites have been determined and discussed by means of charge distribution. This study provides insight on both the roles of Mg2+ and K+ vacancies and Li+ ion in the local structural properties around Cr3+ centers in KMgF3.

The role of predictability and structure in word stress processing: an ERP study on Cairene Arabic and a cross-linguistic comparison

PubMed Central

Domahs, Ulrike; Knaus, Johannes A.; El Shanawany, Heba; Wiese, Richard

2014-01-01

This article presents neurolinguistic data on word stress perception in Cairene Arabic, in comparison to previous results on German and Turkish. The main goal is to investigate how central properties of stress systems such as predictability of stress and metrical structure are reflected in the prosodic processing of words. Cairene Arabic is a language with a regular foot-based word stress system, leading to highly predictable placement of word stress. An ERP study on Cairene Arabic is reported, in which a stress violation paradigm is used to investigate the factors predictability of stress and foot structure. The results of the experiment show that for Cairene Arabic the internal structure of prosodic words in terms of feet determines prosodic processing. This structure effect is complemented by a frequency effect for stress patterns. PMID:25374546

Structure-based inhibitors of tau aggregation

NASA Astrophysics Data System (ADS)

Seidler, P. M.; Boyer, D. R.; Rodriguez, J. A.; Sawaya, M. R.; Cascio, D.; Murray, K.; Gonen, T.; Eisenberg, D. S.

2018-02-01

Aggregated tau protein is associated with over 20 neurological disorders, which include Alzheimer's disease. Previous work has shown that tau's sequence segments VQIINK and VQIVYK drive its aggregation, but inhibitors based on the structure of the VQIVYK segment only partially inhibit full-length tau aggregation and are ineffective at inhibiting seeding by full-length fibrils. Here we show that the VQIINK segment is the more powerful driver of tau aggregation. Two structures of this segment determined by the cryo-electron microscopy method micro-electron diffraction explain its dominant influence on tau aggregation. Of practical significance, the structures lead to the design of inhibitors that not only inhibit tau aggregation but also inhibit the ability of exogenous full-length tau fibrils to seed intracellular tau in HEK293 biosensor cells into amyloid. We also raise the possibility that the two VQIINK structures represent amyloid polymorphs of tau that may account for a subset of prion-like strains of tau.

Reverse engineering the cooperative machinery of human hemoglobin.

PubMed

Ren, Zhong

2013-01-01

Hemoglobin transports molecular oxygen from the lungs to all human tissues for cellular respiration. Its α2β2 tetrameric assembly undergoes cooperative binding and releasing of oxygen for superior efficiency and responsiveness. Over past decades, hundreds of hemoglobin structures were determined under a wide range of conditions for investigation of molecular mechanism of cooperativity. Based on a joint analysis of hemoglobin structures in the Protein Data Bank (Ren, companion article), here I present a reverse engineering approach to elucidate how two subunits within each dimer reciprocate identical motions that achieves intradimer cooperativity, how ligand-induced structural signals from two subunits are integrated to drive quaternary rotation, and how the structural environment at the oxygen binding sites alter their binding affinity. This mechanical model reveals the intricate design that achieves the cooperative mechanism and has previously been masked by inconsistent structural fluctuations. A number of competing theories on hemoglobin cooperativity and broader protein allostery are reconciled and unified.

Structure of Toxoplasma gondii fructose-1,6-bisphosphate aldolase.

PubMed

Boucher, Lauren E; Bosch, Jürgen

2014-09-01

The apicomplexan parasite Toxoplasma gondii must invade host cells to continue its lifecycle. It invades different cell types using an actomyosin motor that is connected to extracellular adhesins via the bridging protein fructose-1,6-bisphosphate aldolase. During invasion, aldolase serves in the role of a structural bridging protein, as opposed to its normal enzymatic role in the glycolysis pathway. Crystal structures of the homologous Plasmodium falciparum fructose-1,6-bisphosphate aldolase have been described previously. Here, T. gondii fructose-1,6-bisphosphate aldolase has been crystallized in space group P22121, with the biologically relevant tetramer in the asymmetric unit, and the structure has been determined via molecular replacement to a resolution of 2.0 Å. An analysis of the quality of the model and of the differences between the four chains in the asymmetric unit and a comparison between the T. gondii and P. falciparum aldolase structures is presented.

Analysis of the Structures and Properties of (GaSb)n (n = 4-9) Clusters through Density Functional Theory.

PubMed

Lu, Qi Liang; Luo, Qi Quan; Huang, Shou Guo; Li, Yi De; Wan, Jian Guo

2016-07-07

An optimization strategy combining global semiempirical quantum mechanical search with all-electron density functional theory was adopted to determine the lowest energy structure of (GaSb)n clusters up to n = 9. The growth pattern of the clusters differed from those of previously reported group III-V binary clusters. A cagelike configuration was found for cluster sizes n ≤ 7. The structure of (GaSb)6 deviated from that of other III-V clusters. Competition existed between core-shell and hollow cage structures of (GaSb)7. Novel noncagelike structures were energetically preferred over the cages for the (GaSb)8 and (GaSb)9 clusters. Electronic properties, such as vertical ionization potential, adiabatic electron affinities, HOMO-LUMO gaps, and average on-site charges on Ga or Sb atoms, as well as binding energies, were computed.

Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease.

PubMed

Carss, Keren J; Arno, Gavin; Erwood, Marie; Stephens, Jonathan; Sanchis-Juan, Alba; Hull, Sarah; Megy, Karyn; Grozeva, Detelina; Dewhurst, Eleanor; Malka, Samantha; Plagnol, Vincent; Penkett, Christopher; Stirrups, Kathleen; Rizzo, Roberta; Wright, Genevieve; Josifova, Dragana; Bitner-Glindzicz, Maria; Scott, Richard H; Clement, Emma; Allen, Louise; Armstrong, Ruth; Brady, Angela F; Carmichael, Jenny; Chitre, Manali; Henderson, Robert H H; Hurst, Jane; MacLaren, Robert E; Murphy, Elaine; Paterson, Joan; Rosser, Elisabeth; Thompson, Dorothy A; Wakeling, Emma; Ouwehand, Willem H; Michaelides, Michel; Moore, Anthony T; Webster, Andrew R; Raymond, F Lucy

2017-01-05

Inherited retinal disease is a common cause of visual impairment and represents a highly heterogeneous group of conditions. Here, we present findings from a cohort of 722 individuals with inherited retinal disease, who have had whole-genome sequencing (n = 605), whole-exome sequencing (n = 72), or both (n = 45) performed, as part of the NIHR-BioResource Rare Diseases research study. We identified pathogenic variants (single-nucleotide variants, indels, or structural variants) for 404/722 (56%) individuals. Whole-genome sequencing gives unprecedented power to detect three categories of pathogenic variants in particular: structural variants, variants in GC-rich regions, which have significantly improved coverage compared to whole-exome sequencing, and variants in non-coding regulatory regions. In addition to previously reported pathogenic regulatory variants, we have identified a previously unreported pathogenic intronic variant in CHM in two males with choroideremia. We have also identified 19 genes not previously known to be associated with inherited retinal disease, which harbor biallelic predicted protein-truncating variants in unsolved cases. Whole-genome sequencing is an increasingly important comprehensive method with which to investigate the genetic causes of inherited retinal disease. Copyright © 2017. Published by Elsevier Inc.

Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data.

PubMed

Xu, Nan; Veesler, David; Doerschuk, Peter C; Johnson, John E

2018-05-01

The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways. First, instead of imposing icosahedral symmetry on every particle in the data set during the variance analysis, we only assume that the data set as a whole has icosahedral symmetry. This change removes artifacts of high variance along icosahedral symmetry axes, but retains all of the features previously reported in the HK97 data set. Second we present a covariance analysis that reveals correlations in structural dynamics (variance) between the interior of the HK97 procapsid with the protease and regions of the exterior (not seen in the absence of the protease). The latter analysis corresponds well with hydrogen deuterium exchange studies previously published that reveal the same correlation. Copyright © 2018 Elsevier Inc. All rights reserved.

GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition

PubMed Central

2011-01-01

Background Calculation of the root mean square deviation (RMSD) between the atomic coordinates of two optimally superposed structures is a basic component of structural comparison techniques. We describe a quaternion based method, GPU-Q-J, that is stable with single precision calculations and suitable for graphics processor units (GPUs). The application was implemented on an ATI 4770 graphics card in C/C++ and Brook+ in Linux where it was 260 to 760 times faster than existing unoptimized CPU methods. Source code is available from the Compbio website http://software.compbio.washington.edu/misc/downloads/st_gpu_fit/ or from the author LHH. Findings The Nutritious Rice for the World Project (NRW) on World Community Grid predicted de novo, the structures of over 62,000 small proteins and protein domains returning a total of 10 billion candidate structures. Clustering ensembles of structures on this scale requires calculation of large similarity matrices consisting of RMSDs between each pair of structures in the set. As a real-world test, we calculated the matrices for 6 different ensembles from NRW. The GPU method was 260 times faster that the fastest existing CPU based method and over 500 times faster than the method that had been previously used. Conclusions GPU-Q-J is a significant advance over previous CPU methods. It relieves a major bottleneck in the clustering of large numbers of structures for NRW. It also has applications in structure comparison methods that involve multiple superposition and RMSD determination steps, particularly when such methods are applied on a proteome and genome wide scale. PMID:21453553

1.8 Å structure of murine GITR ligand dimer expressed in Drosophila melanogaster S2 cells

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

Chattopadhyay, Kausik; Ramagopal, Udupi A.; Nathenson, Stanley G., E-mail: nathenso@aecom.yu.edu

2009-05-01

1.8 Å X-ray crystal structure of mouse GITRL expressed in D. melanogaster S2 cells shows an identical ‘strand-exchanged’ dimeric assembly similar to that observed previously for the E. coli-expressed protein. Glucocorticoid-induced TNF receptor ligand (GITRL), a prominent member of the TNF superfamily, activates its receptor on both effector and regulatory T cells to generate critical costimulatory signals that have been implicated in a wide range of T-cell immune functions. The crystal structures of murine and human orthologs of GITRL recombinantly expressed in Escherichia coli have previously been determined. In contrast to all classical TNF structures, including the human GITRL structure,more » murine GITRL demonstrated a unique ‘strand-exchanged’ dimeric organization. Such a novel assembly behavior indicated a dramatic impact on receptor activation as well as on the signaling mechanism associated with the murine GITRL costimulatory system. In this present work, the 1.8 Å resolution crystal structure of murine GITRL expressed in Drosophila melanogaster S2 cells is reported. The eukaryotic protein-expression system allows transport of the recombinant protein into the extracellular culture medium, thus maximizing the possibility of obtaining correctly folded material devoid of any folding/assembly artifacts that are often suspected with E. coli-expressed proteins. The S2 cell-expressed murine GITRL adopts an identical ‘strand-exchanged’ dimeric structure to that observed for the E. coli-expressed protein, thus conclusively demonstrating the novel quaternary structure assembly behavior of murine GITRL.« less

X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: evidence for photoreductive dissociation of the iron-cyanide bond

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

de Serrano, V.S.; Davis, M.F.; Gaff, J.F.

X-ray crystal structures of the metcyano form of dehaloperoxidase-hemoglobin (DHP A) from Amphitrite ornata (DHPCN) and the C73S mutant of DHP A (C73SCN) were determined using synchrotron radiation in order to further investigate the geometry of diatomic ligands coordinated to the heme iron. The DHPCN structure was also determined using a rotating-anode source. The structures show evidence of photoreduction of the iron accompanied by dissociation of bound cyanide ion (CN{sup -}) that depend on the intensity of the X-ray radiation and the exposure time. The electron density is consistent with diatomic molecules located in two sites in the distal pocketmore » of DHPCN. However, the identities of the diatomic ligands at these two sites are not uniquely determined by the electron-density map. Consequently, density functional theory calculations were conducted in order to determine whether the bond lengths, angles and dissociation energies are consistent with bound CN{sup -} or O{sub 2} in the iron-bound site. In addition, molecular-dynamics simulations were carried out in order to determine whether the dynamics are consistent with trapped CN{sup -} or O{sub 2} in the second site of the distal pocket. Based on these calculations and comparison with a previously determined X-ray crystal structure of the C73S-O{sub 2} form of DHP [de Serrano et al. (2007), Acta Cryst. D63, 1094-1101], it is concluded that CN{sup -} is gradually replaced by O{sub 2} as crystalline DHP is photoreduced at 100 K. The ease of photoreduction of DHP A is consistent with the reduction potential, but suggests an alternative activation mechanism for DHP A compared with other peroxidases, which typically have reduction potentials that are 0.5 V more negative. The lability of CN{sup -} at 100 K suggests that the distal pocket of DHP A has greater flexibility than most other hemoglobins.« less

Experimental correlation of melt structures, nucleation rates, and thermal histories of silicate melts

NASA Technical Reports Server (NTRS)

Boynton, W. V.; DRAKE; HILDEBRAND; JONES; LEWIS; TREIMAN; WARK

1987-01-01

The theory and measurement of the structure of liquids is an important aspect of modern metallurgy and igneous petrology. Liquid structure exerts strong controls on both the types of crystals that may precipitate from melts and on the chemical composition of those crystals. An interesting aspect of melt structure studies is the problem of melt memories; that is, a melt can retain a memory of previous thermal history. This memory can influence both nucleation behavior and crystal composition. This melt memory may be characterized quantitatively with techniques such as Raman, infrared and NMR spectroscopy to provide information on short-range structure. Melt structure studies at high temperature will take advantage of the microgravity conditions of the Space Station to perform containerless experiments. Melt structure determinations at high temperature (experiments that are greatly facilitated by containerless technology) will provide invaluable information for materials science, glass technology, and geochemistry. In conjunction with studies of nucleation behavior and nucleation rates, information relevant to nucleation in magma chambers in terrestrial planets will be acquired.

Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1

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

Lewis-Ballester, Ariel; Pham, Khoa N.; Batabyal, Dipanwita

Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an attractive cancer immunotherapeutic target owing to its role in promoting tumoral immune escape. However, drug development has been hindered by limited structural information. Here, we report the crystal structures of hIDO1 in complex with its substrate, Trp, an inhibitor, epacadostat, and/or an effector, indole ethanol (IDE). The data reveal structural features of the active site (Sa) critical for substrate activation; in addition, they disclose a new inhibitor-binding mode and a distinct small molecule binding site (Si). Structure-guided mutation of a critical residue, F270, to glycine perturbs the Si site, allowing structural determination ofmore » an inhibitory complex, where both the Sa and Si sites are occupied by Trp. The Si site offers a novel target site for allosteric inhibitors and a molecular explanation for the previously baffling substrate-inhibition behavior of the enzyme. Taken together, the data open exciting new avenues for structure-based drug design.« less

Revision of the Li13Si4 structure.

PubMed

Zeilinger, Michael; Fässler, Thomas F

2013-11-06

Besides Li17Si4, Li16.42Si4, and Li15Si4, another lithium-rich representative in the Li-Si system is the phase Li13Si4 (trideca-lithium tetra-silicide), the structure of which has been determined previously [Frank et al. (1975 ▶). Z. Naturforsch. Teil B, 30, 10-13]. A careful analysis of X-ray diffraction patterns of Li13Si4 revealed discrepancies between experimentally observed and calculated Bragg positions. Therefore, we redetermined the structure of Li13Si4 on the basis of single-crystal X-ray diffraction data. Compared to the previous structure report, decisive differences are (i) the introduction of a split position for one Li site [occupancy ratio 0.838 (7):0.162 (7)], (ii) the anisotropic refinement of atomic displacement parameters for all atoms, and (iii) a high accuracy of atom positions and unit-cell parameters. The asymmetric unit of Li13Si4 contains two Si and seven Li atoms. Except for one Li atom situated on a site with symmetry 2/m, all other atoms are on mirror planes. The structure consists of isolated Si atoms as well as Si-Si dumbbells surrounded by Li atoms. Each Si atom is either 12- or 13-coordinated. The isolated Si atoms are situated in the ab plane at z = 0 and are strictly separated from the Si-Si dumbbells at z = 0.5.

Identification and structural characterization of O-beta-ribosyl-(1"----2')-adenosine-5"-phosphate in yeast methionine initiator tRNA.

PubMed Central

Keith, G; Glasser, A L; Desgrès, J; Kuo, K C; Gehrke, C W

1990-01-01

We report in this paper on the complete structure determination of the modified nucleotide A*, now called Ar(p), that was previously identified in yeast methionine initiator tRNA as an isomeric form of O-ribosyl-adenosine bearing an additional phosphoryl-monoester group on its ribose2 moiety. By using the chemical procedure of periodate oxidation and subsequent beta-elimination with cyclohexylamine on mono- and dinucleotides containing Ar(p), we characterized the location of the phosphate group on the C-5" of the ribose2 moiety, and the linkage between the two riboses as a (1"----2')-glycosidic bond. Since the structural difference between phosphatase treated Ar(p) and authentic O-alpha-ribosyl-(1"----2')-adenosine from poly(ADP-Ribose) was previously assigned to an isomeric difference in the ribose2-ribose1 linkage, the (1"----2')-glycosidic bond of Ar(p) was deduced to have a beta-spatial configuration. Thus, final chemical structure for Ar(p) at the position 64 in yeast initiator tRNA(Met) has been established as O-beta-ribosyl-(1"----2')-adenosine-5"-phosphate. This nucleotide is linked by a 3',5'-phosphodiester bond to G at the position 65. PMID:2235481

Unraveling the meaning of chemical shifts in protein NMR.

PubMed

Berjanskii, Mark V; Wishart, David S

2017-11-01

Chemical shifts are among the most informative parameters in protein NMR. They provide wealth of information about protein secondary and tertiary structure, protein flexibility, and protein-ligand binding. In this report, we review the progress in interpreting and utilizing protein chemical shifts that has occurred over the past 25years, with a particular focus on the large body of work arising from our group and other Canadian NMR laboratories. More specifically, this review focuses on describing, assessing, and providing some historical context for various chemical shift-based methods to: (1) determine protein secondary and super-secondary structure; (2) derive protein torsion angles; (3) assess protein flexibility; (4) predict residue accessible surface area; (5) refine 3D protein structures; (6) determine 3D protein structures and (7) characterize intrinsically disordered proteins. This review also briefly covers some of the methods that we previously developed to predict chemical shifts from 3D protein structures and/or protein sequence data. It is hoped that this review will help to increase awareness of the considerable utility of NMR chemical shifts in structural biology and facilitate more widespread adoption of chemical-shift based methods by the NMR spectroscopists, structural biologists, protein biophysicists, and biochemists worldwide. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV

NASA Technical Reports Server (NTRS)

Lim, Kap; Ho, Joseph X.; Keeling, Kim; Gilliland, Gary L.; Ji, Xinhua; Rueker, Florian; Carter, Daniel C.

1994-01-01

The 3-dimensional crystal structure of glutathione S-transferase (GST) of Schistosoma japonicum (Sj) fused with a conserved neutralizing epitope on gp41 (glycoprotein, 41 kDa) of human immunodeficiency virus type 1 (HIV-1) was determined at 2.5 A resolution. The structure of the 3-3 isozyme rat GST of the mu gene class was used as a molecular replacement model. The structure consists of a 4-stranded beta-sheet and 3 alpha-helices in domain 1 and 5 alpha-helices in domain 2. The space group of the Sj GST crystal is P4(sub 3)2(sub 1)2 with unit cell dimensions of a = b = 94.7 A, and c = 58.1 A. The crystal has 1 GST monomer per asymmetric unit, and 2 monomers that form an active dimer are related by crystallographic 2-fold symmetry. In the binding site, the ordered structure of reduced glutathione is observed. The gp41 peptide (Glu-Leu-Asp-Lys-Trp-Ala) fused to the C-terminus of Sj GST forms a loop stabilized by symmetry-related GSTs. The Sj GST structure is compared with previously determined GST structures of mammalian gene classes mu, alpha, and pi. Conserved amino acid residues among the 4 GSTs that are important for hydrophobic and hydrophilic interactions for dimer association and glutathione binding are discussed.

A structural analysis of small vapor-deposited 'multiply twinned' gold particles

NASA Technical Reports Server (NTRS)

Yang, C. Y.; Heinemann, K.; Yacaman, M. J.; Poppa, H.

1979-01-01

High resolution selected zone dark field, Bragg reflection imaging and weak beam dark field techniques of transmission electron microscopy were used to determine the structure of small gold particles vapor deposited on NaCl substrates. Attention was focused on the analysis of those particles in the 50-150 A range that have pentagonal or hexagonal bright field profiles. These particles have been previously described as multiply twinned crystallites composed of face-centered cubic tetrahedra. The experimental evidence of the present studies can be interpreted on the assumption that the particle structure is a regular icosahedron or decahedron for the hexagonal or the pentagonal particles respectively. The icosahedron is a multiply twinned rhombohedral crystal and the decahedron is a multiply twinned body-centered orthorhombic crystal, each of which constitutes a slight distortion from the face-centered cubic structure.

Structure-function analysis of the auxilin J-domain reveals an extended Hsc70 interaction interface.

PubMed

Jiang, Jianwen; Taylor, Alexander B; Prasad, Kondury; Ishikawa-Brush, Yumiko; Hart, P John; Lafer, Eileen M; Sousa, Rui

2003-05-20

J-domains are widespread protein interaction modules involved in recruiting and stimulating the activity of Hsp70 family chaperones. We have determined the crystal structure of the J-domain of auxilin, a protein which is involved in uncoating clathrin-coated vesicles. Comparison to the known structures of J-domains from four other proteins reveals that the auxilin J-domain is the most divergent of all J-domain structures described to date. In addition to the canonical J-domain features described previously, the auxilin J-domain contains an extra N-terminal helix and a long loop inserted between helices I and II. The latter loop extends the positively charged surface which forms the Hsc70 binding site, and is shown by directed mutagenesis and surface plasmon resonance to contain side chains important for binding to Hsc70.

Water content and structure in malignant and benign skin tumours

NASA Astrophysics Data System (ADS)

Gniadecka, M.; Nielsen, O. F.; Wulf, H. C.

2003-12-01

Analysis of the low frequency region of Raman spectra enables determination of water structure. It has been previously demonstrated by various techniques that water content and possibly also the water structure is altered in some malignant tumours. To further elucidate possible change in water structure in tumours we performed NIR FT Raman spectroscopy on biopsies from selected benign and malignant skin tumours (benign: seborrheic keratosis, pigmented nevi; malignant: malignant melanoma, basal cell carcinoma). We did not observe any differences in water content between malignant and benign skin tumours with an exception of seborrheic keratosis, in which the water content was decreased. Increase in the tetrahedral (free) water was found in malignant skin tumours and sun-damaged skin relative to normal young skin and benign skin tumours. This finding may add to the understanding of molecular alterations in cancer.

Sequence-dependent effects in drug-DNA interaction: the crystal structure of Hoechst 33258 bound to the d(CGCAAATTTGCG)2 duplex.

PubMed Central

Spink, N; Brown, D G; Skelly, J V; Neidle, S

1994-01-01

The bis-benzimidazole drug Hoechst 33258 has been co-crystallized with the dodecanucleotide sequence d(CGCAAATTTGCG)2. The structure has been solved by molecular replacement and refined to an R factor of 18.5% for 2125 reflections collected on a Xentronics area detector. The drug is bound in the minor groove, at the five base-pair site 5'-ATTTG and is in a unique orientation. This is displaced by one base pair in the 5' direction compared to previously-determined structures of this drug with the sequence d(CGCGAATTCGCG)2. Reasons for this difference in behaviour are discussed in terms of several sequence-dependent structural features of the DNA, with particular reference to differences in propeller twist and minor-groove width. Images PMID:7515488

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

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

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

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

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

Wurzburg, Beth A.; Tarchevskaya, Svetlana S.; Jardetzky, Theodore S.

CD23, the low-affinity receptor for IgE (Fc{var_epsilon}RII), regulates IgE synthesis and also mediates IgE-dependent antigen transport and processing. CD23 is a unique Fc receptor belonging to the C-type lectin-like domain superfamily and binds IgE in an unusual, non-lectin-like manner, requiring calcium but not carbohydrate. We have solved the high-resolution crystal structures of the human CD23 lectin domain in the presence and absence of Ca{sup 2+}. The crystal structures differ significantly from a previously determined NMR structure and show that calcium binding occurs at the principal binding site, but not at an auxiliary site that appears to be absent in humanmore » CD23. Conformational differences between the apo and Ca{sup 2+} bound structures suggest how IgE-Fc binding can be both calcium-dependent and carbohydrate-independent.« less

Crystal Structure of the N-Terminal Half of the Traffic Controller UL37 from Herpes Simplex Virus 1

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

Koenigsberg, Andrea L.; Heldwein, Ekaterina E.; Sandri-Goldin, Rozanne M.

Inner tegument protein UL37 is conserved among all three subfamilies of herpesviruses. Studies of UL37 homologs from two alphaherpesviruses, herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV), have suggested that UL37 plays an essential albeit poorly defined role in intracellular capsid trafficking. At the same time, HSV and PRV homologs cannot be swapped, which suggests that in addition to a conserved function, UL37 homologs also have divergent virus-specific functions. Accurate dissection of UL37 functions requires detailed maps in the form of atomic-resolution structures. Previously, we reported the crystal structure of the N-terminal half of UL37 (UL37N) from PRV. Here,more » we report the crystal structure of HSV-1 UL37N. Comparison of the two structures reveals that UL37 homologs differ in their overall shapes, distributions of surface charges, and locations of projecting loops. In contrast, the previously identified R2 surface region is structurally conserved. We propose that within the N-terminal half of UL37, functional conservation is centered within the R2 surface region, whereas divergent structural elements pinpoint regions mediating virus-specific functions and may engage different binding partners. Together, the two structures can now serve as templates for a structure-guided exploration of both conserved and virus-specific functions of UL37. IMPORTANCEThe ability to move efficiently within host cell cytoplasm is essential for replication in all viruses. It is especially important in the neuroinvasive alphaherpesviruses, such as human herpes simplex virus 1 (HSV-1), HSV-2, and veterinarian pseudorabies virus (PRV), that infect the peripheral nervous system and have to travel long distances along axons. Capsid movement in these viruses is controlled by capsid-associated tegument proteins, yet their specific roles have not yet been defined. Systematic exploration of the roles of tegument proteins in capsid trafficking requires detailed navigational charts in the form of their three-dimensional structures. Here, we determined the crystal structure of the N-terminal half of a conserved tegument protein, UL37, from HSV-1. This structure, along with our previously reported structure of the UL37 homolog from PRV, provides a much needed 3-dimensional template for the dissection of both conserved and virus-specific functions of UL37 in intracellular capsid trafficking.« less

Structural Comparison of Different Antibodies Interacting with Parvovirus Capsids

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

Hafenstein, Susan; Bowman, Valorie D.; Sun, Tao

2009-05-13

The structures of canine parvovirus (CPV) and feline parvovirus (FPV) complexed with antibody fragments from eight different neutralizing monoclonal antibodies were determined by cryo-electron microscopy (cryoEM) reconstruction to resolutions varying from 8.5 to 18 {angstrom}. The crystal structure of one of the Fab molecules and the sequence of the variable domain for each of the Fab molecules have been determined. The structures of Fab fragments not determined crystallographically were predicted by homology modeling according to the amino acid sequence. Fitting of the Fab and virus structures into the cryoEM densities identified the footprints of each antibody on the viral surface.more » As anticipated from earlier analyses, the Fab binding sites are directed to two epitopes, A and B. The A site is on an exposed part of the surface near an icosahedral threefold axis, whereas the B site is about equidistant from the surrounding five-, three-, and twofold axes. One antibody directed to the A site binds CPV but not FPV. Two of the antibodies directed to the B site neutralize the virus as Fab fragments. The differences in antibody properties have been linked to the amino acids within the antibody footprints, the position of the binding site relative to the icosahedral symmetry elements, and the orientation of the Fab structure relative to the surface of the virus. Most of the exposed surface area was antigenic, although each of the antibodies had a common area of overlap that coincided with the positions of the previously mapped escape mutations.« less

A voxel-based asymmetry study of the relationship between hemispheric asymmetry and language dominance in Wada tested patients.

PubMed

Keller, Simon S; Roberts, Neil; Baker, Gus; Sluming, Vanessa; Cezayirli, Enis; Mayes, Andrew; Eldridge, Paul; Marson, Anthony G; Wieshmann, Udo C

2018-03-23

Determining the anatomical basis of hemispheric language dominance (HLD) remains an important scientific endeavor. The Wada test remains the gold standard test for HLD and provides a unique opportunity to determine the relationship between HLD and hemispheric structural asymmetries on MRI. In this study, we applied a whole-brain voxel-based asymmetry (VBA) approach to determine the relationship between interhemispheric structural asymmetries and HLD in a large consecutive sample of Wada tested patients. Of 135 patients, 114 (84.4%) had left HLD, 10 (7.4%) right HLD, and 11 (8.2%) bilateral language representation. Fifty-four controls were also studied. Right-handed controls and right-handed patients with left HLD had comparable structural brain asymmetries in cortical, subcortical, and cerebellar regions that have previously been documented in healthy people. However, these patients and controls differed in structural asymmetry of the mesial temporal lobe and a circumscribed region in the superior temporal gyrus, suggesting that only asymmetries of these regions were due to brain alterations caused by epilepsy. Additional comparisons between patients with left and right HLD, matched for type and location of epilepsy, revealed that structural asymmetries of insula, pars triangularis, inferior temporal gyrus, orbitofrontal cortex, ventral temporo-occipital cortex, mesial somatosensory cortex, and mesial cerebellum were significantly associated with the side of HLD. Patients with right HLD and bilateral language representation were significantly less right-handed. These results suggest that structural asymmetries of an insular-fronto-temporal network may be related to HLD. © 2018 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Structure of Importin-α from a Filamentous Fungus in Complex with a Classical Nuclear Localization Signal.

PubMed

Bernardes, Natalia E; Takeda, Agnes A S; Dreyer, Thiago R; Freitas, Fernanda Z; Bertolini, Maria Célia; Fontes, Marcos R M

2015-01-01

Neurospora crassa is a filamentous fungus that has been extensively studied as a model organism for eukaryotic biology, providing fundamental insights into cellular processes such as cell signaling, growth and differentiation. To advance in the study of this multicellular organism, an understanding of the specific mechanisms for protein transport into the cell nucleus is essential. Importin-α (Imp-α) is the receptor for cargo proteins that contain specific nuclear localization signals (NLSs) that play a key role in the classical nuclear import pathway. Structures of Imp-α from different organisms (yeast, rice, mouse, and human) have been determined, revealing that this receptor possesses a conserved structural scaffold. However, recent studies have demonstrated that the Impα mechanism of action may vary significantly for different organisms or for different isoforms from the same organism. Therefore, structural, functional, and biophysical characterization of different Impα proteins is necessary to understand the selectivity of nuclear transport. Here, we determined the first crystal structure of an Impα from a filamentous fungus which is also the highest resolution Impα structure already solved to date (1.75 Å). In addition, we performed calorimetric analysis to determine the affinity and thermodynamic parameters of the interaction between Imp-α and the classical SV40 NLS peptide. The comparison of these data with previous studies on Impα proteins led us to demonstrate that N. crassa Imp-α possess specific features that are distinct from mammalian Imp-α but exhibit important similarities to rice Imp-α, particularly at the minor NLS binding site.

The constant region affects antigen binding of antibodies to DNA by altering secondary structure.

PubMed

Xia, Yumin; Janda, Alena; Eryilmaz, Ertan; Casadevall, Arturo; Putterman, Chaim

2013-11-01

We previously demonstrated an important role of the constant region in the pathogenicity of anti-DNA antibodies. To determine the mechanisms by which the constant region affects autoantibody binding, a panel of isotype-switch variants (IgG1, IgG2a, IgG2b) was generated from the murine PL9-11 IgG3 autoantibody. The affinity of the PL9-11 antibody panel for histone was measured by surface plasmon resonance (SPR). Tryptophan fluorescence was used to determine wavelength shifts of the antibody panel upon binding to DNA and histone. Finally, circular dichroism spectroscopy was used to measure changes in secondary structure. SPR analysis revealed significant differences in histone binding affinity between members of the PL9-11 panel. The wavelength shifts of tryptophan fluorescence emission were found to be dependent on the antibody isotype, while circular dichroism analysis determined that changes in antibody secondary structure content differed between isotypes upon antigen binding. Thus, the antigen binding affinity is dependent on the particular constant region expressed. Moreover, the effects of antibody binding to antigen were also constant region dependent. Alteration of secondary structures influenced by constant regions may explain differences in fine specificity of anti-DNA antibodies between antibodies with similar variable regions, as well as cross-reactivity of anti-DNA antibodies with non-DNA antigens. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

Li, Yan-Rong; Wang, Jian-Min; Bai, Jin-Ming, E-mail: liyanrong@mail.ihep.ac.cn

Broad emission lines of active galactic nuclei stem from a spatially extended region (broad-line region, BLR) that is composed of discrete clouds and photoionized by the central ionizing continuum. The temporal behaviors of these emission lines are blurred echoes of continuum variations (i.e., reverberation mapping, RM) and directly reflect the structures and kinematic information of BLRs through the so-called transfer function (also known as the velocity-delay map). Based on the previous works of Rybicki and Press and Zu et al., we develop an extended, non-parametric approach to determine the transfer function for RM data, in which the transfer function ismore » expressed as a sum of a family of relatively displaced Gaussian response functions. Therefore, arbitrary shapes of transfer functions associated with complicated BLR geometry can be seamlessly included, enabling us to relax the presumption of a specified transfer function frequently adopted in previous studies and to let it be determined by observation data. We formulate our approach in a previously well-established framework that incorporates the statistical modeling of continuum variations as a damped random walk process and takes into account long-term secular variations which are irrelevant to RM signals. The application to RM data shows the fidelity of our approach.« less

Structures and Activity of New Anabaenopeptins Produced by Baltic Sea Cyanobacteria.

PubMed

Spoof, Lisa; Błaszczyk, Agata; Meriluoto, Jussi; Cegłowska, Marta; Mazur-Marzec, Hanna

2015-12-30

Anabaenopeptins, bioactive cyclic hexapeptides, were isolated by preparative reversed-phase high performance liquid chromatography from an extract of Baltic Sea cyanobacterial bloom material composed of Nodularia spumigena (50%), Aphanizomenon flos-aquae (40%) and Dolichospermum spp. (10%). Five new anabaenopeptins and nine previously known anabaenopeptins were isolated, and their putative structures were determined by tandem mass spectrometry. The activity of the peptides against carboxypeptidase A and protein phosphatase 1 as well as chymotrypsin, trypsin and thrombin was tested. All anabaenopeptins inhibited carboxypeptidase A (apart from one anabaenopeptin variant) and protein phosphatase 1 with varying potency, but no inhibition against chymotrypsin, trypsin and thrombin was observed.

Micro-crystallography comes of age

PubMed Central

Smith, Janet L.; Fischetti, Robert F.; Yamamoto, Masaki

2012-01-01

The latest revolution in macromolecular crystallography was incited by the development of dedicated, user friendly, micro-crystallography beamlines. Brilliant X-ray beams of diameter 20 microns or less, now available at most synchrotron sources, enable structure determination from samples that previously were inaccessible. Relative to traditional crystallography, crystals with one or more small dimensions have diffraction patterns with vastly improved signal-to-noise when recorded with an appropriately matched beam size. Structures can be solved from isolated, well diffracting regions within inhomogeneous samples. This review summarizes the technological requirements and approaches to producing micro-beams and how they continue to change the practice of crystallography. PMID:23021872

Use of Small Angle Neutron Scattering to Study Various Properties of Wool and Mohair Fibres

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

Franklyn, C. B.; Toeroek, Gy.

2011-12-13

To maintain a competitive edge in the wool and mohair industry, a detailed knowledge and understanding of the properties of wool fibres is essential. Standard techniques are used to determine fibre diameter, length and strength; however, properties such as hydroscopicity, lustre and changes in fibre structure following chemical or mechanical treatment are not so well understood. The unique capabilities of small angle neutron scattering to study changes in the supermolecular structure of wool fibres, particularly at the level of the microfibril-matrix complex, have been used to provide previously unknown features of the fibres. The results of these studies are presented.

Flame Structure and Scalar Properties in Microgravity Laminar Fires

NASA Technical Reports Server (NTRS)

Feikema, D. A.; Lim, J.; Sivathanu, Y.

2006-01-01

Recent results from microgravity combustion experiments conducted in the Zero Gravity Facility (ZGF) 5.18 second drop tower are reported. Emission mid-infrared spectroscopy measurements have been completed to quantitatively determine the flame temperature, water and carbon dioxide vapor concentrations, radiative emissive power, and soot concentrations in a microgravity laminar ethylene/air flame. The ethylene/air laminar flame conditions are similar to previously reported experiments including the Flight Project, Laminar Soot Processes (LSP). Soot concentrations and gas temperatures are in reasonable agreement with similar results available in the literature. However, soot concentrations and flame structure dramatically change in long duration microgravity laminar diffusion flames as demonstrated in this paper.

Least-squares sequential parameter and state estimation for large space structures

NASA Technical Reports Server (NTRS)

Thau, F. E.; Eliazov, T.; Montgomery, R. C.

1982-01-01

This paper presents the formulation of simultaneous state and parameter estimation problems for flexible structures in terms of least-squares minimization problems. The approach combines an on-line order determination algorithm, with least-squares algorithms for finding estimates of modal approximation functions, modal amplitudes, and modal parameters. The approach combines previous results on separable nonlinear least squares estimation with a regression analysis formulation of the state estimation problem. The technique makes use of sequential Householder transformations. This allows for sequential accumulation of matrices required during the identification process. The technique is used to identify the modal prameters of a flexible beam.

The CADSS design automation system. [computerized design language for small digital systems

NASA Technical Reports Server (NTRS)

Franke, E. A.

1973-01-01

This research was designed to implement and extend a previously defined design automation system for the design of small digital structures. A description is included of the higher level language developed to describe systems as a sequence of register transfer operations. The system simulator which is used to determine if the original description is correct is also discussed. The design automation system produces tables describing the state transistions of the system and the operation of all registers. In addition all Boolean equations specifying system operation are minimized and converted to NAND gate structures. Suggestions for further extensions to the system are also given.

Evidence that Intraspecific Trait Variation among Nasal Bacteria Shapes the Distribution of Staphylococcus aureus

PubMed Central

Libberton, Ben; Coates, Rosanna E.

2014-01-01

Nasal carriage of Staphylococcus aureus is a risk factor for infection, yet the bacterial determinants required for carriage are poorly defined. Interactions between S. aureus and other members of the bacterial flora may determine colonization and have been inferred in previous studies by using correlated species distributions. However, traits mediating species interactions are often polymorphic, suggesting that understanding how interactions structure communities requires a trait-based approach. We characterized S. aureus growth inhibition by the culturable bacterial aerobe consortia of 60 nasal microbiomes, and this revealed intraspecific variation in growth inhibition and that inhibitory isolates clustered within communities that were culture negative for S. aureus. Across microbiomes, the cumulative community-level growth inhibition was negatively associated with S. aureus incidence. To fully understand the ecological processes structuring microbiomes, it will be crucial to account for intraspecific variation in the traits that mediate species interactions. PMID:24980973

The primary structure of aspartate aminotransferase from pig heart muscle. Partial sequences determined by digestion with thermolysin and elastase

PubMed Central

Bossa, Francesco; Barra, Donatella; Carloni, Massimo; Fasella, Paolo; Riva, Francesca; Doonan, Shawn; Doonan, Hilary J.; Hanford, Robin; Vernon, Charles A.; Walker, John M.

1973-01-01

Peptides produced by thermolytic digestion of aminoethylated aspartate aminotransferase and of the oxidized enzyme were isolated and their amino acid sequences determined. Digestion by elastase of the carboxymethylated enzyme gave peptides representing approximately 40% of the primary structure. Fragments from these digests overlapped with previously reported sequences of peptides obtained by peptic and tryptic digestion (Doonan et al., 1972), giving ten composite peptides containing 395 amino acid residues. The amino acid composition of these composite peptides agrees well with that of the intact enzyme. Confirmatory results for some of the present data have been deposited as Supplementary Publication 50018 at the National Lending Library for Science and Technology, Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1973) 131, 5. PMID:4748834

Characterization of the Deoxyguanosine–Lysine Cross-Link of Methylglyoxal

PubMed Central

2015-01-01

Methylglyoxal is a mutagenic bis-electrophile that is produced endogenously from carbohydrate precursors. Methylglyoxal has been reported to induce DNA–protein cross-links (DPCs) in vitro and in cultured cells. Previous work suggests that these cross-links are formed between guanine and either lysine or cysteine side chains. However, the chemical nature of the methylglyoxal induced DPC have not been determined. We have examined the reaction of methylglyoxal, deoxyguanosine (dGuo), and Nα-acetyllysine (AcLys) and determined the structure of the cross-link to be the N2-ethyl-1-carboxamide with the lysine side chain amino group (1). The cross-link was identified by mass spectrometry and the structure confirmed by comparison to a synthetic sample. Further, the cross-link between methylglyoxal, dGuo, and a peptide (AcAVAGKAGAR) was also characterized. The mechanism of cross-link formation is likely to involve an Amadori rearrangement. PMID:24801980

Estrogenic activity of constituents from the rhizomes of Rheum undulatum Linné.

PubMed

Park, SeonJu; Kim, Yun Na; Kwak, Hee Jae; Jeong, Eun Ju; Kim, Seung Hyun

2018-02-15

Stilbenes have been reported to be phytoestrogen compounds owing to its structural similarity to the estrogenic agent diethylstilbestrol. To find new stilbene-derivative phytoestrogens, isolation of stilbene-rich R. undulatum was performed and led to identify six new compounds (1-5 and 28), one newly determined absolute configurations compound (27) together with 21 previously reported compounds (6-26). The structures of compounds were determined on the basis of extensive spectroscopic methods including 1D and 2D NMR and CD spectra data. All the isolated compounds were tested for their estrogenic activities in HepG2 cells transiently transfected with ERα, ERβ and ERE-reporter plasmid. Among them, stilbene-derivatives, piceatannol 3'-O-β-d-xylopyranoside (12), cis-rhaponticin (16) and rhapontigenin 3'-O-β-d-glucopyranoside (17), showed the more potent binding affinity for estrogen receptors than 17β-estrodiol. Copyright © 2018 Elsevier Ltd. All rights reserved.

An economic prediction of the finer resolution level wavelet coefficients in electronic structure calculations.

PubMed

Nagy, Szilvia; Pipek, János

2015-12-21

In wavelet based electronic structure calculations, introducing a new, finer resolution level is usually an expensive task, this is why often a two-level approximation is used with very fine starting resolution level. This process results in large matrices to calculate with and a large number of coefficients to be stored. In our previous work we have developed an adaptively refined solution scheme that determines the indices, where the refined basis functions are to be included, and later a method for predicting the next, finer resolution coefficients in a very economic way. In the present contribution, we would like to determine whether the method can be applied for predicting not only the first, but also the other, higher resolution level coefficients. Also the energy expectation values of the predicted wave functions are studied, as well as the scaling behaviour of the coefficients in the fine resolution limit.

A putative siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis

PubMed Central

Trindade, Inês B.; Fonseca, Bruno M.; Matias, Pedro M.; Louro, Ricardo O.; Moe, Elin

2016-01-01

Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacterium Shewanella frigidimarina NCIMB 400, the gene tagged as SFRI_RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this protein are reported, together with its preliminary X-ray crystallographic analysis to 1.35 Å resolution. The SIP crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 48.04, b = 78.31, c = 67.71 Å, α = 90, β = 99.94, γ = 90°, and are predicted to contain two molecules per asymmetric unit. Structure determination by molecular replacement and the use of previously determined ∼2 Å resolution SIP structures with ∼30% sequence identity as templates are ongoing. PMID:27599855

Solid-phase extraction NMR studies of chromatographic fractions of saponins from Quillaja saponaria.

PubMed

Nyberg, Nils T; Baumann, Herbert; Kenne, Lennart

2003-01-15

The saponin mixture QH-B from the tree Quillaja saponaria var. Molina was fractionated by RP-HPLC in several steps. The fractions were analyzed by solid-phase extraction NMR (SPE-NMR), a technique combining the workup by solid-phase extraction with on-line coupling to an NMR flow probe. Together with MALDI-TOF mass spectrometry and comparison with chemical shifts of similar saponins, the structures of both major and minor components in QH-B could be obtained. The procedure described is a simple method to determine the structure of components in a complex mixture. The two major fractions of the mixture were found to contain at least 28 saponins, differing in the carbohydrate substructures. Eight of these have not previously been determined. The 28 saponins formed 14 equilibrium pairs by the migration of an O-acyl group between two adjacent positions on a fucosyl residue.

Atomic resolution ADF-STEM imaging of organic molecular crystal of halogenated copper phthalocyanine.

PubMed

Haruta, Mitsutaka; Yoshida, Kaname; Kurata, Hiroki; Isoda, Seiji

2008-05-01

Annular dark-field (ADF) scanning transmission electron microscopy (STEM) measurements are demonstrated for the first time to be applicable for acquiring Z-contrast images of organic molecules at atomic resolution. High-angle ADF imaging by STEM is a new technique that provides incoherent high-resolution Z-contrast images for organic molecules. In the present study, low-angle ADF-STEM is successfully employed to image the molecular crystal structure of hexadecachloro-Cu-phthalocyanine (Cl16-CuPc), an organic molecule. The structures of CuPc derivatives (polyhalogenated CuPc with Br and Cl) are determined quantitatively using the same technique to determine the occupancy of halogens at each chemical site. By comparing the image contrasts of atomic columns, the occupancy of Br is found to be ca. 56% at the inner position, slightly higher than that for random substitution and in good agreement with previous TEM results.

SdsA polymorph isolation and improvement of their crystal quality using nonconventional crystallization techniques

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

De la Mora, Eugenio; Flores-Hernández, Edith; Jakoncic, Jean

SdsA, a sodium dodecyl sulfate hydrolase, from Pseudomonas aeruginosa was crystallized in three different crystal polymorphs and their three-dimensional structure was determined. The different polymorphs present different crystal packing habits. One of the polymorphs suggests the existence of a tetramer, an oligomeric state not observed previously, while the crystal packing of the remaining two polymorphs obstructs the active site entrance but stabilizes flexible regions of the protein. Nonconventional crystallization methods that minimize convection, such as counterdiffusion in polyvinyl alcohol gel coupled with the influence of a 500 MHz (10.2 T) magnetic field, were necessary to isolate the poorest diffracting polymorphmore » and increase its internal order to determine its structure by X-ray diffraction. In conclusion, the results obtained show the effectiveness of nonconventional crystallographic methods to isolate different crystal polymorphs.« less

Structural characterization of the thermally tolerant pectin methylesterase purified from citrus sinensis fruit and its gene sequence.

PubMed

Savary, Brett J; Vasu, Prasanna; Cameron, Randall G; McCollum, T Gregory; Nuñez, Alberto

2013-12-26

Despite the longstanding importance of the thermally tolerant pectin methylesterase (TT-PME) activity in citrus juice processing and product quality, the unequivocal identification of the protein and its corresponding gene has remained elusive. TT-PME was purified from sweet orange [ Citrus sinensis (L.) Osbeck] finisher pulp (8.0 mg/1.3 kg tissue) with an improved purification scheme that provided 20-fold increased enzyme yield over previous results. Structural characterization of electrophoretically pure TT-PME by MALDI-TOF MS determined molecular masses of approximately 47900 and 53000 Da for two principal glycoisoforms. De novo sequences generated from tryptic peptides by MALDI-TOF/TOF MS matched multiple anonymous Citrus EST cDNA accessions. The complete tt-pme cDNA (1710 base pair) was cloned from a fruit mRNA library using RT- and RLM-RACE PCR. Citrus TT-PME is a novel isoform that showed higher sequence identity with the multiply glycosylated kiwifruit PME than to previously described Citrus thermally labile PME isoforms.

Complete Sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta: Gene arrangements indicate that platyhelminths are eutrochozoans

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

von Nickisch-Rosenegk, Markus; Brown, Wesley M.; Boore, Jeffrey L.

2001-01-01

Using ''long-PCR'' we have amplified in overlapping fragments the complete mitochondrial genome of the tapeworm Hymenolepis diminuta (Platyhelminthes: Cestoda) and determined its 13,900 nucleotide sequence. The gene content is the same as that typically found for animal mitochondrial DNA (mtDNA) except that atp8 appears to be lacking, a condition found previously for several other animals. Despite the small size of this mtDNA, there are two large non-coding regions, one of which contains 13 repeats of a 31 nucleotide sequence and a potential stem-loop structure of 25 base pairs with an 11-member loop. Large potential secondary structures are identified also formore » the non-coding regions of two other cestode mtDNAs. Comparison of the mitochondrial gene arrangement of H. diminuta with those previously published supports a phylogenetic position of flatworms as members of the Eutrochozoa, rather than being basal to either a clade of protostomes or a clade of coelomates.« less

Accuracy Assessment in Determining the Location of Corners of Building Structures Using a Combination of Various Measurement Methods

NASA Astrophysics Data System (ADS)

Krzyżek, Robert; Przewięźlikowska, Anna

2017-12-01

When surveys of corners of building structures are carried out, surveyors frequently use a compilation of two surveying methods. The first one involves the determination of several corners with reference to a geodetic control using classical methods of surveying field details. The second method relates to the remaining corner points of a structure, which are determined in sequence from distance-distance intersection, using control linear values of the wall faces of the building, the so-called tie distances. This paper assesses the accuracy of coordinates of corner points of a building structure, determined using the method of distance-distance intersection, based on the corners which had previously been determined by the conducted surveys tied to a geodetic control. It should be noted, however, that such a method of surveying the corners of building structures from linear measures is based on the details of the first-order accuracy, while the regulations explicitly allow such measurement only for the details of the second- and third-order accuracy. Therefore, a question arises whether this legal provision is unfounded, or whether surveyors are acting not only against the applicable standards but also without due diligence while performing surveys? This study provides answers to the formulated problem. The main purpose of the study was to verify whether the actual method which is used in practice for surveying building structures allows to obtain the required accuracy of coordinates of the points being determined, or whether it should be strictly forbidden. The results of the conducted studies clearly demonstrate that the problem is definitely more complex. Eventually, however, it might be assumed that assessment of the accuracy in determining a location of corners of a building using a combination of two different surveying methods will meet the requirements of the regulation [MIA, 2011), subject to compliance with relevant baseline criteria, which have been presented in this study. Observance of the proposed boundary conditions would allow for frequent performance of surveys of building structures by surveyors (from tie distances), while maintaining the applicable accuracy criteria. This would allow for the inclusion of surveying documentation into the national geodetic and cartographic documentation center database pursuant to the legal bases.

Prediction of Ras-effector interactions using position energy matrices.

PubMed

Kiel, Christina; Serrano, Luis

2007-09-01

One of the more challenging problems in biology is to determine the cellular protein interaction network. Progress has been made to predict protein-protein interactions based on structural information, assuming that structural similar proteins interact in a similar way. In a previous publication, we have determined a genome-wide Ras-effector interaction network based on homology models, with a high accuracy of predicting binding and non-binding domains. However, for a prediction on a genome-wide scale, homology modelling is a time-consuming process. Therefore, we here successfully developed a faster method using position energy matrices, where based on different Ras-effector X-ray template structures, all amino acids in the effector binding domain are sequentially mutated to all other amino acid residues and the effect on binding energy is calculated. Those pre-calculated matrices can then be used to score for binding any Ras or effector sequences. Based on position energy matrices, the sequences of putative Ras-binding domains can be scanned quickly to calculate an energy sum value. By calibrating energy sum values using quantitative experimental binding data, thresholds can be defined and thus non-binding domains can be excluded quickly. Sequences which have energy sum values above this threshold are considered to be potential binding domains, and could be further analysed using homology modelling. This prediction method could be applied to other protein families sharing conserved interaction types, in order to determine in a fast way large scale cellular protein interaction networks. Thus, it could have an important impact on future in silico structural genomics approaches, in particular with regard to increasing structural proteomics efforts, aiming to determine all possible domain folds and interaction types. All matrices are deposited in the ADAN database (http://adan-embl.ibmc.umh.es/). Supplementary data are available at Bioinformatics online.

Structural and functional characterization of two unusual endonuclease III enzymes from Deinococcus radiodurans.

PubMed

Sarre, Aili; Ökvist, Mats; Klar, Tobias; Hall, David R; Smalås, Arne O; McSweeney, Sean; Timmins, Joanna; Moe, Elin

2015-08-01

While most bacteria possess a single gene encoding the bifunctional DNA glycosylase Endonuclease III (EndoIII) in their genomes, Deinococcus radiodurans possesses three: DR2438 (DrEndoIII1), DR0289 (DrEndoIII2) and DR0982 (DrEndoIII3). Here we have determined the crystal structures of DrEndoIII1 and an N-terminally truncated form of DrEndoIII3 (DrEndoIII3Δ76). We have also generated a homology model of DrEndoIII2 and measured activity of the three enzymes. All three structures consist of two all α-helical domains, one of which exhibits a [4Fe-4S] cluster and the other a HhH-motif, separated by a DNA binding cleft, similar to previously determined structures of endonuclease III from Escherichia coli and Geobacillus stearothermophilus. However, both DrEndoIII1 and DrEndoIII3 possess an extended HhH motif with extra helical features and an altered electrostatic surface potential. In addition, the DNA binding cleft of DrEndoIII3 seems to be less accessible for DNA interactions, while in DrEndoIII1 it seems to be more open. Analysis of the enzyme activities shows that DrEndoIII2 is most similar to the previously studied enzymes, while DrEndoIII1 seems to be more distant with a weaker activity towards substrate DNA containing either thymine glycol or an abasic site. DrEndoIII3 is the most distantly related enzyme and displays no detectable activity towards these substrates even though the suggested catalytic residues are conserved. Based on a comparative structural analysis, we suggest that the altered surface potential, shape of the substrate-binding pockets and specific amino acid substitutions close to the active site and in the DNA interacting loops may underlie the unexpected differences in activity. Copyright © 2015 Elsevier Inc. All rights reserved.

Crystal structure of tetra-kis-(μ3-2-{[1,1-bis-(hy-droxy-meth-yl)-2-oxidoeth-yl]imino-meth-yl}-6-meth-oxy-phenolato)tetra-kis-[aqua-copper(II)]: a redetermination at 200 K.

PubMed

Buvaylo, Elena A; Vassilyeva, Olga Yu; Skelton, Brian W

2015-10-01

The crystal structure of the tetra-nuclear title compound, [Cu4(C12H15NO5)4(H2O)4], has been previously reported by Back, Oliveira, Canabarro & Iglesias [Z. Anorg. Allg. Chem. (2015), 641, 941-947], based on room-temperature data. In the previously published structure, no standard uncertainties are recorded for the deprotonated hy-droxy-methyl group and water mol-ecule O atoms coordinating to the metal atom indicating that they were not refined; furthermore, the H atoms of some OH groups and water mol-ecules have not been positioned accurately. Since the current structure was determined at a lower temperature, all atoms, including the H atoms of these hy-droxy groups and the water mol-ecule, have been determined more accurately resulting in improved standard uncertainties in the bond lengths and angles. Diffraction data were collected at 200 K, rather than the more usual 100 K, due to apparent disordering at lower temperatures. In addition, it is now possible to report intra- and inter-molecular O-H⋯O inter-actions. In the title complex molecule, which has crystallographic -4 symmetry, the Cu(II) ions are coordinated by the tridentate Schiff base ligands and water mol-ecules, forming a tetra-nuclear Cu4O4 cubane-like core. The Cu(II) ion adopts a CuNO5 elongated octa-hedral environment. The coordination environment of Cu(II) at 200 K displays a small contraction of the Cu-N/O bonds, compared with the room-temperature structure. In the crystal lattice, the neutral clusters are linked by inter-molecular O-H⋯O hydrogen bonds into a one-dimensional hydrogen-bonding network propagating along the b axis.

Characterization of highly efficient heavy-ion mutagenesis in Arabidopsis thaliana.

PubMed

Kazama, Yusuke; Hirano, Tomonari; Saito, Hiroyuki; Liu, Yang; Ohbu, Sumie; Hayashi, Yoriko; Abe, Tomoko

2011-11-15

Heavy-ion mutagenesis is recognised as a powerful technology to generate new mutants, especially in higher plants. Heavy-ion beams show high linear energy transfer (LET) and thus more effectively induce DNA double-strand breaks than other mutagenic techniques. Previously, we determined the most effective heavy-ion LET (LETmax: 30.0 keV μm(-1)) for Arabidopsis mutagenesis by analysing the effect of LET on mutation induction. However, the molecular structure of mutated DNA induced by heavy ions with LETmax remains unclear. Knowledge of the structure of mutated DNA will contribute to the effective exploitation of heavy-ion beam mutagenesis. Dry Arabidopsis thaliana seeds were irradiated with carbon (C) ions with LETmax at a dose of 400 Gy and with LET of 22.5 keV μm(-1) at doses of 250 Gy or 450 Gy. The effects on mutation frequency and alteration of DNA structure were compared. To characterise the structure of mutated DNA, we screened the well-characterised mutants elongated hypocotyls (hy) and glabrous (gl) and identified mutated DNA among the resulting mutants by high-resolution melting curve, PCR and sequencing analyses. The mutation frequency induced by C ions with LETmax was two-fold higher than that with 22.5 keV μm(-1) and similar to the mutation frequency previously induced by ethyl methane sulfonate. We identified the structure of 22 mutated DNAs. Over 80% of the mutations caused by C ions with both LETs were base substitutions or deletions/insertions of less than 100 bp. The other mutations involved large rearrangements. The C ions with LETmax showed high mutation efficiency and predominantly induced base substitutions or small deletions/insertions, most of which were null mutations. These small alterations can be determined by single-nucleotide polymorphism (SNP) detection systems. Therefore, C ions with LETmax might be useful as a highly efficient reverse genetic system in conjunction with SNP detection systems, and will be beneficial for forward genetics and plant breeding.

``Making the Molecular Movie'': First Frames

NASA Astrophysics Data System (ADS)

Miller, R. J. Dwayne

2011-03-01

Femtosecond Electron Diffraction has enabled atomic resolution to structural changes as they occur, essentially watching atoms move in real time--directly observe transition states. This experiment has been referred to as ``making the molecular movie'' and has been previously discussed in the context of a gedanken experiment. With the recent development of femtosecond electron pulses with sufficient number density to execute single shot structure determinations, this experiment has been finally realized. A new concept in electron pulse generation was developed based on a solution to the N-body electron propagation problem involving up to 10,000 interacting electrons that has led to a new generation of extremely bright electron pulsed sources that minimizes space charge broadening effects. Previously thought intractable problems of determining t=0 and fully characterizing electron pulses on the femtosecond time scale have now been solved through the use of the laser pondermotive potential to provide a time dependent scattering source. Synchronization of electron probe and laser excitation pulses is now possible with an accuracy of 10 femtoseconds to follow even the fastest nuclear motions. The camera for the ``molecular movie'' is well in hand based on high bunch charge electron sources. Several movies depicting atomic motions during passage through structural transitions will be shown. Atomic level views of the simplest possible structural transition, melting, will be presented for a number of systems in which both thermal and purely electronically driven atomic displacements can be correlated to the degree of directional bonding. Optical manipulation of charge distributions and effects on interatomic forces/bonding can be directly observed through the ensuing atomic motions. New phenomena involving strongly correlated electron systems will be presented in which an exceptionally cooperative phase transitions has been observed. The primitive origin of molecular cooperativity has also been discovered in recent studies of molecular crystals. These new developments will be discussed in the context of developing the necessary technology to directly observe the structure-function correlation in biomolecules--the fundamental molecular basis of biological systems.

Structural implications of weak Ca2+ block in Drosophila cyclic nucleotide–gated channels

PubMed Central

Lam, Yee Ling; Zeng, Weizhong; Derebe, Mehabaw Getahun

2015-01-01

Calcium permeability and the concomitant calcium block of monovalent ion current (“Ca2+ block”) are properties of cyclic nucleotide–gated (CNG) channel fundamental to visual and olfactory signal transduction. Although most CNG channels bear a conserved glutamate residue crucial for Ca2+ block, the degree of block displayed by different CNG channels varies greatly. For instance, the Drosophila melanogaster CNG channel shows only weak Ca2+ block despite the presence of this glutamate. We previously constructed a series of chimeric channels in which we replaced the selectivity filter of the bacterial nonselective cation channel NaK with a set of CNG channel filter sequences and determined that the resulting NaK2CNG chimeras displayed the ion selectivity and Ca2+ block properties of the parent CNG channels. Here, we used the same strategy to determine the structural basis of the weak Ca2+ block observed in the Drosophila CNG channel. The selectivity filter of the Drosophila CNG channel is similar to that of most other CNG channels except that it has a threonine at residue 318 instead of a proline. We constructed a NaK chimera, which we called NaK2CNG-Dm, which contained the Drosophila selectivity filter sequence. The high resolution structure of NaK2CNG-Dm revealed a filter structure different from those of NaK and all other previously investigated NaK2CNG chimeric channels. Consistent with this structural difference, functional studies of the NaK2CNG-Dm chimeric channel demonstrated a loss of Ca2+ block compared with other NaK2CNG chimeras. Moreover, mutating the corresponding threonine (T318) to proline in Drosophila CNG channels increased Ca2+ block by 16 times. These results imply that a simple replacement of a threonine for a proline in Drosophila CNG channels has likely given rise to a distinct selectivity filter conformation that results in weak Ca2+ block. PMID:26283200

Structural implications of weak Ca2+ block in Drosophila cyclic nucleotide-gated channels.

PubMed

Lam, Yee Ling; Zeng, Weizhong; Derebe, Mehabaw Getahun; Jiang, Youxing

2015-09-01

Calcium permeability and the concomitant calcium block of monovalent ion current ("Ca(2+) block") are properties of cyclic nucleotide-gated (CNG) channel fundamental to visual and olfactory signal transduction. Although most CNG channels bear a conserved glutamate residue crucial for Ca(2+) block, the degree of block displayed by different CNG channels varies greatly. For instance, the Drosophila melanogaster CNG channel shows only weak Ca(2+) block despite the presence of this glutamate. We previously constructed a series of chimeric channels in which we replaced the selectivity filter of the bacterial nonselective cation channel NaK with a set of CNG channel filter sequences and determined that the resulting NaK2CNG chimeras displayed the ion selectivity and Ca(2+) block properties of the parent CNG channels. Here, we used the same strategy to determine the structural basis of the weak Ca(2+) block observed in the Drosophila CNG channel. The selectivity filter of the Drosophila CNG channel is similar to that of most other CNG channels except that it has a threonine at residue 318 instead of a proline. We constructed a NaK chimera, which we called NaK2CNG-Dm, which contained the Drosophila selectivity filter sequence. The high resolution structure of NaK2CNG-Dm revealed a filter structure different from those of NaK and all other previously investigated NaK2CNG chimeric channels. Consistent with this structural difference, functional studies of the NaK2CNG-Dm chimeric channel demonstrated a loss of Ca(2+) block compared with other NaK2CNG chimeras. Moreover, mutating the corresponding threonine (T318) to proline in Drosophila CNG channels increased Ca(2+) block by 16 times. These results imply that a simple replacement of a threonine for a proline in Drosophila CNG channels has likely given rise to a distinct selectivity filter conformation that results in weak Ca(2+) block. © 2015 Lam et al.

Text Mining for Protein Docking

PubMed Central

Badal, Varsha D.; Kundrotas, Petras J.; Vakser, Ilya A.

2015-01-01

The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking). Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu). The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features) approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound benchmark set, significantly increasing the docking success rate. PMID:26650466

X-ray structure of acid-sensing ion channel 1-snake toxin complex reveals open state of a Na(+)-selective channel.

PubMed

Baconguis, Isabelle; Bohlen, Christopher J; Goehring, April; Julius, David; Gouaux, Eric

2014-02-13

Acid-sensing ion channels (ASICs) detect extracellular protons produced during inflammation or ischemic injury and belong to the superfamily of degenerin/epithelial sodium channels. Here, we determine the cocrystal structure of chicken ASIC1a with MitTx, a pain-inducing toxin from the Texas coral snake, to define the structure of the open state of ASIC1a. In the MitTx-bound open state and in the previously determined low-pH desensitized state, TM2 is a discontinuous α helix in which the Gly-Ala-Ser selectivity filter adopts an extended, belt-like conformation, swapping the cytoplasmic one-third of TM2 with an adjacent subunit. Gly 443 residues of the selectivity filter provide a ring of three carbonyl oxygen atoms with a radius of ∼3.6 Å, presenting an energetic barrier for hydrated ions. The ASIC1a-MitTx complex illuminates the mechanism of MitTx action, defines the structure of the selectivity filter of voltage-independent, sodium-selective ion channels, and captures the open state of an ASIC. Copyright © 2014 Elsevier Inc. All rights reserved.

Cocrystal structure of the ICAP1 PTB domain in complex with a KRIT1 peptide

PubMed Central

Liu, Weizhi; Boggon, Titus J.

2013-01-01

Integrin cytoplasmic domain-associated protein-1 (ICAP1) is a suppressor of integrin activation and directly binds to the cytoplasmic tail of β1 integrins; its binding suppresses integrin activation by competition with talin. Krev/Rap1 interaction trapped-1 (KRIT1) releases ICAP1 suppression of integrin activation by sequestering ICAP1 away from integrin cytoplasmic tails. Here, the cocrystal structure of the PTB domain of ICAP1 in complex with a 29-­amino-acid fragment (residues 170–198) of KRIT1 is presented to 1.7 Å resolution [the resolution at which 〈I/σ(I)〉 = 2.9 was 1.83 Å]. In previous studies, the structure of ICAP1 with integrin β1 was determined to 3.0 Å resolution and that of ICAP1 with the N-terminal portion of KRIT1 (residues 1–­198) was determined to 2.54 Å resolution; therefore, this study provides the highest resolution structure yet of ICAP1 and allows further detailed analysis of the interaction of ICAP1 with its minimal binding region in KRIT1. PMID:23695561

CIT-7, a crystalline, molecular sieve with pores bounded by 8 and 10-membered rings† †Electronic supplementary information (ESI) available: Details of the synthesis and characterization of all materials as well as details on the synchrotron and RED data collection and structure determination, including the cif file. See DOI: 10.1039/c4sc03935a Click here for additional data file.

PubMed Central

Schmidt, Joel E.; Xie, Dan; Rea, Thomas

2015-01-01

A new crystalline molecular sieve, denoted CIT-7, is synthesized using an imidazolium-based diquaternary organic structure directing agent (OSDA). The framework structure is determined from a combination of rotation electron diffraction and synchrotron X-ray powder diffraction data. The structure has 10 crystallographically unique tetrahedral atoms (T-atoms) in the unit cell, and can be described as an ordered arrangement of the [425462] mtw building unit and a previously unreported [4452] building unit. The framework contains a 2-dimensional pore system that is bounded by 10 T-atom rings (10-ring, 5.1 Å × 6.2 Å opening) that are connected with oval 8-rings (2.9 Å × 5.5 Å opening) through medium-sized cavities (∼7.9 Å) at the channel intersections. CIT-7 can be synthesized over a broad range of compositions including pure-silica and heteroatom, e.g., aluminosilicate and titanosilicate, containing variants. PMID:29163872

Rigidity of transmembrane proteins determines their cluster shape

NASA Astrophysics Data System (ADS)

Jafarinia, Hamidreza; Khoshnood, Atefeh; Jalali, Mir Abbas

2016-01-01

Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as α -helices and β -sheets have different structural rigidities. We use molecular dynamics simulation of a coarse-grained model of protein-embedded lipid membranes to investigate the mechanisms of protein clustering. For a variety of protein concentrations, our simulations under thermal equilibrium conditions reveal that the structural rigidity of transmembrane domains dramatically affects interactions and changes the shape of the cluster. We have observed stable large aggregates even in the absence of hydrophobic mismatch, which has been previously proposed as the mechanism of protein aggregation. According to our results, semiflexible proteins aggregate to form two-dimensional clusters, while rigid proteins, by contrast, form one-dimensional string-like structures. By assuming two probable scenarios for the formation of a two-dimensional triangular structure, we calculate the lipid density around protein clusters and find that the difference in lipid distribution around rigid and semiflexible proteins determines the one- or two-dimensional nature of aggregates. It is found that lipids move faster around semiflexible proteins than rigid ones. The aggregation mechanism suggested in this paper can be tested by current state-of-the-art experimental facilities.

Low temperature structures of dCpG-proflavine. Conformational and hydration effects.

PubMed Central

Schneider, B; Ginell, S L; Berman, H M

1992-01-01

The structure of the complex of dCpG with proflavine was determined using x-ray data taken at -130 degrees C (low temperature) and at -2 degrees C (cold temperature) and compared with the structure of the complex determined previously at room temperature (Shieh, H. S., H. M. Berman, M. Dabrow, and S. Neidle. 1980. Nucleic Acids Res. 8:85-97). Low temperature was refined with 5,125 reflections between 8.0 and 0.93 A, Anisotropically modeled temperature factors were used for DNA/drug atoms and isotropic ones for water oxygens to R factor of 12.2% in P2(1)2(1)2; a = 32.853, b = 21.760, c = 13.296 A. Cold temperature was refined isotropically with 2,846 reflections 8.0-0.89 A to R = 15.1% in P2(1)2(1)2; a = 32.867, b = 22.356, c = 13.461 A. Both structures are very similar to the room temperature one, though some important differences were observed: one guanine sugar moiety is disordered and additional water molecules have been located that give rise to infinite polyhedral hydration networks. Images FIGURE 2 PMID:1489914

Low temperature structures of dCpG-proflavine.

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

Schneider, B.; Ginell, S. L.; Berman, H. M.

1992-12-01

The structure of the complex of dCpG with proflavine was determined using x-ray data taken at -130 degrees C (low temperature) and at -2 degrees C (cold temperature) and compared with the structure of the complex determined previously at room temperature (Shieh, H. S., H. M. Berman, M. Dabrow, and S. Neidle. 1980. Nucleic Acids Res. 8:85-97). Low temperature was refined with 5,125 reflections between 8.0 and 0.93 A, Anisotropically modeled temperature factors were used for DNA/drug atoms and isotropic ones for water oxygens to R factor of 12.2% in P2(1)2(1)2; a = 32.853, b = 21.760, c = 13.296more » A. Cold temperature was refined isotropically with 2,846 reflections 8.0-0.89 A to R = 15.1% in P2(1)2(1)2; a = 32.867, b = 22.356, c = 13.461 A. Both structures are very similar to the room temperature one, though some important differences were observed: one guanine sugar moiety is disordered and additional water molecules have been located that give rise to infinite polyhedral hydration networks.« less

Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.

PubMed

Zhang, Qian; Xu, Zhijian; Shi, Jiye; Zhu, Weiliang

2017-07-24

Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishing of experimentally determined XBs in PDB. In our previous study, we showed that side-chain XBs forming with protein side chains are underestimated in PDB on the basis of the phenomenon that the proportion of side-chain XBs to overall XBs decreases as structural resolution becomes lower and lower. However, whether the dominant backbone XBs forming with protein backbone are overlooked is still a mystery. Here, with the help of the ratio (R F ) of the observed XBs' frequency of occurrence to their frequency expected at random, we demonstrated that backbone XBs are largely overlooked in PDB, too. Furthermore, three cases were discovered possessing backbone XBs in high resolution structures while losing the XBs in low resolution structures. In the last two cases, even at 1.80 Å resolution, the backbone XBs were lost, manifesting the urgent need to consider XBs in the refinement process during X-ray crystallography study.

Design Criteria for Low Profile Flange Calculations

NASA Technical Reports Server (NTRS)

Leimbach, K. R.

1973-01-01

An analytical method and a design procedure to develop flanged separable pipe connectors are discussed. A previously established algorithm is the basis for calculating low profile flanges. The characteristics and advantages of the low profile flange are analyzed. The use of aluminum, titanium, and plastics for flange materials is described. Mathematical models are developed to show the mechanical properties of various flange configurations. A computer program for determining the structural stability of the flanges is described.

An alternative view of protein fold space.

PubMed

Shindyalov, I N; Bourne, P E

2000-02-15

Comparing and subsequently classifying protein structures information has received significant attention concurrent with the increase in the number of experimentally derived 3-dimensional structures. Classification schemes have focused on biological function found within protein domains and on structure classification based on topology. Here an alternative view is presented that groups substructures. Substructures are long (50-150 residue) highly repetitive near-contiguous pieces of polypeptide chain that occur frequently in a set of proteins from the PDB defined as structurally non-redundant over the complete polypeptide chain. The substructure classification is based on a previously reported Combinatorial Extension (CE) algorithm that provides a significantly different set of structure alignments than those previously described, having, for example, only a 40% overlap with FSSP. Qualitatively the algorithm provides longer contiguous aligned segments at the price of a slightly higher root-mean-square deviation (rmsd). Clustering these alignments gives a discreet and highly repetitive set of substructures not detectable by sequence similarity alone. In some cases different substructures represent all or different parts of well known folds indicative of the Russian doll effect--the continuity of protein fold space. In other cases they fall into different structure and functional classifications. It is too early to determine whether these newly classified substructures represent new insights into the evolution of a structural framework important to many proteins. What is apparent from on-going work is that these substructures have the potential to be useful probes in finding remote sequence homology and in structure prediction studies. The characteristics of the complete all-by-all comparison of the polypeptide chains present in the PDB and details of the filtering procedure by pair-wise structure alignment that led to the emergent substructure gallery are discussed. Substructure classification, alignments, and tools to analyze them are available at http://cl.sdsc.edu/ce.html.

Three novel approaches to structural identifiability analysis in mixed-effects models.

PubMed

Janzén, David L I; Jirstrand, Mats; Chappell, Michael J; Evans, Neil D

2016-05-06

Structural identifiability is a concept that considers whether the structure of a model together with a set of input-output relations uniquely determines the model parameters. In the mathematical modelling of biological systems, structural identifiability is an important concept since biological interpretations are typically made from the parameter estimates. For a system defined by ordinary differential equations, several methods have been developed to analyse whether the model is structurally identifiable or otherwise. Another well-used modelling framework, which is particularly useful when the experimental data are sparsely sampled and the population variance is of interest, is mixed-effects modelling. However, established identifiability analysis techniques for ordinary differential equations are not directly applicable to such models. In this paper, we present and apply three different methods that can be used to study structural identifiability in mixed-effects models. The first method, called the repeated measurement approach, is based on applying a set of previously established statistical theorems. The second method, called the augmented system approach, is based on augmenting the mixed-effects model to an extended state-space form. The third method, called the Laplace transform mixed-effects extension, is based on considering the moment invariants of the systems transfer function as functions of random variables. To illustrate, compare and contrast the application of the three methods, they are applied to a set of mixed-effects models. Three structural identifiability analysis methods applicable to mixed-effects models have been presented in this paper. As method development of structural identifiability techniques for mixed-effects models has been given very little attention, despite mixed-effects models being widely used, the methods presented in this paper provides a way of handling structural identifiability in mixed-effects models previously not possible. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Distinguishing tautomerism in the crystal structure of (Z)-N-(5-ethyl-2,3-di-hydro-1,3,4-thiadiazol-2-ylidene) -4-methylbenzenesulfonamide using DFT-D calculations and {sup 13}C solid-state NMR

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

Li, Xiaozhou; Bond, Andrew D.; Johansson, Kristoffer E.

2014-08-01

The crystal structure of (Z)-N-(5-ethyl-2,3-di-hydro-1,3,4-thiadiazol-2-ylidene) -4-methylbenzenesulfonamide contains an imine tautomer, rather than the previously reported amine tautomer. The tautomers can be distinguished using dispersion-corrected density functional theory calculations and by comparison of calculated and measured {sup 13}C solid-state NMR spectra. The crystal structure of the title compound, C{sub 11}H{sub 13}N{sub 3}O{sub 2}S{sub 2}, has been determined previously on the basis of refinement against laboratory powder X-ray diffraction (PXRD) data, supported by comparison of measured and calculated {sup 13}C solid-state NMR spectra [Hangan et al. (2010 ▶). Acta Cryst. B66, 615–621]. The mol@@ecule is tautomeric, and was reported as an aminemore » tautomer [systematic name: N-(5-ethyl-1,3,4-thia@@diazol-2-yl)-p-toluene@@sulfonamide], rather than the correct imine tautomer. The protonation site on the mol@@ecule’s 1,3,4-thia@@diazole ring is indicated by the inter@@molecular contacts in the crystal structure: N—H⋯O hydrogen bonds are established at the correct site, while the alternative protonation site does not establish any notable inter molecular inter@@actions. The two tautomers provide essentially identical Rietveld fits to laboratory PXRD data, and therefore they cannot be directly distinguished in this way. However, the correct tautomer can be distinguished from the incorrect one by previously reported qu@@anti@@tative criteria based on the extent of structural distortion on optimization of the crystal structure using dispersion-corrected density functional theory (DFT-D) calculations. Calculation of the {sup 13}C SS-NMR spectrum based on the correct imine tautomer also provides considerably better agreement with the measured {sup 13}C SS-NMR spectrum.« less

Construction patterns of birds’ nests provide insight into nest-building behaviours

PubMed Central

Goodman, Adrian M.

2017-01-01

Previous studies have suggested that birds and mammals select materials needed for nest building based on their thermal or structural properties, although the amounts or properties of the materials used have been recorded for only a very small number of species. Some of the behaviours underlying the construction of nests can be indirectly determined by careful deconstruction of the structure and measurement of the biomechanical properties of the materials used. Here we examined this idea in an investigation of Bullfinch (Pyrrhula pyrrhula) nests as a model for open-nesting songbird species that construct a “twig” nest, and tested the hypothesis that materials in different parts of nests serve different functions. The quantities of materials present in the nest base, sides and cup were recorded before structural analysis. Structural analysis showed that the base of the outer nests were composed of significantly thicker, stronger and more rigid materials compared to the side walls, which in turn were significantly thicker, stronger and more rigid than materials used in the cup. These results suggest that the placement of particular materials in nests may not be random, but further work is required to determine if the final structure of a nest accurately reflects the construction process. PMID:28265501

Structural and functional salivary disorders in type 2 diabetic patients.

PubMed

Carda, Carmen; Mosquera-Lloreda, Nezly; Salom, Lucas; Gomez de Ferraris, Maria Elsa; Peydró, Amando

2006-07-01

Diabetes mellitus type 2 is the most common metabolic disorder and it causes an important morbimortality. The structural modifications in the parotid gland (sialosis) had already been described in these patients and could result in variations in the salivary composition, as well as an increase in periodontal and dental pathology. To compare the biochemical findings in the saliva and to correlate these biochemical disturbances with the morphologic findings previously described. Clinical information were gathered about 33 patients, 17 had type 2 diabetes. Samples of whole saliva were obtained for biochemical analysis and serum samples to determine metabolic control. In the diabetics saliva we found urea and total proteins increased and reduced levels of microalbumina. Salivary glucose was only augmented in patients with poor metabolic control. Clinical symptoms of xerostomia were present in 76,4% and dental and periodontal disease in 100%. The parotid gland was characterised by the presence of small acini, lipid intracytoplasmic droplets, as well as adipose stroma infiltration. The acinar cytoqueratins expression was heterogeneous and very positive in the hyperplasic ducts. These biochemical disorders in the saliva of the type 2 diabetic patients would be related with the structural changes previously observed in parotid glands.

3D Anisotropy of Solar Wind Turbulence, Tubes, or Ribbons?

NASA Astrophysics Data System (ADS)

Verdini, Andrea; Grappin, Roland; Alexandrova, Olga; Lion, Sonny

2018-01-01

We study the anisotropy with respect to the local magnetic field of turbulent magnetic fluctuations at magnetofluid scales in the solar wind. Previous measurements in the fast solar wind obtained axisymmetric anisotropy, despite that the analysis method allows nonaxisymmetric structures. These results are probably contaminated by the wind expansion that introduces another symmetry axis, namely, the radial direction, as indicated by recent numerical simulations. These simulations also show that while the expansion is strong, the principal fluctuations are in the plane perpendicular to the radial direction. Using this property, we separate 11 yr of Wind spacecraft data into two subsets characterized by strong and weak expansion and determine the corresponding turbulence anisotropy. Under strong expansion, the small-scale anisotropy is consistent with the Goldreich & Sridhar critical balance. As in previous works, when the radial symmetry axis is not eliminated, the turbulent structures are field-aligned tubes. Under weak expansion, we find 3D anisotropy predicted by the Boldyrev model, that is, turbulent structures are ribbons and not tubes. However, the very basis of the Boldyrev phenomenology, namely, a cross-helicity increasing at small scales, is not observed in the solar wind: the origin of the ribbon formation is unknown.

Complete theory of symmetry-based indicators of band topology.

PubMed

Po, Hoi Chun; Vishwanath, Ashvin; Watanabe, Haruki

2017-06-30

The interplay between symmetry and topology leads to a rich variety of electronic topological phases, protecting states such as the topological insulators and Dirac semimetals. Previous results, like the Fu-Kane parity criterion for inversion-symmetric topological insulators, demonstrate that symmetry labels can sometimes unambiguously indicate underlying band topology. Here we develop a systematic approach to expose all such symmetry-based indicators of band topology in all the 230 space groups. This is achieved by first developing an efficient way to represent band structures in terms of elementary basis states, and then isolating the topological ones by removing the subset of atomic insulators, defined by the existence of localized symmetric Wannier functions. Aside from encompassing all earlier results on such indicators, including in particular the notion of filling-enforced quantum band insulators, our theory identifies symmetry settings with previously hidden forms of band topology, and can be applied to the search for topological materials.Understanding the role of topology in determining electronic structure can lead to the discovery, or appreciation, of materials with exotic properties such as protected surface states. Here, the authors present a framework for identifying topologically distinct band-structures for all 3D space groups.

Age- and bite-structured models for vector-borne diseases.

PubMed

Rock, K S; Wood, D A; Keeling, M J

2015-09-01

The biology and behaviour of biting insects is a vitally important aspect in the spread of vector-borne diseases. This paper aims to determine, through the use of mathematical models, what effect incorporating vector senescence and realistic feeding patterns has on disease. A novel model is developed to enable the effects of age- and bite-structure to be examined in detail. This original PDE framework extends previous age-structured models into a further dimension to give a new insight into the role of vector biting and its interaction with vector mortality and spread of disease. Through the PDE model, the roles of the vector death and bite rates are examined in a way which is impossible under the traditional ODE formulation. It is demonstrated that incorporating more realistic functions for vector biting and mortality in a model may give rise to different dynamics than those seen under a more simple ODE formulation. The numerical results indicate that the efficacy of control methods that increase vector mortality may not be as great as predicted under a standard host-vector model, whereas other controls including treatment of humans may be more effective than previously thought. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Aggregation Properties and Liquid Crystal Phase of a Dye Based on Naphthalenetetracarboxylic Acid

NASA Astrophysics Data System (ADS)

Tomasik, Michelle; Collings, Peter

2007-03-01

R003 is a dye produced for thin film optical components by Optiva, Inc.^1 made from the sulfonation of the dibenzimidazole derivative of naphthalenetetracarboxylic acid. Its molecular structure is very different from the aggregating food dye previously investigated in our laboratory^2 and R003 forms a liquid crystal phase at significantly lower concentrations. We have performed polarizing microscopy, absorption spectroscopy, and x-ray diffraction experiments in order to determine the phase diagram and aggregate structure. In addition, we have included both translational and orientational entropy in the theoretical analysis of the aggregation process, and have used a more realistic lineshape in analyzing the absorption data. Our results indicate that the ``bond energy'' for molecules in an aggregate is even larger than for the previously studied dye and that the aggregate structure has a cross-sectional area equal to two or three molecular areas rather than one.^1Lazarev, P., N. Ovchinnikova, M. Paukshto, SID Int. Symp. Digest of Tech. Papers, San Jose, California, June XXXII, 571 (2001).^2V. R. Horowitz, L. A. Janowitz, A. L. Modic, P. A. Heiney, and P. J. Collings, Phys. Rev. E 72, 041710 (2005).

Millimeter-Wave Spectroscopy, X-ray Crystal Structure, and Quantum Chemical Studies of Diketene: Resolving Ambiguities Concerning the Structure of the Ketene Dimer.

PubMed

Orr, Vanessa L; Esselman, Brian J; Dorman, P Matisha; Amberger, Brent K; Guzei, Ilia A; Woods, R Claude; McMahon, Robert J

2016-10-06

The pure rotational spectrum of diketene has been studied in the millimeter-wave region from ∼240 to 360 GHz. For the ground vibrational state and five vibrationally excited satellites (ν 24 , 2ν 24 , 3ν 24 , 4ν 24 , and ν 16 ), the observed spectrum allowed for the measurement, assignment, and least-squares fitting a total of more than 10 000 distinct rotational transitions. In each case, the transitions were fit to single-state, complete or near-complete sextic centrifugally distorted rotor models to near experimental error limits using Kisiel's ASFIT. Additionally, we obtained less satisfactory least-squares fits to single-state centrifugally distorted rotor models for three additional vibrational states: ν 24 + ν 16 , ν 23 , and 5ν 24 . The structure of diketene was optimized at the CCSD(T)/ANO1 level, and the vibration-rotation interaction (α i ) values for each normal mode were determined with a CCSD(T)/ANO1 VPT2 anharmonic frequency calculation. These α i values were helpful in identifying the previously unreported ν 16 and ν 23 fundamental states. We obtained a single-crystal X-ray structure of diketene at -173 °C. The bond distances are increased in precision by more than an order of magnitude compared to those in the 1958 X-ray crystal structure. The improved accuracy of the crystal structure geometry resolves the discrepancy between previous computational and experimental structures. The rotational transition frequencies provided herein should be useful for a millimeter-wave or terahertz search for diketene in the interstellar medium.

Complex band structure and electronic transmission eigenchannels

NASA Astrophysics Data System (ADS)

Jensen, Anders; Strange, Mikkel; Smidstrup, Søren; Stokbro, Kurt; Solomon, Gemma C.; Reuter, Matthew G.

2017-12-01

It is natural to characterize materials in transport junctions by their conductance length dependence, β. Theoretical estimations of β are made employing two primary theories: complex band structure and density functional theory (DFT) Landauer transport. It has previously been shown that the β value derived from total Landauer transmission can be related to the β value from the smallest |ki| complex band; however, it is an open question whether there is a deeper relationship between the two. Here we probe the details of the relationship between transmission and complex band structure, in this case individual eigenchannel transmissions and different complex bands. We present calculations of decay constants for the two most conductive states as determined by complex band structure and standard DFT Landauer transport calculations for one semi-conductor and two molecular junctions. The molecular junctions show that both the length dependence of the total transmission and the individual transmission eigenvalues can be, almost always, found through the complex band structure. The complex band structure of the semi-conducting material, however, does not predict the length dependence of the total transmission but only of the individual channels, at some k-points, due to multiple channels contributing to transmission. We also observe instances of vertical bands, some of which are the smallest |ki| complex bands, that do not contribute to transport. By understanding the deeper relationship between complex bands and individual transmission eigenchannels, we can make a general statement about when the previously accepted wisdom linking transmission and complex band structure will fail, namely, when multiple channels contribute significantly to the transmission.

Independent movement, dimerization and stability of tandem repeats of chicken brain alpha-spectrin

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

Kusunoki, H.; Minasov, G.; Macdonald, R.I.

Previous X-ray crystal structures have shown that linkers of five amino acid residues connecting pairs of chicken brain {alpha}-spectrin and human erythroid {beta}-spectrin repeats can undergo bending without losing their {alpha}-helical structure. To test whether bending at one linker can influence bending at an adjacent linker, the structures of two and three repeat fragments of chicken brain {alpha}-spectrin have been determined by X-ray crystallography. The structure of the three-repeat fragment clearly shows that bending at one linker can occur independently of bending at an adjacent linker. This observation increases the possible trajectories of modeled chains of spectrin repeats. Furthermore, themore » three-repeat molecule crystallized as an antiparallel dimer with a significantly smaller buried interfacial area than that of {alpha}-actinin, a spectrin-related molecule, but large enough and of a type indicating biological specificity. Comparison of the structures of the spectrin and {alpha}-actinin dimers supports weak association of the former, which could not be detected by analytical ultracentrifugation, versus strong association of the latter, which has been observed by others. To correlate features of the structure with solution properties and to test a previous model of stable spectrin and dystrophin repeats, the number of inter-helical interactions in each repeat of several spectrin structures were counted and compared to their thermal stabilities. Inter-helical interactions, but not all interactions, increased in parallel with measured thermal stabilities of each repeat and in agreement with the thermal stabilities of two and three repeats and also partial repeats of spectrin.« less

Local Crystal Structure of Antiferroelectric Bi2Mn4/3Ni2/3O6 in Commensurate and Incommensurate Phases Described by Pair Distribution Function (PDF) and Reverse Monte Carlo (RMC) Modeling.

PubMed

Szczecinski, Robert J; Chong, Samantha Y; Chater, Philip A; Hughes, Helen; Tucker, Matthew G; Claridge, John B; Rosseinsky, Matthew J

2014-04-08

The functional properties of materials can arise from local structural features that are not well determined or described by crystallographic methods based on long-range average structural models. The room temperature (RT) structure of the Bi perovskite Bi 2 Mn 4/3 Ni 2/3 O 6 has previously been modeled as a locally polar structure where polarization is suppressed by a long-range incommensurate antiferroelectric modulation. In this study we investigate the short-range local structure of Bi 2 Mn 4/3 Ni 2/3 O 6 , determined through reverse Monte Carlo (RMC) modeling of neutron total scattering data, and compare the results with the long-range incommensurate structure description. While the incommensurate structure has equivalent B site environments for Mn and Ni, the local structure displays a significantly Jahn-Teller distorted environment for Mn 3+ . The local structure displays the rock-salt-type Mn/Ni ordering of the related Bi 2 MnNiO 6 high pressure phase, as opposed to Mn/Ni clustering observed in the long-range average incommensurate model. RMC modeling reveals short-range ferroelectric correlations between Bi 3+ cations, giving rise to polar regions that are quantified for the first time as existing within a distance of approximately 12 Å. These local correlations persist in the commensurate high temperature (HT) phase, where the long-range average structure is nonpolar. The local structure thus provides information about cation ordering and B site structural flexibility that may stabilize Bi 3+ on the A site of the perovskite structure and reveals the extent of the local polar regions created by this cation.

Challenges in the Structure Determination of Self-Assembled Metallacages: What Do Cage Cavities Contain, Internal Vapor Bubbles or Solvent and/or Counterions?

PubMed

Givelet, Cecile C; Dron, Paul I; Wen, Jin; Magnera, Thomas F; Zamadar, Matibur; Čépe, Klára; Fujiwara, Hiroki; Shi, Yue; Tuchband, Michael R; Clark, Noel; Zbořil, Radek; Michl, Josef

2016-05-25

Proving the structures of charged metallacages obtained by metal ion coordination-driven solution self-assembly is challenging, and the common use of routine NMR spectroscopy and mass spectrometry is unreliable. Carefully determined diffusion coefficients from diffusion-ordered proton magnetic resonance (DOSY NMR) for six cages of widely differing sizes lead us to propose a structural reassignment of two molecular cages from a previously favored trimer to a pentamer or hexamer, and another from a trimer to a much higher oligomer, possibly an intriguing tetradecamer. In the former case, strong support for the reassignment to a larger cage is provided by an observation of a slow reversible transformation of the initially formed cage into a smaller but spectrally very similar one upon dilution. In the latter case, freeze-fracture transmission electron micrographs demonstrate that at least some of the solutions are colloidal, and high-resolution electron transmission and atomic force microscopy images are compatible with a tetradecamer but not a trimer. Comparison of solute partial molar volumes deduced from measurement of solution density with volumes anticipated from molecular models argues strongly against the presence of large voids (solvent vapor bubbles) in cages dissolved in nitromethane. The presence of bubbles was previously proposed in an attempt to account for the bilinear nature of the Eyring plot of the rate constant for pyridine ligand edge exchange reaction in one of the cages and for the unusual activation parameters in the high-temperature regime. An alternative interpretation is proposed now.

Asymmetric structure of five and six membered DNA hairpin loops

NASA Technical Reports Server (NTRS)

Baumann, U.; Chang, S.

1995-01-01

The tertiary structure of nucleic acid hairpins was elucidated by means of the accessibility of the single-strand-specific nuclease from mung bean. This molecular probe has proven especially useful in determining details of the structural arrangement of the nucleotides within a loop. In this study 3'-labeling is introduced to complement previously used 5'-labeling in order to assess and to exclude possible artifacts of the method. Both labeling procedures result in mutually consistent cleavage patterns. Therefore, methodological artifacts can be excluded and the potential of the nuclease as structural probe is increased. DNA hairpins with five and six membered loops reveal an asymmetric loop structure with a sharp bend of the phosphate-ribose backbone between the second and third nucleotide on the 3'-side of a loop. These hairpin structures differ from smaller loops with 3 or 4 members, which reveal this type of bend between the first and second 3' nucleotide, and resemble with respect to the asymmetry anticodon loops of tRNA.

Murine Leukemia Virus Reverse Transcriptase: Structural Comparison with HIV-1 Reverse Transcriptase

PubMed Central

Coté, Marie L.; Roth, Monica J.

2008-01-01

Recent X-ray crystal structure determinations of Moloney murine leukemia virus reverse transcriptase (MoMLV RT) have allowed for more accurate structure/function comparisons to HIV-1 RT than were formerly possible. Previous biochemical studies of MoMLV RT in conjunction with knowledge of sequence homologies to HIV-1 RT and overall fold similarities to RTs in general, provided a foundation upon which to build. In addition, numerous crystal structures of the MoMLV RT fingers/palm subdomain had also shed light on one of the critical functions of the enzyme, specifically polymerization. Now in the advent of new structural information, more intricate examination of MoMLV RT in its entirety can be realized, and thus the comparisons with HIV-1 RT may be more critically elucidated. Here, we will review the similarities and differences between MoMLV RT and HIV-1 RT via structural analysis, and propose working models for the MoMLV RT based upon that information. PMID:18294720

Transmembrane Helices Tilt, Bend, Slide, Torque, and Unwind between Functional States of Rhodopsin

PubMed Central

Ren, Zhong; Ren, Peter X.; Balusu, Rohith; Yang, Xiaojing

2016-01-01

The seven-helical bundle of rhodopsin and other G-protein coupled receptors undergoes structural rearrangements as the transmembrane receptor protein is activated. These structural changes are known to involve tilting and bending of various transmembrane helices. However, the cause and effect relationship among structural events leading to a cytoplasmic crevasse for G-protein binding is less well defined. Here we present a mathematical model of the protein helix and a simple procedure to determine multiple parameters that offer precise depiction of a helical conformation. A comprehensive survey of bovine rhodopsin structures shows that the helical rearrangements during the activation of rhodopsin involve a variety of angular and linear motions such as torsion, unwinding, and sliding in addition to the previously reported tilting and bending. These hitherto undefined motion components unify the results obtained from different experimental approaches, and demonstrate conformational similarity between the active opsin structure and the photoactivated structures in crystallo near the retinal anchor despite their marked differences. PMID:27658480

Structure of a Trypanosoma Brucei Alpha/Beta--Hydrolase Fold Protein With Unknown Function

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

Merritt, E.A.; Holmes, M.; Buckner, F.S.

2009-05-26

The structure of a structural genomics target protein, Tbru020260AAA from Trypanosoma brucei, has been determined to a resolution of 2.2 {angstrom} using multiple-wavelength anomalous diffraction at the Se K edge. This protein belongs to Pfam sequence family PF08538 and is only distantly related to previously studied members of the {alpha}/{beta}-hydrolase fold family. Structural superposition onto representative {alpha}/{beta}-hydrolase fold proteins of known function indicates that a possible catalytic nucleophile, Ser116 in the T. brucei protein, lies at the expected location. However, the present structure and by extension the other trypanosomatid members of this sequence family have neither sequence nor structural similaritymore » at the location of other active-site residues typical for proteins with this fold. Together with the presence of an additional domain between strands {beta}6 and {beta}7 that is conserved in trypanosomatid genomes, this suggests that the function of these homologs has diverged from other members of the fold family.« less

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

PubMed Central

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

2014-01-01

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

Complex structure of a bacterial class 2 histone deacetylase homologue with a trifluoromethylketone inhibitor

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

Nielsen, Tine Kragh; Hildmann, Christian; Riester, Daniel

2007-04-01

The crystal structure of HDAH FB188 in complex with a trifluoromethylketone at 2.2 Å resolution is reported and compared to a previously determined inhibitor complex. Histone deacetylases (HDACs) have emerged as attractive targets in anticancer drug development. To date, a number of HDAC inhibitors have been developed and most of them are hydroxamic acid derivatives, typified by suberoylanilide hydroxamic acid (SAHA). Not surprisingly, structural information that can greatly enhance the design of novel HDAC inhibitors is so far only available for hydroxamic acids in complex with HDAC or HDAC-like enzymes. Here, the first structure of an enzyme complex with amore » nonhydroxamate HDAC inhibitor is presented. The structure of the trifluoromethyl ketone inhibitor 9,9,9-trifluoro-8-oxo-N-phenylnonanamide in complex with bacterial FB188 HDAH (histone deacetylase-like amidohydrolase from Bordetella/Alcaligenes strain FB188) has been determined. HDAH reveals high sequential and functional homology to human class 2 HDACs and a high structural homology to human class 1 HDACs. Comparison with the structure of HDAH in complex with SAHA reveals that the two inhibitors superimpose well. However, significant differences in binding to the active site of HDAH were observed. In the presented structure the O atom of the trifluoromethyl ketone moiety is within binding distance of the Zn atom of the enzyme and the F atoms participate in interactions with the enzyme, thereby involving more amino acids in enzyme–inhibitor binding.« 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.

Psychometric properties of the Liebowitz Social Anxiety Scale (LSAS) in a longitudinal study of African Americans with anxiety disorders.

PubMed

Beard, Courtney; Rodriguez, Benjamin F; Moitra, Ethan; Sibrava, Nicholas J; Bjornsson, Andri; Weisberg, Risa B; Keller, Martin B

2011-06-01

The Liebowitz Social Anxiety Scale (LSAS) is a widely used measure of social anxiety. However, no study has examined the psychometric properties of the LSAS in an African American sample. The current study examined the LSAS characteristics in 97 African Americans diagnosed with an anxiety disorder. Overall, the original LSAS subscales showed excellent internal consistency and temporal stability. Similar to previous reports, fear and avoidance subscales were so highly correlated that they yielded redundant information. Confirmatory factor analyses for three previously proposed models failed to demonstrate an excellent fit to our data. However, a four-factor model showed minimally acceptable fit. Overall, the LSAS performed similarly in our African American sample as in previous European American samples. Exploratory factor analyses are warranted to determine whether a better factor structure exists for African Americans. Copyright © 2011 Elsevier Ltd. All rights reserved.

Unexpectedly large mass loss during the thermal pulse cycle of the red giant star R Sculptoris.

PubMed

Maercker, M; Mohamed, S; Vlemmings, W H T; Ramstedt, S; Groenewegen, M A T; Humphreys, E; Kerschbaum, F; Lindqvist, M; Olofsson, H; Paladini, C; Wittkowski, M; de Gregorio-Monsalvo, I; Nyman, L-A

2012-10-11

The asymptotic-giant-branch star R Sculptoris is surrounded by a detached shell of dust and gas. The shell originates from a thermal pulse during which the star underwent a brief period of increased mass loss. It has hitherto been impossible to constrain observationally the timescales and mass-loss properties during and after a thermal pulse--parameters that determine the lifetime of the asymptotic giant branch and the amount of elements returned by the star. Here we report observations of CO emission from the circumstellar envelope and shell around R Sculptoris with an angular resolution of 1.3″. What was previously thought to be only a thin, spherical shell with a clumpy structure is revealed to also contain a spiral structure. Spiral structures associated with circumstellar envelopes have been previously seen, leading to the conclusion that the systems must be binaries. Combining the observational data with hydrodynamic simulations, we conclude that R Sculptoris is a binary system that underwent a thermal pulse about 1,800 years ago, lasting approximately 200 years. About 3 × 10(-3) solar masses of material were ejected at a velocity of 14.3 km s(-1) and at a rate around 30 times higher than the pre-pulse mass-loss rate. This shows that about three times more mass was returned to the interstellar medium during and immediately after the pulse than previously thought.

Observation of J/ψϕ Structures Consistent with Exotic States from Amplitude Analysis of B^{+}→J/ψϕK^{+} Decays.

PubMed

Aaij, R; Adeva, B; Adinolfi, M; Ajaltouni, Z; Akar, S; Albrecht, J; Alessio, F; Alexander, M; Ali, S; Alkhazov, G; Alvarez Cartelle, P; Alves, A A; Amato, S; Amerio, S; Amhis, Y; An, L; Anderlini, L; Andreassi, G; Andreotti, M; Andrews, J E; Appleby, R B; Aquines Gutierrez, O; Archilli, F; d'Argent, P; Arnau Romeu, J; Artamonov, A; Artuso, M; Aslanides, E; Auriemma, G; Baalouch, M; Babuschkin, I; Bachmann, S; Back, J J; Badalov, A; Baesso, C; Baldini, W; Barlow, R J; Barschel, C; Barsuk, S; Barter, W; Batozskaya, V; Batsukh, B; Battista, V; Bay, A; Beaucourt, L; Beddow, J; Bedeschi, F; Bediaga, I; Bel, L J; Bellee, V; Belloli, N; Belous, K; Belyaev, I; Ben-Haim, E; Bencivenni, G; Benson, S; Benton, J; Berezhnoy, A; Bernet, R; Bertolin, A; Betti, F; Bettler, M-O; van Beuzekom, M; Bezshyiko, I; Bifani, S; Billoir, P; Bird, T; Birnkraut, A; Bitadze, A; Bizzeti, A; Blake, T; Blanc, F; Blouw, J; Blusk, S; Bocci, V; Boettcher, T; Bondar, A; Bondar, N; Bonivento, W; Borgheresi, A; Borghi, S; Borisyak, M; Borsato, M; Bossu, F; Boubdir, M; Bowcock, T J V; Bowen, E; Bozzi, C; Braun, S; Britsch, M; Britton, T; Brodzicka, J; Buchanan, E; Burr, C; Bursche, A; Buytaert, J; Cadeddu, S; Calabrese, R; Calvi, M; Calvo Gomez, M; Campana, P; Campora Perez, D; Capriotti, L; Carbone, A; Carboni, G; Cardinale, R; Cardini, A; Carniti, P; Carson, L; Carvalho Akiba, K; Casse, G; Cassina, L; Castillo Garcia, L; Cattaneo, M; Cauet, Ch; Cavallero, G; Cenci, R; Charles, M; Charpentier, Ph; Chatzikonstantinidis, G; Chefdeville, M; Chen, S; Cheung, S-F; Chobanova, V; Chrzaszcz, M; Cid Vidal, X; Ciezarek, G; Clarke, P E L; Clemencic, M; Cliff, H V; Closier, J; Coco, V; Cogan, J; Cogneras, E; Cogoni, V; Cojocariu, L; Collazuol, G; Collins, P; Comerma-Montells, A; Contu, A; Cook, A; Coquereau, S; Corti, G; Corvo, M; Costa Sobral, C M; Couturier, B; Cowan, G A; Craik, D C; Crocombe, A; Cruz Torres, M; Cunliffe, S; Currie, R; D'Ambrosio, C; Dall'Occo, E; Dalseno, J; David, P N Y; Davis, A; De Aguiar Francisco, O; De Bruyn, K; De Capua, S; De Cian, M; De Miranda, J M; De Paula, L; De Serio, M; De Simone, P; Dean, C-T; Decamp, D; Deckenhoff, M; Del Buono, L; Demmer, M; Derkach, D; Deschamps, O; Dettori, F; Dey, B; Di Canto, A; Dijkstra, H; Dordei, F; Dorigo, M; Dosil Suárez, A; Dovbnya, A; Dreimanis, K; Dufour, L; Dujany, G; Dungs, K; Durante, P; Dzhelyadin, R; Dziurda, A; Dzyuba, A; Déléage, N; Easo, S; Egede, U; Egorychev, V; Eidelman, S; Eisenhardt, S; Eitschberger, U; Ekelhof, R; Eklund, L; Elsasser, Ch; Ely, S; Esen, S; Evans, H M; Evans, T; Falabella, A; Farley, N; Farry, S; Fay, R; Fazzini, D; Ferguson, D; Fernandez Albor, V; Ferrari, F; Ferreira Rodrigues, F; Ferro-Luzzi, M; Filippov, S; Fini, R A; Fiore, M; Fiorini, M; Firlej, M; Fitzpatrick, C; Fiutowski, T; Fleuret, F; Fohl, K; Fontana, M; Fontanelli, F; Forshaw, D C; Forty, R; Frank, M; Frei, C; Fu, J; Furfaro, E; Färber, C; Gallas Torreira, A; Galli, D; Gallorini, S; Gambetta, S; Gandelman, M; Gandini, P; Gao, Y; García Pardiñas, J; Garra Tico, J; Garrido, L; Garsed, P J; Gascon, D; Gaspar, C; Gavardi, L; Gazzoni, G; Gerick, D; Gersabeck, E; Gersabeck, M; Gershon, T; Ghez, Ph; Gianì, S; Gibson, V; Girard, O G; Giubega, L; Gizdov, K; Gligorov, V V; Golubkov, D; Golutvin, A; Gomes, A; Gorelov, I V; Gotti, C; Grabalosa Gándara, M; Graciani Diaz, R; Granado Cardoso, L A; Graugés, E; Graverini, E; Graziani, G; Grecu, A; Griffith, P; Grillo, L; Gruberg Cazon, B R; Grünberg, O; Gushchin, E; Guz, Yu; Gys, T; Göbel, C; Hadavizadeh, T; Hadjivasiliou, C; Haefeli, G; Haen, C; Haines, S C; Hall, S; Hamilton, B; Han, X; Hansmann-Menzemer, S; Harnew, N; Harnew, S T; Harrison, J; Hatch, M; He, J; Head, T; Heister, A; Hennessy, K; Henrard, P; Henry, L; Hernando Morata, J A; van Herwijnen, E; Heß, M; Hicheur, A; Hill, D; Hombach, C; Hulsbergen, W; Humair, T; Hushchyn, M; Hussain, N; Hutchcroft, D; Idzik, M; Ilten, P; Jacobsson, R; Jaeger, A; Jalocha, J; Jans, E; Jawahery, A; John, M; Johnson, D; Jones, C R; Joram, C; Jost, B; Jurik, N; Kandybei, S; Kanso, W; Karacson, M; Kariuki, J M; Karodia, S; Kecke, M; Kelsey, M; Kenyon, I R; Kenzie, M; Ketel, T; Khairullin, E; Khanji, B; Khurewathanakul, C; Kirn, T; Klaver, S; Klimaszewski, K; Koliiev, S; Kolpin, M; Komarov, I; Koopman, R F; Koppenburg, P; Kozachuk, A; Kozeiha, M; Kravchuk, L; Kreplin, K; Kreps, M; Krokovny, P; Kruse, F; Krzemien, W; Kucewicz, W; Kucharczyk, M; Kudryavtsev, V; Kuonen, A K; Kurek, K; Kvaratskheliya, T; Lacarrere, D; Lafferty, G; Lai, A; Lambert, D; Lanfranchi, G; Langenbruch, C; Langhans, B; Latham, T; Lazzeroni, C; Le Gac, R; van Leerdam, J; Lees, J-P; Leflat, A; Lefrançois, J; Lefèvre, R; Lemaitre, F; Lemos Cid, E; Leroy, O; Lesiak, T; Leverington, B; Li, Y; Likhomanenko, T; Lindner, R; Linn, C; Lionetto, F; Liu, B; Liu, X; Loh, D; Longstaff, I; Lopes, J H; Lucchesi, D; Lucio Martinez, M; Luo, H; Lupato, A; Luppi, E; Lupton, O; Lusiani, A; Lyu, X; Machefert, F; Maciuc, F; Maev, O; Maguire, K; Malde, S; Malinin, A; Maltsev, T; Manca, G; Mancinelli, G; Manning, P; Maratas, J; Marchand, J F; Marconi, U; Marin Benito, C; Marino, P; Marks, J; Martellotti, G; Martin, M; Martinelli, M; Martinez Santos, D; Martinez Vidal, F; Martins Tostes, D; Massacrier, L M; Massafferri, A; Matev, R; Mathad, A; Mathe, Z; Matteuzzi, C; Mauri, A; Maurin, B; Mazurov, A; McCann, M; McCarthy, J; McNab, A; McNulty, R; Meadows, B; Meier, F; Meissner, M; Melnychuk, D; Merk, M; Merli, A; Michielin, E; Milanes, D A; Minard, M-N; Mitzel, D S; Molina Rodriguez, J; Monroy, I A; Monteil, S; Morandin, M; Morawski, P; Mordà, A; Morello, M J; Moron, J; Morris, A B; Mountain, R; Muheim, F; Mulder, M; Mussini, M; Müller, D; Müller, J; Müller, K; Müller, V; Naik, P; Nakada, T; Nandakumar, R; Nandi, A; Nasteva, I; Needham, M; Neri, N; Neubert, S; Neufeld, N; Neuner, M; Nguyen, A D; Nguyen-Mau, C; Nieswand, S; Niet, R; Nikitin, N; Nikodem, T; Novoselov, A; O'Hanlon, D P; Oblakowska-Mucha, A; Obraztsov, V; Ogilvy, S; Oldeman, R; Onderwater, C J G; Otalora Goicochea, J M; Otto, A; Owen, P; Oyanguren, A; Pais, P R; Palano, A; Palombo, F; Palutan, M; Panman, J; Papanestis, A; Pappagallo, M; Pappalardo, L L; Pappenheimer, C; Parker, W; Parkes, C; Passaleva, G; Pastore, A; Patel, G D; Patel, M; Patrignani, C; Pearce, A; Pellegrino, A; Penso, G; Pepe Altarelli, M; Perazzini, S; Perret, P; Pescatore, L; Petridis, K; Petrolini, A; Petrov, A; Petruzzo, M; Picatoste Olloqui, E; Pietrzyk, B; Pikies, M; Pinci, D; Pistone, A; Piucci, A; Playfer, S; Plo Casasus, M; Poikela, T; Polci, F; Poluektov, A; Polyakov, I; Polycarpo, E; Pomery, G J; Popov, A; Popov, D; Popovici, B; Potterat, C; Price, E; Price, J D; Prisciandaro, J; Pritchard, A; Prouve, C; Pugatch, V; Puig Navarro, A; Punzi, G; Qian, W; Quagliani, R; Rachwal, B; Rademacker, J H; Rama, M; Ramos Pernas, M; Rangel, M S; Raniuk, I; Raven, G; Redi, F; Reichert, S; Dos Reis, A C; Remon Alepuz, C; Renaudin, V; Ricciardi, S; Richards, S; Rihl, M; Rinnert, K; Rives Molina, V; Robbe, P; Rodrigues, A B; Rodrigues, E; Rodriguez Lopez, J A; Rodriguez Perez, P; Rogozhnikov, A; Roiser, S; Romanovskiy, V; Romero Vidal, A; Ronayne, J W; Rotondo, M; Ruf, T; Ruiz Valls, P; Saborido Silva, J J; Sadykhov, E; Sagidova, N; Saitta, B; Salustino Guimaraes, V; Sanchez Mayordomo, C; Sanmartin Sedes, B; Santacesaria, R; Santamarina Rios, C; Santimaria, M; Santovetti, E; Sarti, A; Satriano, C; Satta, A; Saunders, D M; Savrina, D; Schael, S; Schellenberg, M; Schiller, M; Schindler, H; Schlupp, M; Schmelling, M; Schmelzer, T; Schmidt, B; Schneider, O; Schopper, A; Schubert, K; Schubiger, M; Schune, M-H; Schwemmer, R; Sciascia, B; Sciubba, A; Semennikov, A; Sergi, A; Serra, N; Serrano, J; Sestini, L; Seyfert, P; Shapkin, M; Shapoval, I; Shcheglov, Y; Shears, T; Shekhtman, L; Shevchenko, V; Shires, A; Siddi, B G; Silva Coutinho, R; Silva de Oliveira, L; Simi, G; Simone, S; Sirendi, M; Skidmore, N; Skwarnicki, T; Smith, E; Smith, I T; Smith, J; Smith, M; Snoek, H; Sokoloff, M D; Soler, F J P; Souza, D; Souza De Paula, B; Spaan, B; Spradlin, P; Sridharan, S; Stagni, F; Stahl, M; Stahl, S; Stefko, P; Stefkova, S; Steinkamp, O; Stenyakin, O; Stevenson, S; Stoica, S; Stone, S; Storaci, B; Stracka, S; Straticiuc, M; Straumann, U; Sun, L; Sutcliffe, W; Swientek, K; Syropoulos, V; Szczekowski, M; Szumlak, T; T'Jampens, S; Tayduganov, A; Tekampe, T; Tellarini, G; Teubert, F; Thomas, C; Thomas, E; van Tilburg, J; Tisserand, V; Tobin, M; Tolk, S; Tomassetti, L; Tonelli, D; Topp-Joergensen, S; Toriello, F; Tournefier, E; Tourneur, S; Trabelsi, K; Traill, M; Tran, M T; Tresch, M; Trisovic, A; Tsaregorodtsev, A; Tsopelas, P; Tully, A; Tuning, N; Ukleja, A; Ustyuzhanin, A; Uwer, U; Vacca, C; Vagnoni, V; Valat, S; Valenti, G; Vallier, A; Vazquez Gomez, R; Vazquez Regueiro, P; Vecchi, S; van Veghel, M; Velthuis, J J; Veltri, M; Veneziano, G; Venkateswaran, A; Vernet, M; Vesterinen, M; Viaud, B; Vieira, D; Vieites Diaz, M; Vilasis-Cardona, X; Volkov, V; Vollhardt, A; Voneki, B; Voong, D; Vorobyev, A; Vorobyev, V; Voß, C; de Vries, J A; Vázquez Sierra, C; Waldi, R; Wallace, C; Wallace, R; Walsh, J; Wang, J; Ward, D R; Wark, H M; Watson, N K; Websdale, D; Weiden, A; Whitehead, M; Wicht, J; Wilkinson, G; Wilkinson, M; Williams, M; Williams, M P; Williams, M; Williams, T; Wilson, F F; Wimberley, J; Wishahi, J; Wislicki, W; Witek, M; Wormser, G; Wotton, S A; Wraight, K; Wright, S; Wyllie, K; Xie, Y; Xing, Z; Xu, Z; Yang, Z; Yin, H; Yu, J; Yuan, X; Yushchenko, O; Zangoli, M; Zarebski, K A; Zavertyaev, M; Zhang, L; Zhang, Y; Zhang, Y; Zhelezov, A; Zheng, Y; Zhokhov, A; Zhukov, V; Zucchelli, S

2017-01-13

The first full amplitude analysis of B^{+}→J/ψϕK^{+} with J/ψ→μ^{+}μ^{-}, ϕ→K^{+}K^{-} decays is performed with a data sample of 3  fb^{-1} of pp collision data collected at sqrt[s]=7 and 8 TeV with the LHCb detector. The data cannot be described by a model that contains only excited kaon states decaying into ϕK^{+}, and four J/ψϕ structures are observed, each with significance over 5 standard deviations. The quantum numbers of these structures are determined with significance of at least 4 standard deviations. The lightest has mass consistent with, but width much larger than, previous measurements of the claimed X(4140) state.

Around the macrolide - Impact of 3D structure of macrocycles on lipophilicity and cellular accumulation.

PubMed

Koštrun, Sanja; Munic Kos, Vesna; Matanović Škugor, Maja; Palej Jakopović, Ivana; Malnar, Ivica; Dragojević, Snježana; Ralić, Jovica; Alihodžić, Sulejman

2017-06-16

The aim of this study was to investigate lipophilicity and cellular accumulation of rationally designed azithromycin and clarithromycin derivatives at the molecular level. The effect of substitution site and substituent properties on a global physico-chemical profile and cellular accumulation of investigated compounds was studied using calculated structural parameters as well as experimentally determined lipophilicity. In silico models based on the 3D structure of molecules were generated to investigate conformational effect on studied properties and to enable prediction of lipophilicity and cellular accumulation for this class of molecules based on non-empirical parameters. The applicability of developed models was explored on a validation and test sets and compared with previously developed empirical models. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Retrosynthetic Analysis-Guided Breaking Tile Symmetry for the Assembly of Complex DNA Nanostructures.

PubMed

Wang, Pengfei; Wu, Siyu; Tian, Cheng; Yu, Guimei; Jiang, Wen; Wang, Guansong; Mao, Chengde

2016-10-11

Current tile-based DNA self-assembly produces simple repetitive or highly symmetric structures. In the case of 2D lattices, the unit cell often contains only one basic tile because the tiles often are symmetric (in terms of either the backbone or the sequence). In this work, we have applied retrosynthetic analysis to determine the minimal asymmetric units for complex DNA nanostructures. Such analysis guides us to break the intrinsic structural symmetries of the tiles to achieve high structural complexities. This strategy has led to the construction of several DNA nanostructures that are not accessible from conventional symmetric tile designs. Along with previous studies, herein we have established a set of four fundamental rules regarding tile-based assembly. Such rules could serve as guidelines for the design of DNA nanostructures.

Structure of the Si(111)-(5×2)-Au Surface

NASA Astrophysics Data System (ADS)

Abukawa, Tadashi; Nishigaya, Yoshiki

2013-01-01

The structure of the Si(111)-(5×2)-Au surface, one of the long-standing problems in surface science, has been solved by means of Weissenberg reflection high-energy electron diffraction. The arrangement of the Au atoms and their positions with respect to the substrate were determined from a three-dimensional Patterson function with a lateral resolution of 0.3 Å based on a large amount of diffraction data. The new structural model consists of six Au atoms in a 5×2 unit, which agrees with the recently confirmed Au coverage of 0.6 ML [I. Barke , Phys. Rev. B 79, 155301 (2009).PRBMDO1098-0121]. The model has a distinct ×2 periodicity, and includes a Au dimer. The model is also compatible with previously obtained STM images.

Gamma-Ray Pulsar Light Curves as Probes of Magnetospheric Structure

NASA Technical Reports Server (NTRS)

Harding, A. K.

2016-01-01

The large number of gamma-ray pulsars discovered by the Fermi Gamma-Ray Space Telescope since its launch in 2008 dwarfs the handful that were previously known. The variety of observed light curves makes possible a tomography of both the ensemble-averaged field structure and the high-energy emission regions of a pulsar magnetosphere. Fitting the gamma-ray pulsar light curves with model magnetospheres and emission models has revealed that most of the high-energy emission, and the particles acceleration, takes place near or beyond the light cylinder, near the current sheet. As pulsar magnetosphere models become more sophisticated, it is possible to probe magnetic field structure and emission that are self-consistently determined. Light curve modeling will continue to be a powerful tool for constraining the pulsar magnetosphere physics.

Structural prerequisites for G-protein activation by the neurotensin receptor

DOE PAGES

Krumm, Brian E.; White, Jim F.; Shah, Priyanka; ...

2015-07-24

We previously determined the structure of neurotensin receptor NTSR1 in an active-like conformation with six thermostabilizing mutations bound to the peptide agonist neurotensin. This receptor was unable to activate G proteins, indicating that the mutations restricted NTSR1 to relate agonist binding to G-protein activation. Here we analyse the effect of three of those mutations (E166A 3.49, L310A 6.37, F358A 7.42) and present two structures of NTSR1 able to catalyse nucleotide exchange at Gα. The presence of F358 7.42 causes the conserved W321 6.48 to adopt a side chain orientation parallel to the lipid bilayer sealing the collapsed Na+ ion pocketmore » and linking the agonist with residues in the lower receptor part implicated in GPCR activation. In the intracellular receptor half, the bulkier L310 6.37 side chain dictates the position of R167 3.50 of the highly conserved D/ERY motif. These residues, together with the presence of E166 3.49 provide determinants for G-protein activation by NTSR1.« less

Distinct peptide binding specificities of Src homology 3 (SH3) protein domains can be determined by modulation of local energetics across the binding interface.

PubMed

Gorelik, Maryna; Davidson, Alan R

2012-03-16

The yeast Nbp2p SH3 and Bem1p SH3b domains bind certain target peptides with similar high affinities, yet display vastly different affinities for other targets. To investigate this unusual behavior, we have solved the structure of the Nbp2p SH3-Ste20 peptide complex and compared it with the previously determined structure of the Bem1p SH3b bound to the same peptide. Although the Ste20 peptide interacts with both domains in a structurally similar manner, extensive in vitro studies with domain and peptide mutants revealed large variations in interaction strength across the binding interface of the two complexes. Whereas the Nbp2p SH3 made stronger contacts with the peptide core RXXPXXP motif, the Bem1p SH3b domain made stronger contacts with residues flanking the core motif. Remarkably, this modulation of local binding energetics can explain the distinct and highly nuanced binding specificities of these two domains.

Comparison of S. cerevisiae F-BAR domain structures reveals a conserved inositol phosphate binding site

PubMed Central

Moravcevic, Katarina; Alvarado, Diego; Schmitz, Karl R.; Kenniston, Jon A.; Mendrola, Jeannine M.; Ferguson, Kathryn M.; Lemmon, Mark A.

2015-01-01

SUMMARY F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here, we compare membrane-binding properties of the S. cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound to an inositol phosphate. The structures explain phospholipid-binding selectivity differences, and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip, and is partly retained in certain other F-BAR domains. Our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity, and provide a basis for its prediction from sequence. PMID:25620000

Crystallization of a pentapeptide-repeat protein by reductive cyclic pentylation of free amines with glutaraldehyde

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

Vetting, Matthew W., E-mail: vetting@aecom.yu.edu; Hegde, Subray S.; Blanchard, John S.

2009-05-01

A method to modify proteins with glutaraldehyde under reducing conditions is presented. Treatment with glutaraldehyde and dimethylaminoborane was found to result in cyclic pentylation of free amines and facilitated the structural determination of a protein previously recalcitrant to the formation of diffraction quality crystals. The pentapeptide-repeat protein EfsQnr from Enterococcus faecalis protects DNA gyrase from inhibition by fluoroquinolones. EfsQnr was cloned and purified to homogeneity, but failed to produce diffraction-quality crystals in initial crystallization screens. Treatment of EfsQnr with glutaraldehyde and the strong reducing agent borane–dimethylamine resulted in a derivatized protein which produced crystals that diffracted to 1.6 Å resolution;more » their structure was subsequently determined by single-wavelength anomalous dispersion. Analysis of the derivatized protein using Fourier transform ion cyclotron resonance mass spectrometry indicated a mass increase of 68 Da per free amino group. Electron-density maps about a limited number of structurally ordered lysines indicated that the modification was a cyclic pentylation of free amines, producing piperidine groups.« less

Magnetic structures in potential multiferroic GdCrO3

NASA Astrophysics Data System (ADS)

Manuel, Pascal; Chapon, Laurent; Khalyavin, Dmitry; Xueyun, Wang; Cheong, Sang-Wook

2015-03-01

For the past decade, multiferroics materials have atracted a lot of attention in the condensed matter community because of potential applications for devices. A somewhat ambiguous addition to the multiferroics family was recently reported in the peroskite based GdCrO3 in both bulk and thin film samples. Indeed, ferroelectricity was evidenced by a strong enhancement of the capacitance in a field but significant leakage and no well developed P-E hysteresis blurred the picture. Our own measurements clearly indicate the existence of a polar phase below 2K. To complete the understanding of this material, the determination of the magnetic structure is required but is hampered by the fact Gd is a strong neutron absorber. We will present some neutron diffraction data collected on an isotopic 160GdCrO3 sample at the WISH diffractometer at ISIS which confirm the presence of three successive magnetic phases, previously only seen by magnetization, as a function of temperature. We will compare our determined structures against predictions based on group theoretical considerations and experimental work on other rare-earth ortho-chromates and discuss the mechanism for multiferroicity.

Structural determination of a 5-acetamido-3,5,7, 9-tetradeoxy-7-(3-hydroxybutyramido)-L-glycero-L-manno-nonulos onic acid-containing homopolysaccharide isolated from Sinorhizobium fredii HH103.

PubMed Central

Gil-Serrano, A M; Rodríguez-Carvajal, M A; Tejero-Mateo, P; Espartero, J L; Menendez, M; Corzo, J; Ruiz-Sainz, J E; BuendíA-Clavería, A M

1999-01-01

The structure of a polysaccharide from Sinorhizobium fredii HH103 has been determined. This polysaccharide was isolated by following the protocol for lipopolysaccharide extraction. On the basis of monosaccharide analysis, methylation analysis, fast atom bombardment MS, matrix-assisted laser desorption ionization MS, electron-impact high-resolution MS, one-dimensional (1)H-NMR and (13)C-NMR and two-dimensional NMR experiments, the structure was shown to consist of a homopolymer of a 3:1 mixture of 5-acetamido-3,5,7, 9-tetradeoxy-7-[(R)- and (S)-3-hydroxybutyramido]-l-glycero-l-manno-nonulosonic acid. The sugar residues are attached via a glycosidic linkage to the OH group of the 3-hydroxybutyramido substituent and thus the monomers are linked via both glycosidic and amidic linkages. In contrast with the Sinorhizobium K-antigens previously reported, which are composed of a disaccharide repeating unit, the K-antigen polysacharide of S. fredii HH103 is a homopolysaccharide. PMID:10477263

Structural prerequisites for G-protein activation by the neurotensin receptor

PubMed Central

Krumm, Brian E.; White, Jim F.; Shah, Priyanka; Grisshammer, Reinhard

2015-01-01

We previously determined the structure of neurotensin receptor NTSR1 in an active-like conformation with six thermostabilizing mutations bound to the peptide agonist neurotensin. This receptor was unable to activate G proteins, indicating that the mutations restricted NTSR1 to relate agonist binding to G-protein activation. Here we analyse the effect of three of those mutations (E166A3.49, L310A6.37, F358A7.42) and present two structures of NTSR1 able to catalyse nucleotide exchange at Gα. The presence of F3587.42 causes the conserved W3216.48 to adopt a side chain orientation parallel to the lipid bilayer sealing the collapsed Na+ ion pocket and linking the agonist with residues in the lower receptor part implicated in GPCR activation. In the intracellular receptor half, the bulkier L3106.37 side chain dictates the position of R1673.50 of the highly conserved D/ERY motif. These residues, together with the presence of E1663.49 provide determinants for G-protein activation by NTSR1. PMID:26205105

Structural prerequisites for G-protein activation by the neurotensin receptor

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

Krumm, Brian E.; White, Jim F.; Shah, Priyanka

We previously determined the structure of neurotensin receptor NTSR1 in an active-like conformation with six thermostabilizing mutations bound to the peptide agonist neurotensin. This receptor was unable to activate G proteins, indicating that the mutations restricted NTSR1 to relate agonist binding to G-protein activation. Here we analyse the effect of three of those mutations (E166A 3.49, L310A 6.37, F358A 7.42) and present two structures of NTSR1 able to catalyse nucleotide exchange at Gα. The presence of F358 7.42 causes the conserved W321 6.48 to adopt a side chain orientation parallel to the lipid bilayer sealing the collapsed Na+ ion pocketmore » and linking the agonist with residues in the lower receptor part implicated in GPCR activation. In the intracellular receptor half, the bulkier L310 6.37 side chain dictates the position of R167 3.50 of the highly conserved D/ERY motif. These residues, together with the presence of E166 3.49 provide determinants for G-protein activation by NTSR1.« less

Significant Centers of Tectonic Activity as Identified by Wrinkle Ridges for the Western Hemisphere of Mars

NASA Technical Reports Server (NTRS)

Anderson, R.C.; Haldemann, A. F. C.; Golombek, M. P.; Franklin, B. J.; Dohm, J. M.; Lias, J.

2000-01-01

The western hemisphere region of Mars has been the site of numerous scientific investigations regarding its tectonic evolution. For this region of Mars, the dominant tectonic region is the Tharsis province. Tharsis is characterized by an enormous system of radiating grabens and a circumferential system of wrinkle ridges. Past investigations of grabens associated with Tharsis have identified specific centers of tectonic activity. A recent structural analysis of the western hemisphere region of Mars which includes the Tharsis region, utilized 25,000 structures to determine the history of local and regional centers of tectonic activity based primarily on the spatial and temporal relationships of extensional features. This investigation revealed that Tharsis is more structurally complex (heterogeneous) than has been previously identified: it consists of numerous regional and local centers of tectonic activity (some are more dominant and/or more long lived than others). Here we use the same approach as Anderson et al. to determine whether the centers of tectonic activity that formed the extensional features also contributed to wrinkle ridge (compressional) formation.

A new crystal form of a hyperthermophilic endocellulase

PubMed Central

Kataoka, Misumi; Ishikawa, Kazuhiko

2014-01-01

The hyperthermophilic glycoside hydrolase family endocellulase 12 from the archaeon Pyrococcus furiosus (EGPf; Gene ID PF0854; EC 3.2.1.4) catalyzes the hydrolytic cleavage of the β-1,4-glucosidic linkage in β-glucan in lignocellulose biomass. A crystal of EGPf was previously prepared at pH 9.0 and its structure was determined at an atomic resolution of 1.07 Å. This article reports the crystallization of EGPf at the more physiologically relevant pH of 5.5. Structure determination showed that this new crystal form has the symmetry of space group C2. Two molecules of the enzyme are observed in the asymmetric unit. Crystal packing is weak at pH 5.5 owing to two flexible interfaces between symmetry-related molecules. Comparison of the EGPf structures obtained at pH 9.0 and pH 5.5 reveals a significant conformational difference at the active centre and in the surface loops. The interfaces in the vicinity of the flexible surface loops impact the quality of the EGPf crystal. PMID:25005081

Relationships between residue Voronoi volume and sequence conservation in proteins.

PubMed

Liu, Jen-Wei; Cheng, Chih-Wen; Lin, Yu-Feng; Chen, Shao-Yu; Hwang, Jenn-Kang; Yen, Shih-Chung

2018-02-01

Functional and biophysical constraints can cause different levels of sequence conservation in proteins. Previously, structural properties, e.g., relative solvent accessibility (RSA) and packing density of the weighted contact number (WCN), have been found to be related to protein sequence conservation (CS). The Voronoi volume has recently been recognized as a new structural property of the local protein structural environment reflecting CS. However, for surface residues, it is sensitive to water molecules surrounding the protein structure. Herein, we present a simple structural determinant termed the relative space of Voronoi volume (RSV); it uses the Voronoi volume and the van der Waals volume of particular residues to quantify the local structural environment. RSV (range, 0-1) is defined as (Voronoi volume-van der Waals volume)/Voronoi volume of the target residue. The concept of RSV describes the extent of available space for every protein residue. RSV and Voronoi profiles with and without water molecules (RSVw, RSV, VOw, and VO) were compared for 554 non-homologous proteins. RSV (without water) showed better Pearson's correlations with CS than did RSVw, VO, or VOw values. The mean correlation coefficient between RSV and CS was 0.51, which is comparable to the correlation between RSA and CS (0.49) and that between WCN and CS (0.56). RSV is a robust structural descriptor with and without water molecules and can quantitatively reflect evolutionary information in a single protein structure. Therefore, it may represent a practical structural determinant to study protein sequence, structure, and function relationships. Copyright © 2017 Elsevier B.V. All rights reserved.

Relationships between attitudes toward and achievement in science for rural middle school students: Patterns across gender

NASA Astrophysics Data System (ADS)

Mattern, Nancy Page Garland

Four causal models describing the relationships between attitudes and achievement have been proposed in the literature. The cross-effects, or reciprocal effects, model highlights the effects of prior attitudes on later achievement (over and above the effect of previous achievement) and of prior achievement on later attitudes (above the effect of previous attitudes). In the achievement predominant model, the effect of prior achievement on later attitudes is emphasized, controlling for the effect of previous attitudes. The effect of prior attitudes on later achievement, controlling for the effect of previous achievement, is emphasized in the attitudes predominant model. In the no cross-effects model there are no significant cross paths from prior attitudes to later achievement or from prior achievement to later attitudes. To determine the best-fitting model for rural seventh and eighth grade science girls and boys, the causal relationships over time between attitudes toward science and achievement in science were examined by gender using structural equation modeling. Data were collected in two waves, over one school year. A baseline measurement model was estimated in simultaneous two-group solutions and was a good fit to the data. Next, the four structural models were estimated and model fits compared. The three models nested within the structural cross-effects model showed significant decay of fit when compared to the fit of the cross-effects model. The cross-effects model was the best fit overall for middle school girls and boys. The cross-effects model was then tested for invariance across gender. There was significant decay of fit when model form, factor path loadings, and structural paths were constrained to be equal for girls and boys. Two structural paths, the path from prior achievement to later attitudes, and the path from prior attitudes to later attitudes, were the sources of gender non-invariance. Separate models were estimated for girls and boys, and the fits of nested models were compared. The no cross-effects model was the best-fitting model for rural middle school girls. The new no attitudes-path model was the best-fitting model for boys. Implications of these findings for teaching middle school students were discussed.

Structures and kinetics for plant nucleoside triphosphate diphosphohydrolases support a domain motion catalytic mechanism.

PubMed

Summers, Emma L; Cumming, Mathew H; Oulavallickal, Tifany; Roberts, Nicholas J; Arcus, Vickery L

2017-08-01

Extracellular nucleoside triphosphate diphosphohydrolases (NTPDases) are enzymes that hydrolyze extracellular nucleotides to the respective monophosphate nucleotides. In the past 20 years, NTPDases belonging to mammalian, parasitic and prokaryotic domains of life have been discovered, cloned and characterized. We reveal the first structures of NTPDases from the legume plant species Trifolium repens (7WC) and Vigna unguiculata subsp. cylindrica (DbLNP). Four crystal structures of 7WC and DbLNP were determined at resolutions between 1.9 and 2.6 Å. For 7WC, structures were determined for an -apo form (1.89 Å) and with the product AMP (2.15 Å) and adenine and phosphate (1.76 Å) bound. For DbLNP, a structure was solved with phosphate and manganese bound (2.60 Å). Thorough kinetic data and analysis is presented. The structure of 7WC and DbLNP reveals that these NTPDases can adopt two conformations depending on the molecule and co-factor bound in the active site. A central hinge region creates a "butterfly-like" motion of the domains that reduces the width of the inter-domain active site cleft upon molecule binding. This phenomenon has been previously described in Rattus norvegicus and Legionella pneumophila NTPDaseI and Toxoplasma gondii NTPDaseIII suggesting a common catalytic mechanism across the domains of life. © 2017 The Protein Society.

Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site.

PubMed

Roston, Daniel; Demapan, Darren; Cui, Qiang

2016-06-15

A reaction's transition state (TS) structure plays a critical role in determining reactivity and has important implications for the design of catalysts, drugs, and other applications. Here, we explore TS structure in the enzyme alkaline phosphatase using hybrid Quantum Mechanics/Molecular Mechanics simulations. We find that minor perturbations to the substrate have major effects on TS structure and the way the enzyme stabilizes the TS. Substrates with good leaving groups (LGs) have little cleavage of the phosphorus-LG bond at the TS, while substrates with poor LGs have substantial cleavage of that bond. The results predict nonlinear free energy relationships for a single rate-determining step, and substantial differences in kinetic isotope effects for different substrates; both trends were observed in previous experimental studies, although the original interpretations differed from the present model. Moreover, due to different degrees of phosphorus-LG bond cleavage at the TS for different substrates, the LG is stabilized by different interactions at the TS: while a poor LG is directly stabilized by an active site zinc ion, a good LG is mainly stabilized by active site water molecules. Our results demonstrate the considerable plasticity of TS structure and stabilization in enzymes. Furthermore, perturbations to reactivity that probe TS structure experimentally (i.e., substituent effects) may substantially perturb the TS they aim to probe, and thus classical experimental approaches such as free energy relations should be interpreted with care.

Crystal structure of TBC1D15 GTPase‐activating protein (GAP) domain and its activity on Rab GTPases

PubMed Central

Chen, Yan‐Na; Gu, Xin; Zhou, X. Edward; Wang, Weidong; Cheng, Dandan; Ge, Yinghua; Ye, Fei

2017-01-01

Abstract TBC1D15 belongs to the TBC (Tre‐2/Bub2/Cdc16) domain family and functions as a GTPase‐activating protein (GAP) for Rab GTPases. So far, the structure of TBC1D15 or the TBC1D15·Rab complex has not been determined, thus, its catalytic mechanism on Rab GTPases is still unclear. In this study, we solved the crystal structures of the Shark and Sus TBC1D15 GAP domains, to 2.8 Å and 2.5 Å resolution, respectively. Shark‐TBC1D15 and Sus‐TBC1D15 belong to the same subfamily of TBC domain‐containing proteins, and their GAP‐domain structures are highly similar. This demonstrates the evolutionary conservation of the TBC1D15 protein family. Meanwhile, the newly determined crystal structures display new variations compared to the structures of yeast Gyp1p Rab GAP domain and TBC1D1. GAP assays show that Shark and Sus GAPs both have higher catalytic activity on Rab11a·GTP than Rab7a·GTP, which differs from the previous study. We also demonstrated the importance of arginine and glutamine on the catalytic sites of Shark GAP and Sus GAP. When arginine and glutamine are changed to alanine or lysine, the activities of Shark GAP and Sus GAP are lost. PMID:28168758

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation

PubMed Central

Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L.; Freund, Stefan M.; Menzel, Andreas; Fersht, Alan R.; Jemth, Per; van der Spoel, David; Davidsson, Jan

2015-01-01

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution. PMID:25946337

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation.

PubMed

Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L; Freund, Stefan M; Menzel, Andreas; Fersht, Alan R; Jemth, Per; van der Spoel, David; Davidsson, Jan

2015-01-01

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution.

Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils.

PubMed

Long, Xi-En; Yao, Huaiying; Wang, Juan; Huang, Ying; Singh, Brajesh K; Zhu, Yong-Guan

2015-06-16

Previous studies suggested that microbial photosynthesis plays a potential role in paddy fields, but little is known about chemoautotrophic carbon fixers in drained paddy soils. We conducted a microcosm study using soil samples from five paddy fields to determine the environmental factors and quantify key functional microbial taxa involved in chemoautotrophic carbon fixation. We used stable isotope probing in combination with phospholipid fatty acid (PLFA) and molecular approaches. The amount of microbial (13)CO2 fixation was determined by quantification of (13)C-enriched fatty acid methyl esters and ranged from 21.28 to 72.48 ng of (13)C (g of dry soil)(-1), and the corresponding ratio (labeled PLFA-C:total PLFA-C) ranged from 0.06 to 0.49%. The amount of incorporationof (13)CO2 into PLFAs significantly increased with soil pH except at pH 7.8. PLFA and high-throughput sequencing results indicated a dominant role of Gram-negative bacteria or proteobacteria in (13)CO2 fixation. Correlation analysis indicated a significant association between microbial community structure and carbon fixation. We provide direct evidence of chemoautotrophic C fixation in soils with statistical evidence of microbial community structure regulation of inorganic carbon fixation in the paddy soil ecosystem.

A putative siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIMB 400: cloning, expression, purification, crystallization and X-ray diffraction analysis

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

Trindade, Inês B.; Fonseca, Bruno M.; Matias, Pedro M.

The gene encoding a putative siderophore-interacting protein from the marine bacterium S. frigidimarina was successfully cloned, followed by expression and purification of the gene product. Optimized crystals diffracted to 1.35 Å resolution and preliminary crystallographic analysis is promising with respect to structure determination and increased insight into the poorly understood molecular mechanisms underlying iron acquisition. Siderophore-binding proteins (SIPs) perform a key role in iron acquisition in multiple organisms. In the genome of the marine bacterium Shewanella frigidimarina NCIMB 400, the gene tagged as SFRI-RS12295 encodes a protein from this family. Here, the cloning, expression, purification and crystallization of this proteinmore » are reported, together with its preliminary X-ray crystallographic analysis to 1.35 Å resolution. The SIP crystals belonged to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 48.04, b = 78.31, c = 67.71 Å, α = 90, β = 99.94, γ = 90°, and are predicted to contain two molecules per asymmetric unit. Structure determination by molecular replacement and the use of previously determined ∼2 Å resolution SIP structures with ∼30% sequence identity as templates are ongoing.« less

Jet-cooled laser-induced fluorescence spectroscopy of cyclohexoxy: rotational and fine structure of molecules in nearly degenerate electronic States.

PubMed

Liu, Jinjun; Miller, Terry A

2014-12-26

The rotational structure of the previously observed B̃(2)A' ← X̃(2)A″ and B̃(2)A' ← Ã(2)A' laser-induced fluorescence spectra of jet-cooled cyclohexoxy radical (c-C6H11O) [ Zu, L.; Liu, J.; Tarczay, G.; Dupré, P; Miller, T. A. Jet-cooled laser spectroscopy of the cyclohexoxy radical. J. Chem. Phys. 2004 , 120 , 10579 ] has been analyzed and simulated using a spectroscopic model that includes the coupling between the nearly degenerate X̃ and à states separated by ΔE. The rotational and fine structure of these two states is reproduced by a 2-fold model using one set of molecular constants including rotational constants, spin-rotation constants (ε's), the Coriolis constant (Aζt), the quenched spin-orbit constant (aζed), and the vibronic energy separation between the two states (ΔE0). The energy level structure of both states can also be reproduced using an isolated-state asymmetric top model with rotational constants and effective spin-rotation constants (ε's) and without involving Coriolis and spin-orbit constants. However, the spin-orbit interaction introduces transitions that have no intensity using the isolated-state model but appear in the observed spectra. The line intensities are well simulated using the 2-fold model with an out-of-plane (b-) transition dipole moment for the B̃ ← X̃ transitions and in-plane (a and c) transition dipole moment for the B̃ ← à transitions, requiring the symmetry for the X̃ (Ã) state to be A″ (A'), which is consistent with a previous determination and opposite to that of isopropoxy, the smallest secondary alkoxy radical. The experimentally determined Ã-X̃ separation and the energy level ordering of these two states with different (A' and A″) symmetries are consistent with quantum chemical calculations. The 2-fold model also enables the independent determination of the two contributions to the Ã-X̃ separation: the relativistic spin-orbit interaction (magnetic effect) and the nonrelativistic vibronic separation between the lowest vibrational energy levels of these two states due to both electrostatic interaction (Coulombic effect) and difference in zero-point energies (kinetic effect).

Rotational and Fine Structure of Pseudo-Jahn Molecules with C_1 Symmetry

NASA Astrophysics Data System (ADS)

Liu, Jinjun

2016-06-01

It has been found in our previous works that rotational and fine-structure analysis of spectra involving nearly degenerate electronic states may aid in interpretation and analysis of the vibronic structure, specifically in the case of pseudo-Jahn-Teller (pJT) molecules with C_s symmetry. The spectral analysis of pJT derivatives (isopropoxy and cyclohexoxy of a prototypical JT molecule (the methoxy radical) allowed for quantitative determination of various contributions to the energy separation between the nearly degenerate electronic states, including the relativistic spin-orbit (SO) effect, the electrostatic interaction, and their zero-point energy difference. These states are coupled by SO and Coriolis interactions, which can also be determined accurately in rotational and fine structure analysis. Most recently, the spectroscopic model for rotational analysis of pJT molecules has been extended for analysis of molecules with C_1 symmetry, i.e., no symmetry. This model includes the six independently determinable components of the spin-rotation (SR) tensor and the three components of the SO and Coriolis interactions. It has been employed to simulate and fit high-resolution laser-induced fluorescence (LIF) spectra of jet-cooled alkoxy radicals with C_1 symmetry, including the 2-hexoxy and the 2-pentoxy radicals, as well as previously recorded LIF spectrum of the trans-conformer (defined by its OCCC dihedral angle) of the 2-butoxy radical. Although the LIF spectra can be reproduced by using either the SR constants or SO and Coriolis constants, the latter simulation offers results that are physically more meaningful whereas the SR constants have to be regarded as effective constants. Furthermore, we will review the SO and Coriolis constants of alkoxy radicals that have been investigated, starting from the well-studied methoxy radical (CH_3O). J. Liu, D. Melnik, and T. A. Miller, J. Chem. Phys. 139, 094308 (2013) J. Liu and T. A. Miller, J. Phys. Chem. A 118, 11871-11890 (2014) L. Stakhursky, L. Zu, J. Liu, and T. A. Miller, J. Chem. Phys. 125, 094316 (2006)

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

Electronic structure and mechanical properties of osmium borides, carbides and nitrides from first principles

NASA Astrophysics Data System (ADS)

Liang, Yongcheng; Zhao, Jianzhi; Zhang, Bin

2008-06-01

The stabilities, mechanical properties and electronic structures of osmium boride (OsB), carbide (OsC) and nitride (OsN), in the tungsten carbide (WC), rocksalt (NaCl), cesium chloride (CsCl) and zinc blende (ZnS) structures respectively, are systematically predicted by calculations from first-principles. Only four phases, namely, OsB(WC), OsB(CsCl), OsC(WC), and OsC(ZnS), are mechanically stable, and none is a superhard compound, contrary to previous speculation. Most importantly, we find that the changing trends of bulk modulus and shear modulus are completely different for OsB, OsC and OsN in same hexagonal WC structure, which indicates that the underlying sources of hardness and incompressibility are fundamentally different: the former is determined by bonding nature while the latter is closely associated with valence electron density.

Hubble space telescope observations and geometric models of compact multipolar planetary nebulae

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

Hsia, Chih-Hao; Chau, Wayne; Zhang, Yong

2014-05-20

We report high angular resolution Hubble Space Telescope observations of 10 compact planetary nebulae (PNs). Many interesting internal structures, including multipolar lobes, arcs, two-dimensional rings, tori, and halos, are revealed for the first time. These results suggest that multipolar structures are common among PNs, and these structures develop early in their evolution. From three-dimensional geometric models, we have determined the intrinsic dimensions of the lobes. Assuming the lobes are the result of interactions between later-developed fast winds and previously ejected asymptotic giant branch winds, the geometric structures of these PNs suggest that there are multiple phases of fast winds separatedmore » by temporal variations and/or directional changes. A scenario of evolution from lobe-dominated to cavity-dominated stages is presented. The results reported here will provide serious constraints on any dynamical models of PNs.« less

Structure of a CLC chloride ion channel by cryo-electron microscopy

PubMed Central

Park, Eunyong; Campbell, Ernest B.; MacKinnon, Roderick

2017-01-01

CLC proteins transport chloride (Cl−) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC proteins are channels that conduct Cl− ions passively, whereas others are secondary active transporters that exchange two Cl− ions for one H+. The structural basis underlying these distinctive transport mechanisms is puzzling because CLC channels and transporters are expected to share the same architecture based on sequence homology. To solve this puzzle we determined the structure of a mammalian CLC channel (CLC-K) using cryo-electron microscopy. A conserved loop in the Cl− transport pathway shows a structure markedly different from that of CLC transporters. Consequently, the cytosolic constriction for Cl− passage is widened in CLC-K such that the kinetic barrier previously postulated for Cl−/H+ transporter function would be reduced. Thus, reduction of a kinetic barrier in CLC channels enables fast flow of Cl− down its electrochemical gradient. PMID:28002411

Magnetic structure of NiS2 -xSex

NASA Astrophysics Data System (ADS)

Yano, S.; Louca, Despina; Yang, J.; Chatterjee, U.; Bugaris, D. E.; Chung, D. Y.; Peng, L.; Grayson, M.; Kanatzidis, Mercouri G.

2016-01-01

NiS2 -2 xSex is revisited to determine the magnetic structure using neutron diffraction and magnetic representational analysis. Upon cooling, the insulating parent compound, NiS2, becomes antiferromagnetic with two successive magnetic transitions. The first transition (M 1 ) occurs at TN˜39 K with Γ1ψ1 symmetry and a magnetic propagation vector of k =(000 ) . The second transition (M 2 ) occurs at TN˜30 K with k =(0.5 ,0.5 ,0.5 ) and a Γ1ψ2 symmetry with face-centered translations, giving rise to four possible magnetic domains. With doping, the system becomes metallic. The transition to the M 2 state is suppressed prior to x =0.4 while the M 1 state persists. The M 1 magnetic structure gradually vanishes by x ˜0.8 at a lower concentration than previously reported. The details of the magnetic structures are provided.

Systematic data interpretation of remote sensing in the reception of hydrocarbons, volume 1. M.S. Thesis

NASA Technical Reports Server (NTRS)

Demiranda, F. P. (Principal Investigator)

1984-01-01

The utilization of MSS-LANDSAT and RADAR imagery in the definition of morphostructural anomalies, which are indicative of hydrocarbon entrapment sites in the limit of the Middle and Lower Amazons basins was systemized. The identification and classification of the morphostructural anomalies were accomplished by means of the drainage network interpretation, based on the criteria previously proposed. Thirty anomalies were recognized, being subdivided into twenty domes, two fault controlled domes, six structural depressions, one fault controlled structural depression and one structure developed on a tilted fault block. Many anomalies are not randomly located. Rather, they seem to be aligned according to directions ENE and NNW, suggesting the presence of morphstructural trends in this part of the Amazons Basin. Significant orientations of lineaments were determined through statistical analysis, which defined many regional trends. The directions coincide with morphostructural trends orientations and with the directions of important structures in the Precambrian basement.

The structure of Escherichia coli signal recognition particle revealed by scanning transmission electron microscopy.

PubMed

Mainprize, Iain L; Beniac, Daniel R; Falkovskaia, Elena; Cleverley, Robert M; Gierasch, Lila M; Ottensmeyer, F Peter; Andrews, David W

2006-12-01

Structural studies on various domains of the ribonucleoprotein signal recognition particle (SRP) have not converged on a single complete structure of bacterial SRP consistent with the biochemistry of the particle. We obtained a three-dimensional structure for Escherichia coli SRP by cryoscanning transmission electron microscopy and mapped the internal RNA by electron spectroscopic imaging. Crystallographic data were fit into the SRP reconstruction, and although the resulting model differed from previous models, they could be rationalized by movement through an interdomain linker of Ffh, the protein component of SRP. Fluorescence resonance energy transfer experiments determined interdomain distances that were consistent with our model of SRP. Docking our model onto the bacterial ribosome suggests a mechanism for signal recognition involving interdomain movement of Ffh into and out of the nascent chain exit site and suggests how SRP could interact and/or compete with the ribosome-bound chaperone, trigger factor, for a nascent chain during translation.