Extended Lipkin-type models with residual proton-neutron interaction

International Nuclear Information System (INIS)

Stoica, S.

1999-01-01

Extended Lipkin-Meshkov-Glick (LMG) models for testing the Random Phase Approximation (RPA) and proton-neutron Random Phase Approximation (pnRPA) methods are developed taking into account explicitly the proton and neutron degrees of freedom. First, an extended LMG model for testing RPA is developed. The proton and neutron Hamiltonians are taken to be of the LMG form and, in addition, a residual proton-neutron interaction is included. Exact solutions in a SU(2) x SU(2) basis as well as the RPA solutions for the energy spectrum of the model Hamiltonian are obtained. Then, the behaviour of the first collective excited state is studied as a function of the interaction parameters of the model using the exact and RPA methods. Secondly, an extended LMG model for testing pnRPA method is developed. Besides the proton and neutron single particle terms two types of residual proton-neutron interactions, one simulating a particle-particle and the other a particle-hole interaction, are included in the model Hamiltonian, so that the model is exactly solvable in an isospin SU(2) x SU(2) basis. The exact and pnRPA spectra of the model Hamiltonian are calculated as a function of the model parameters and compared to each other. Furthermore, charge-changing operators simulating a nuclear beta decay and their action on eigenfunctions of the model Hamiltonian are defined, and transition amplitude of them are calculated using exact and pnRPA wave functions. The best agreement between the exact RPA-type calculations for spectra and transitions, was obtained when the correlated RPA ground state, instead of the uncorrelated HF ground state was employed and when both kinds of residual interactions (i.e. like- and unlike-particle two-body interactions) are included in the model Hamiltonians. (author)

Identification of residue pairing in interacting β-strands from a predicted residue contact map.

Science.gov (United States)

Mao, Wenzhi; Wang, Tong; Zhang, Wenxuan; Gong, Haipeng

2018-04-19

Despite the rapid progress of protein residue contact prediction, predicted residue contact maps frequently contain many errors. However, information of residue pairing in β strands could be extracted from a noisy contact map, due to the presence of characteristic contact patterns in β-β interactions. This information may benefit the tertiary structure prediction of mainly β proteins. In this work, we propose a novel ridge-detection-based β-β contact predictor to identify residue pairing in β strands from any predicted residue contact map. Our algorithm RDb 2 C adopts ridge detection, a well-developed technique in computer image processing, to capture consecutive residue contacts, and then utilizes a novel multi-stage random forest framework to integrate the ridge information and additional features for prediction. Starting from the predicted contact map of CCMpred, RDb 2 C remarkably outperforms all state-of-the-art methods on two conventional test sets of β proteins (BetaSheet916 and BetaSheet1452), and achieves F1-scores of ~ 62% and ~ 76% at the residue level and strand level, respectively. Taking the prediction of the more advanced RaptorX-Contact as input, RDb 2 C achieves impressively higher performance, with F1-scores reaching ~ 76% and ~ 86% at the residue level and strand level, respectively. In a test of structural modeling using the top 1 L predicted contacts as constraints, for 61 mainly β proteins, the average TM-score achieves 0.442 when using the raw RaptorX-Contact prediction, but increases to 0.506 when using the improved prediction by RDb 2 C. Our method can significantly improve the prediction of β-β contacts from any predicted residue contact maps. Prediction results of our algorithm could be directly applied to effectively facilitate the practical structure prediction of mainly β proteins. All source data and codes are available at http://166.111.152.91/Downloads.html or the GitHub address of https://github.com/wzmao/RDb2C .

The residual proton-neutron interaction and nuclear collectivity

International Nuclear Information System (INIS)

Casten, R.F.

1990-01-01

The essential role of the valence, residual p-n interaction in the development of collectivity, though long known in general terms, has recently become increasingly apparent. A brief review of the p-n interaction is given, including some very basic nuclear data that illustrate its effects and the phenomenological N p N n scheme and the P-factor. This is followed by a discussion of recent experimental extractions of p-n matrix elements throughout the periodic table and theoretical efforts to understand them, in terms of both Shell and Nilsson models. 20 refs., 13 figs

Residual correlation in two-proton interferometry from Λ-proton strong interactions

International Nuclear Information System (INIS)

Wang, Fuqiang

1999-01-01

We investigate the residual effect of Λp strong interactions in pp correlations with one proton from Λ decays. It is found that the residual correlation is about 10% of the Λp correlation strength, and has a broad distribution centered around q≅40 MeV/c. The residual correlation cannot explain the observed structure on the tail of the recently measured pp correlation function in central Pb+Pb collisions by NA49 at the Super Proton Synchrotron. (c) 1999 The American Physical Society

Weak-interaction contributions to hyperfine splitting and Lamb shift

International Nuclear Information System (INIS)

Eides, M.I.

1996-01-01

Weak-interaction contributions to hyperfine splitting and the Lamb shift in hydrogen and muonium are discussed. The problem of sign of the weak-interaction contribution to HFS is clarified, and simple physical arguments that make this sign evident are presented. It is shown that weak-interaction contributions to HFS in hydrogen and muonium have opposite signs. A weak-interaction contribution to the Lamb shift is obtained. copyright 1996 The American Physical Society

Improved Interaction Potentials for Charged Residues in Proteins

DEFF Research Database (Denmark)

Kepp, Kasper Planeta

2008-01-01

Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self-consistent, exper......Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self......, TIP4P or TIP3P; i.e., each water model requires specific water-charged molecule interaction potentials. New models (models 1 and 3) are thus described for both water models. Uncertainties in relative free energies of charged residues are ~2 kcal/mol with the new parameters, due to variations in system...

Interplay between symmetries and residual interactions in rotating nuclei

International Nuclear Information System (INIS)

Cwiok, S.; Kvasil, J.; Nazmitdinov, R.G.

1990-01-01

Using the space rotation and translation invariance of the nuclear Hamiltonian, the residual interactions for a rotating nucleus are constructed. The connection is found between the Goldstone modes of motion (spurious states) and the symmetries of equations of motion in Random Phase Approximation for states near the yrast line. (author). 18 figs

gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.

Science.gov (United States)

Serçinoglu, Onur; Ozbek, Pemra

2018-05-25

Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the role played by each in the context of MD simulations, we present a stand-alone software called gRINN (get Residue Interaction eNergies and Networks). gRINN features graphical user interfaces (GUIs) and a command-line interface for generating and analyzing pairwise residue interaction energies and energy correlations from protein MD simulation trajectories. gRINN utilizes the features of NAMD or GROMACS MD simulation packages and automatizes the steps necessary to extract residue-residue interaction energies from user-supplied simulation trajectories, greatly simplifying the analysis for the end-user. A GUI, including an embedded molecular viewer, is provided for visualization of interaction energy time-series, distributions, an interaction energy matrix, interaction energy correlations and a residue correlation matrix. gRINN additionally offers construction and analysis of Protein Energy Networks, providing residue-based metrics such as degrees, betweenness-centralities, closeness centralities as well as shortest path analysis. gRINN is free and open to all users without login requirement at http://grinn.readthedocs.io.

Computational design, construction, and characterization of a set of specificity determining residues in protein-protein interactions.

Science.gov (United States)

Nagao, Chioko; Izako, Nozomi; Soga, Shinji; Khan, Samia Haseeb; Kawabata, Shigeki; Shirai, Hiroki; Mizuguchi, Kenji

2012-10-01

Proteins interact with different partners to perform different functions and it is important to elucidate the determinants of partner specificity in protein complex formation. Although methods for detecting specificity determining positions have been developed previously, direct experimental evidence for these amino acid residues is scarce, and the lack of information has prevented further computational studies. In this article, we constructed a dataset that is likely to exhibit specificity in protein complex formation, based on available crystal structures and several intuitive ideas about interaction profiles and functional subclasses. We then defined a "structure-based specificity determining position (sbSDP)" as a set of equivalent residues in a protein family showing a large variation in their interaction energy with different partners. We investigated sequence and structural features of sbSDPs and demonstrated that their amino acid propensities significantly differed from those of other interacting residues and that the importance of many of these residues for determining specificity had been verified experimentally. Copyright © 2012 Wiley Periodicals, Inc.

Identification of transmembrane domain 6 & 7 residues that contribute to the binding pocket of the urotensin II receptor.

Science.gov (United States)

Holleran, Brian J; Domazet, Ivana; Beaulieu, Marie-Eve; Yan, Li Ping; Guillemette, Gaétan; Lavigne, Pierre; Escher, Emanuel; Leduc, Richard

2009-04-15

Urotensin II (U-II), a cyclic undecapeptide, is the natural ligand of the urotensin II (UT) receptor, a G protein-coupled receptor. In the present study, we used the substituted-cysteine accessibility method to identify specific residues in transmembrane domains (TMDs) six and seven of the rat urotensin II receptor (rUT) that contribute to the formation of the binding pocket of the receptor. Each residue in the R256(6.32)-Q283(6.59) fragment of TMD6 and the A295(7.31)-T321(7.57) fragment of TMD7 was mutated, individually, to a cysteine. The resulting mutants were expressed in COS-7 cells, which were subsequently treated with the positively charged methanethiosulfonate-ethylammonium (MTSEA) or the negatively charged methanethiosulfonate-ethylsulfonate (MTSES) sulfhydryl-specific alkylating agents. MTSEA treatment resulted in a significant reduction in the binding of TMD6 mutants F268C(6.44) and W278C(6.54) and TMD7 mutants L298C(7.34), T302C(7.38), and T303C(7.39) to (125)I-U-II. MTSES treatment resulted in a significant reduction in the binding of two additional mutants, namely L282C(6.58) in TMD6 and Y300C(7.36) in TMD7. These results suggest that specific residues orient themselves within the water-accessible binding pocket of the rUT receptor. This approach, which allowed us to identify key determinants in TMD6 and TMD7 that contribute to the UT receptor binding pocket, enabled us to further refine our homology-based model of how U-II interacts with its cognate receptor.

Amino acid residues that contribute to substrate specificity of class A beta-lactamase SME-1.

Science.gov (United States)

Majiduddin, Fahd K; Palzkill, Timothy

2005-08-01

Carbapenem antibiotics are used as antibiotics of last resort because they possess a broad spectrum of antimicrobial activity and are not easily hydrolyzed by beta-lactamases. Recently, class A enzymes, such as the SME-1, NMC-A, and IMI-1 beta-lactamases, have been identified with the capacity to hydrolyze carbapenem antibiotics. Traditional class A beta-lactamases, such as TEM-1 and SHV-1, are unable to hydrolyze carbapenem antibiotics and exhibit some differences in sequence from those that are able to hydrolyze carbapenem antibiotics. The positions that differ may contribute to the unique substrate specificity of the class A carbapenemase SME-1. Codons in the SME-1 gene representing residues 104, 105, 132, 167, 237, and 241 were randomized by site-directed mutagenesis, and functional mutants were selected for the ability to hydrolyze imipenem, ampicillin, or cefotaxime. Although several positions are important for hydrolysis of beta-lactam antibiotics, no single position was found to uniquely contribute to carbapenem hydrolysis. The results of this study support a model whereby the carbapenemase activity of SME-1 is due to a highly distributed set of interactions that subtly alter the structure of the active-site pocket.

Amino Acid Residues That Contribute to Substrate Specificity of Class A β-Lactamase SME-1

Science.gov (United States)

Majiduddin, Fahd K.; Palzkill, Timothy

2005-01-01

Carbapenem antibiotics are used as antibiotics of last resort because they possess a broad spectrum of antimicrobial activity and are not easily hydrolyzed by β-lactamases. Recently, class A enzymes, such as the SME-1, NMC-A, and IMI-1 β-lactamases, have been identified with the capacity to hydrolyze carbapenem antibiotics. Traditional class A β-lactamases, such as TEM-1 and SHV-1, are unable to hydrolyze carbapenem antibiotics and exhibit some differences in sequence from those that are able to hydrolyze carbapenem antibiotics. The positions that differ may contribute to the unique substrate specificity of the class A carbapenemase SME-1. Codons in the SME-1 gene representing residues 104, 105, 132, 167, 237, and 241 were randomized by site-directed mutagenesis, and functional mutants were selected for the ability to hydrolyze imipenem, ampicillin, or cefotaxime. Although several positions are important for hydrolysis of β-lactam antibiotics, no single position was found to uniquely contribute to carbapenem hydrolysis. The results of this study support a model whereby the carbapenemase activity of SME-1 is due to a highly distributed set of interactions that subtly alter the structure of the active-site pocket. PMID:16048956

MOLECULAR MODELING STUDY OF THE CONTRIBUTIONS OF SIDE AMINO ACID RESIDUES OF POLYMYXIN B3 TO ITS BINDING WITH E.COLI OUTER MEMBRANE LIPOPOLYSACCHARIDE

Directory of Open Access Journals (Sweden)

Lisnyak Yu. V.

2014-12-01

Full Text Available Last decades, antimicrobial peptides (AMPs are the subject of intense investigations aimed to develop effective drugs against extremely resistant nosocomial bacterial pathogens (especially Gram-negative bacteria. In particular, there has been greatly renewed interest to polymyxins, the representatives of AMPs which are specific and highly potent against Gram-negative bacteria, but have potential nephrotoxic side effect. A prerequisite of purposeful enhancement of therapeutic properties of polymyxins is a detailed knowledge of the molecular mechanisms of their interactions with cell targets. Lipopolysaccharide (LPS, the main component of the outer leaflet of outer membrane of gram-negative bacteria, is a primary cell target of polymyxins. The aim of the paper was to study the peculiarities of molecular interactions of polymyxin В3 with lipopolysaccharide of the outer membrane of gram-negative bacterium. Materials and methods The complexes of polymyxin В3 (PmВ3 and its alaninederivatives with E. coli outer membrane lipopolysaccharide were built and studied by molecular modeling methods (minimization, simulated annealing, docking. Atom coordinates of polymyxin В3 and LPS structures were taken from nuclear magnetic resonance and X-ray crystallography experiments, respectively. The AMBER03 force field was used with a 1.05 nm force cutoff. Longrange electrostatic interactions were treated by the Particle Mesh Ewald method. Results and discussion Alanine scanning of PmВ3 molecule has been carried out and the role of its side amino acid residues in the formation of complex with lipopolysaccharide has been investigated. It has been shown that substitutions of polymyxin’s Dab residues in positions 1, 3, 5, 8 and 9 for alanine markedly reduce the binding energy of PmB3-LPS complex, where as the similar substitutions of residues in positions 2, 6, 7 and 10 leave the binding energy virtually unchanged. Structural aspects of antimicrobial action of

Agrochemical residue-biota interactions in soil and aquatic ecosystems

International Nuclear Information System (INIS)

1980-01-01

Two FAO/IAEA coordinated research programmes are concerned with isotopic tracer-aided studies of agrochemical residue-biota interactions in soils and aquatic ecosystems. They currently involve 18 studies in 14 countries: Brazil, Canada, Egypt, F.R. Germany, Hungary, India, Indonesia, Iraq, Israel, Malaysia, Thailand, Turkey, USA and USSR. The aim was to develop, standardize and apply labelled substrate techniques for comparative assays of primary autotrophic and microheterotrophic production and decay, and complementary tracer techniques to determine the fate, persistence and bioconcentration of trace contaminants. Comparable data were studied concerning the current status of water bodies and likely changes due to contaminants. Soil capacity to decompose undesirable contaminants and residues, and to promote desirable transformations were studied. The techniques were also applied as a diagnostic and prognostic tool, with priority given to rice ecosystems

Contributions to the workshop `Residual ponds from open pit brown coal mining`; Beitraege zum Workshop ``Braunkohlebergbaurestseen``

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-12-31

The contributions to the workshop ``Investigations on flooding in residual ponds from open-pit mining`` deal, inter alia, with the hydrochemical development of flushing waters, the stability of the water quality of residual lakes, especially under the impact of land contamination, the influence of brine receipts by flushed residual lakes, and with the microbiological ecology of residual lakes from mining. Furthermore, geophysical studies for demonstrating paths of flow and for calculating the depth and volume of residual lakes from open-pit mining are discussed. (MSK) [Deutsch] Die Beitraege zu dem Workshop `Untersuchungen zu Flutungen in Tagebaurestseen` befassen sich unter anderem mit der hydrochemischen Entwicklung von Flutungsgewaessern, mit der Qualitaetsstabilitaet von Restseewaessern - insbesonders bei Einwirkung von Altlasten - und mit den Einfluessen von Solezufluessen bei Restseeflutung sowie mit Untersuchungen zur mikrobiologischen Oekologie in Bergbaurestseen. Desweiteren werden geophysikalische Untersuchungen zum Nachweis von Fliesswegen und die Tiefen- und Volumenberechnung eines Tagebaurestlochsees erlaeutert. (MSK)

Contributions to the workshop `Residual ponds from open pit brown coal mining`; Beitraege zum Workshop ``Braunkohlebergbaurestseen``

Energy Technology Data Exchange (ETDEWEB)

NONE

1996-12-31

The contributions to the workshop ``Investigations on flooding in residual ponds from open-pit mining`` deal, inter alia, with the hydrochemical development of flushing waters, the stability of the water quality of residual lakes, especially under the impact of land contamination, the influence of brine receipts by flushed residual lakes, and with the microbiological ecology of residual lakes from mining. Furthermore, geophysical studies for demonstrating paths of flow and for calculating the depth and volume of residual lakes from open-pit mining are discussed. (MSK) [Deutsch] Die Beitraege zu dem Workshop `Untersuchungen zu Flutungen in Tagebaurestseen` befassen sich unter anderem mit der hydrochemischen Entwicklung von Flutungsgewaessern, mit der Qualitaetsstabilitaet von Restseewaessern - insbesonders bei Einwirkung von Altlasten - und mit den Einfluessen von Solezufluessen bei Restseeflutung sowie mit Untersuchungen zur mikrobiologischen Oekologie in Bergbaurestseen. Desweiteren werden geophysikalische Untersuchungen zum Nachweis von Fliesswegen und die Tiefen- und Volumenberechnung eines Tagebaurestlochsees erlaeutert. (MSK)

The RING 2.0 web server for high quality residue interaction networks.

Science.gov (United States)

Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C E

2016-07-08

Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain-domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π-π stacking and π-cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The empirical residual proton-neutron interaction and the onset of collectivity in nuclei

International Nuclear Information System (INIS)

Casten, R.F.

1991-01-01

The critical role of the residual valence p-n interaction in the development and evolution of collectivity, and the onset of shape/phase transitions, is discussed from the standpoint of phenomenological approaches, and empirical extraction of individual p-n interaction strengths, and simple model calculation of them. 22 refs., 18 figs

Contribution to the study of the interactions between residual stresses and oxygen dissolution in a reactive deformable solid

International Nuclear Information System (INIS)

Raceanu, Laura

2011-01-01

The aim of this PhD work is to highlight the interactions between the mechanical stress and the chemical composition within diffusion of matter process for a reactive solid. The chronological evolution of our work goes from a parametric numerical study to an experimental study and reveals the role of mechanical stresses on the oxygen diffusion process. Different origins of mechanical stress were first numerically analysed from the point of view of their impacts on the process of oxygen diffusion into a metal (Zr) or a ceramic (UO 2 ) subjected to an oxidizing environment. This approach allowed us: - to identify a surface treatment (shot-peening) able to generate a residual specific stress field, as a starting point for an experimental study implementation in order to validate the numerical study conclusions; - to highlight the ability of the stress field on the stabilisation of the morphology of an undulated metal/oxide interface (case of Zr). In the experimental approach, different techniques were used to characterize the material (GDOS, SEM, TGA, hole-drilling method, micro-hardness tests). They permitted the detection of a strong influence of shot-peening on the oxidation rate. The comparison of experimental and numerical simulation results reveals strong interactions between stress and compositions fields induced by the different treatments (shot-peening and/or pre-oxidation). This study opens up many opportunities in the understanding of multi-physics coupling effects being very useful for the optimization of mechanical and chemical surface-treatments, able furthermore to favour the diffusion (nitriding, cementation) or to slow it down (corrosion). (author) [fr

A single arginine residue is required for the interaction of the electron transferring flavoprotein (ETF) with three of its dehydrogenase partners.

Science.gov (United States)

Parker, Antony R

2003-12-01

The interaction of several dehydrogenases with the electron transferring flavoprotein (ETF) is a crucial step required for the successful transfer of electrons into the electron transport chain. The exact determinants regarding the interaction of ETF with its dehydrogenase partners are still unknown. Chemical modification of ETF with arginine-specific reagents resulted in the loss, to varying degrees, of activity with medium chain acyl-coenzyme A dehydrogenase (MCAD). The kinetic profiles showed the inactivations followed pseudo-first-order kinetics for all reagents used. For activity with MCAD, maximum inactivation of ETF was accomplished by 2,3-butanedione (4% residual activity after 120 min) and it was shown that modification of one arginine residue was responsible for the inactivation. Almost 100% restoration of this ETF activity was achieved upon incubation with free arginine. However, the same 2,3-butanedione modified ETF only possessed decreased activity with dimethylglycine-(DMGDH, 44%) and sarcosine- (SDH, 27%) dehydrogenases unlike the abolition with MCAD. Full protection of ETF from arginine modification by 2,3-butanedione was achieved using substrate-protected DMGDH, MCAD and SDH respectively. Cross-protection studies of ETF with the three dehydrogenases implied use of the same single arginine residue in the binding of all three dehydrogenases. These results lead us to conclude that this single arginine residue is essential in the binding of the ETF to MCAD, but only contributes partially to the binding of ETF to SDH and DMGDH and thus, the determinants of the dehydrogenase binding sites overlap but are not identical.

The differences in hadronic cross-sections and the residues of secondary reggeons in the quark-gluon model for strong interactions

International Nuclear Information System (INIS)

Kaidalov, A.B.; Volkovitsky, P.E.

1981-01-01

In the framework of the quark-gluon picture for strong interactions based on the topological expansion and the string model, the relations between t differences of hadronic cross- section are obtained. The system of equations for the contribution of secondary reggeons (rho, ω, f, A 2 and phi and f' poles) to the elastic scattering amplitudes for arbitrary hadrons is derived. It is shown that this system has a factorized solution and the secondary reggeon residues for all hadrons are expressed in terms of the universal function g(t). The model predictions are in a good agreement with experimental data [ru

Weak interaction contribution to the energy spectrum of two-lepton system

International Nuclear Information System (INIS)

Martynenko, A.P.; Saleev, V.A.

1995-01-01

The contribution of neutral currents to the weak interaction quasi-potential of two leptons is investigated. The exact expression for the weak interaction operator of the system for arbitrary biding energies in one-boson approximation is obtained. The weak interaction contribution to the S-levels displacement of hydrogen-like atom. 14 refs

Ensemble Architecture for Prediction of Enzyme-ligand Binding Residues Using Evolutionary Information.

Science.gov (United States)

Pai, Priyadarshini P; Dattatreya, Rohit Kadam; Mondal, Sukanta

2017-11-01

Enzyme interactions with ligands are crucial for various biochemical reactions governing life. Over many years attempts to identify these residues for biotechnological manipulations have been made using experimental and computational techniques. The computational approaches have gathered impetus with the accruing availability of sequence and structure information, broadly classified into template-based and de novo methods. One of the predominant de novo methods using sequence information involves application of biological properties for supervised machine learning. Here, we propose a support vector machines-based ensemble for prediction of protein-ligand interacting residues using one of the most important discriminative contributing properties in the interacting residue neighbourhood, i. e., evolutionary information in the form of position-specific- scoring matrix (PSSM). The study has been performed on a non-redundant dataset comprising of 9269 interacting and 91773 non-interacting residues for prediction model generation and further evaluation. Of the various PSSM-based models explored, the proposed method named ROBBY (pRediction Of Biologically relevant small molecule Binding residues on enzYmes) shows an accuracy of 84.0 %, Matthews Correlation Coefficient of 0.343 and F-measure of 39.0 % on 78 test enzymes. Further, scope of adding domain knowledge such as pocket information has also been investigated; results showed significant enhancement in method precision. Findings are hoped to boost the reliability of small-molecule ligand interaction prediction for enzyme applications and drug design. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery.

Directory of Open Access Journals (Sweden)

Robert Kalescky

2016-04-01

Full Text Available Intra-protein information is transmitted over distances via allosteric processes. This ubiquitous protein process allows for protein function changes due to ligand binding events. Understanding protein allostery is essential to understanding protein functions. In this study, allostery in the second PDZ domain (PDZ2 in the human PTP1E protein is examined as model system to advance a recently developed rigid residue scan method combining with configurational entropy calculation and principal component analysis. The contributions from individual residues to whole-protein dynamics and allostery were systematically assessed via rigid body simulations of both unbound and ligand-bound states of the protein. The entropic contributions of individual residues to whole-protein dynamics were evaluated based on covariance-based correlation analysis of all simulations. The changes of overall protein entropy when individual residues being held rigid support that the rigidity/flexibility equilibrium in protein structure is governed by the La Châtelier's principle of chemical equilibrium. Key residues of PDZ2 allostery were identified with good agreement with NMR studies of the same protein bound to the same peptide. On the other hand, the change of entropic contribution from each residue upon perturbation revealed intrinsic differences among all the residues. The quasi-harmonic and principal component analyses of simulations without rigid residue perturbation showed a coherent allosteric mode from unbound and bound states, respectively. The projection of simulations with rigid residue perturbation onto coherent allosteric modes demonstrated the intrinsic shifting of ensemble distributions supporting the population-shift theory of protein allostery. Overall, the study presented here provides a robust and systematic approach to estimate the contribution of individual residue internal motion to overall protein dynamics and allostery.

Constraints on Non-Standard Contributions to the Charged-Current Interactions

CERN Document Server

Hagiwara, K; Hagiwara, Kaoru; Matsumoto, Seiji

1998-01-01

The success of the quantum level predictions of the Standard Model on the $Z$ boson properties, on $\\mw$ and on $\\mt$, which makes use of the muon lifetime as an input, implies a stringent constraint on new physics contributions to the $V-A$ charged-current interactions among leptons. Observed unitarity of the CKM matrix elements then implies constraints on non-standard contributions to the lepton-quark charged-current interactions. By using the recent electroweak data as inputs, we find the 95% CL limits for the corresponding contact interactions: $\\Lambda_{CC,+}^{\\ell\\ell}>7.5$ TeV and the lepton-quark contact interactions.

A computational tool to predict the evolutionarily conserved protein-protein interaction hot-spot residues from the structure of the unbound protein.

Science.gov (United States)

Agrawal, Neeraj J; Helk, Bernhard; Trout, Bernhardt L

2014-01-21

Identifying hot-spot residues - residues that are critical to protein-protein binding - can help to elucidate a protein's function and assist in designing therapeutic molecules to target those residues. We present a novel computational tool, termed spatial-interaction-map (SIM), to predict the hot-spot residues of an evolutionarily conserved protein-protein interaction from the structure of an unbound protein alone. SIM can predict the protein hot-spot residues with an accuracy of 36-57%. Thus, the SIM tool can be used to predict the yet unknown hot-spot residues for many proteins for which the structure of the protein-protein complexes are not available, thereby providing a clue to their functions and an opportunity to design therapeutic molecules to target these proteins. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Aging/Systems Interaction Study, Component Residual Lifetime Evaluation and Feasibility of Relicensing. Progress report, FY 1985

International Nuclear Information System (INIS)

Close, J.A.; Jacobs, P.T.; Korth, G.E.; Mudlin, J.M.; Server, W.L.; Spaletta, H.W.

1985-10-01

This report documents the work performed on four research tasks in Fiscal Year 1985 (FY-1985) which were part of the Aging/Systems Interaction Study, Component Residual Lifetime Evaluation and Feasibility of Relicensing Project. The technical and management/institutional objectives for the project are described, followed by a description of the results of each task. The work on Task 1 involved identifying and prioritizing new research activities for the Nuclear Regulatory Commission (NRC) Nuclear Plant Aging Research (NPAR) Program. A proposed methodology and plan for aging-system interaction studies was developed in Task 2. The description of Task 3 work comprises a summary of nuclear plant life extension activities in the US, the technical basis associated with the residual life of metallic materials and a proposed plan for research on residual life assessment. Task 4 describes the initial evaluation of selected Standard Review Plan (NUREG-0800) sections to investigate the feasibility of relicensing. 14 refs., 13 figs., 20 tabs

Modulating Transmembrane α-Helix Interactions through pH-Sensitive Boundary Residues.

Science.gov (United States)

Ng, Derek P; Deber, Charles M

2016-08-09

Changes in pH can alter the structure and activity of proteins and may be used by the cell to control molecular function. This coupling can also be used in non-native applications through the design of pH-sensitive biomolecules. For example, the pH (low) insertion peptide (pHLIP) can spontaneously insert into a lipid bilayer when the pH decreases. We have previously shown that the α-helicity and helix-helix interactions of the TM2 α-helix of the proteolipid protein (PLP) are sensitive to the local hydrophobicity at its C-terminus. Given that there is an ionizable residue (Glu-88) at the C-terminus of this transmembrane (TM) segment, we hypothesized that changing the ionization state of this residue through pH may alter the local hydrophobicity of the peptide enough to affect both its secondary structure and helix-helix interactions. To examine this phenomenon, we synthesized peptide analogues of the PLP TM2 α-helix (wild-type sequence (66)AFQYVIYGTASFFFLYGALLLAEGF(90)). Using circular dichroism and Förster resonance energy transfer in the membrane-mimetic detergent sodium dodecyl sulfate, we found that a decrease in pH increases both peptide α-helicity and the extent of self-association. This pH-dependent effect is due specifically to the presence of Glu-88 at the C-terminus. Additional experiments in which Phe-90 was mutated to residues of varying hydrophobicities indicated that the strength of this effect is dependent on the local hydrophobicity near Glu-88. Our results have implications for the design of TM peptide switches and improve our understanding of how membrane protein structure and activity can be regulated through local molecular environmental changes.

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.

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Gabrielle Stetz

2017-01-01

Full Text Available Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of

Protein-protein docking with dynamic residue protonation states.

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Krishna Praneeth Kilambi

2014-12-01

Full Text Available Protein-protein interactions depend on a host of environmental factors. Local pH conditions influence the interactions through the protonation states of the ionizable residues that can change upon binding. In this work, we present a pH-sensitive docking approach, pHDock, that can sample side-chain protonation states of five ionizable residues (Asp, Glu, His, Tyr, Lys on-the-fly during the docking simulation. pHDock produces successful local docking funnels in approximately half (79/161 the protein complexes, including 19 cases where standard RosettaDock fails. pHDock also performs better than the two control cases comprising docking at pH 7.0 or using fixed, predetermined protonation states. On average, the top-ranked pHDock structures have lower interface RMSDs and recover more native interface residue-residue contacts and hydrogen bonds compared to RosettaDock. Addition of backbone flexibility using a computationally-generated conformational ensemble further improves native contact and hydrogen bond recovery in the top-ranked structures. Although pHDock is designed to improve docking, it also successfully predicts a large pH-dependent binding affinity change in the Fc-FcRn complex, suggesting that it can be exploited to improve affinity predictions. The approaches in the study contribute to the goal of structural simulations of whole-cell protein-protein interactions including all the environmental factors, and they can be further expanded for pH-sensitive protein design.

Similarity of multi-fragmentation of residual nucleus created in nucleus-nucleus interactions at high energies

International Nuclear Information System (INIS)

Abdel-Hafiez, A.; Chernyavski, M.M.; Orlova, G.I.; Gulamov, K.G.; Navotny, V.SH.; Uzhinskii, V.V.

2000-01-01

Experimental data on multi-fragmentation of residual krypton nuclei created in the interactions of the krypton nuclei with photoemulsion nuclei ut energy of 0.9 GeV per nucleon are presented in a comparison with the analogous data on fragmentation of gold residual nuclei at the energy of 10.7 GeV/nucleon. It is shown for the first time that there are two regimes of nuclear multifragmentation: the former is when less than one-half of nucleons of projectile nucleus are knocked out, the later is when more than one-half of nucleons are knocked out. Residual nuclei with closed masses created at different reactions are fragmenting practically simultaneously when more than one-half of nucleons of original nuclei are knocked out. The evidence of existence of a radial flow of the spectator fragment at the decay of residual krypton nuclei is found

Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces.

Science.gov (United States)

Zerbe, Brandon S; Hall, David R; Vajda, Sandor; Whitty, Adrian; Kozakov, Dima

2012-08-27

In the context of protein-protein interactions, the term "hot spot" refers to a residue or cluster of residues that makes a major contribution to the binding free energy, as determined by alanine scanning mutagenesis. In contrast, in pharmaceutical research, a hot spot is a site on a target protein that has high propensity for ligand binding and hence is potentially important for drug discovery. Here we examine the relationship between these two hot spot concepts by comparing alanine scanning data for a set of 15 proteins with results from mapping the protein surfaces for sites that can bind fragment-sized small molecules. We find the two types of hot spots are largely complementary; the residues protruding into hot spot regions identified by computational mapping or experimental fragment screening are almost always themselves hot spot residues as defined by alanine scanning experiments. Conversely, a residue that is found by alanine scanning to contribute little to binding rarely interacts with hot spot regions on the partner protein identified by fragment mapping. In spite of the strong correlation between the two hot spot concepts, they fundamentally differ, however. In particular, while identification of a hot spot by alanine scanning establishes the potential to generate substantial interaction energy with a binding partner, there are additional topological requirements to be a hot spot for small molecule binding. Hence, only a minority of hot spots identified by alanine scanning represent sites that are potentially useful for small inhibitor binding, and it is this subset that is identified by experimental or computational fragment screening.

Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution.

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Amanda Tse

Full Text Available Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib and promiscuous (Bosutinib, Dasatinib kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations

Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

Science.gov (United States)

Tse, Amanda; Verkhivker, Gennady M.

2015-01-01

Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib) and promiscuous (Bosutinib, Dasatinib) kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations of key mediating

The disordered C-terminal domain of human DNA glycosylase NEIL1 contributes to its stability via intramolecular interactions.

Science.gov (United States)

Hegde, Muralidhar L; Tsutakawa, Susan E; Hegde, Pavana M; Holthauzen, Luis Marcelo F; Li, Jing; Oezguen, Numan; Hilser, Vincent J; Tainer, John A; Mitra, Sankar

2013-07-10

NEIL1 [Nei (endonuclease VIII)-like protein 1], one of the five mammalian DNA glycosylases that excise oxidized DNA base lesions in the human genome to initiate base excision repair, contains an intrinsically disordered C-terminal domain (CTD; ~100 residues), not conserved in its Escherichia coli prototype Nei. Although dispensable for NEIL1's lesion excision and AP lyase activities, this segment is required for efficient in vivo enzymatic activity and may provide an interaction interface for many of NEIL1's interactions with other base excision repair proteins. Here, we show that the CTD interacts with the folded domain in native NEIL1 containing 389 residues. The CTD is poised for local folding in an ordered structure that is induced in the purified fragment by osmolytes. Furthermore, deletion of the disordered tail lacking both Tyr and Trp residues causes a red shift in NEIL1's intrinsic Trp-specific fluorescence, indicating a more solvent-exposed environment for the Trp residues in the truncated protein, which also exhibits reduced stability compared to the native enzyme. These observations are consistent with stabilization of the native NEIL1 structure via intramolecular, mostly electrostatic, interactions that were disrupted by mutating a positively charged (Lys-rich) cluster of residues (amino acids 355-360) near the C-terminus. Small-angle X-ray scattering (SAXS) analysis confirms the flexibility and dynamic nature of NEIL1's CTD, a feature that may be critical to providing specificity for NEIL1's multiple, functional interactions. Copyright © 2013 Elsevier Ltd. All rights reserved.

On the importance of polar interactions for complexes containing intrinsically disordered proteins.

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Eric T C Wong

Full Text Available There is a growing recognition for the importance of proteins with large intrinsically disordered (ID segments in cell signaling and regulation. ID segments in these proteins often harbor regions that mediate molecular recognition. Coupled folding and binding of the recognition regions has been proposed to confer high specificity to interactions involving ID segments. However, researchers recently questioned the origin of the interaction specificity of ID proteins because of the overrepresentation of hydrophobic residues in their interaction interfaces. Here, we focused on the role of polar and charged residues in interactions mediated by ID segments. Making use of the extended nature of most ID segments when in complex with globular proteins, we first identified large numbers of complexes between globular proteins and ID segments by using radius-of-gyration-based selection criteria. Consistent with previous studies, we found the interfaces of these complexes to be enriched in hydrophobic residues, and that these residues contribute significantly to the stability of the interaction interface. However, our analyses also show that polar interactions play a larger role in these complexes than in structured protein complexes. Computational alanine scanning and salt-bridge analysis indicate that interfaces in ID complexes are highly complementary with respect to electrostatics, more so than interfaces of globular proteins. Follow-up calculations of the electrostatic contributions to the free energy of binding uncovered significantly stronger Coulombic interactions in complexes harbouring ID segments than in structured protein complexes. However, they are counter-balanced by even higher polar-desolvation penalties. We propose that polar interactions are a key contributing factor to the observed high specificity of ID segment-mediated interactions.

Substantial conformational change mediated by charge-triad residues of the death effector domain in protein-protein interactions.

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Edward C Twomey

Full Text Available Protein conformational changes are commonly associated with the formation of protein complexes. The non-catalytic death effector domains (DEDs mediate protein-protein interactions in a variety of cellular processes, including apoptosis, proliferation and migration, and glucose metabolism. Here, using NMR residual dipolar coupling (RDC data, we report a conformational change in the DED of the phosphoprotein enriched in astrocytes, 15 kDa (PEA-15 protein in the complex with a mitogen-activated protein (MAP kinase, extracellular regulated kinase 2 (ERK2, which is essential in regulating ERK2 cellular distribution and function in cell proliferation and migration. The most significant conformational change in PEA-15 happens at helices α2, α3, and α4, which also possess the highest flexibility among the six-helix bundle of the DED. This crucial conformational change is modulated by the D/E-RxDL charge-triad motif, one of the prominent structural features of DEDs, together with a number of other electrostatic and hydrogen bonding interactions on the protein surface. Charge-triad motif promotes the optimal orientation of key residues and expands the binding interface to accommodate protein-protein interactions. However, the charge-triad residues are not directly involved in the binding interface between PEA-15 and ERK2.

Short-term contributions of cover crop surface residue return to soil carbon and nitrogen contents in temperate Australia.

Science.gov (United States)

Zhou, Xiaoqi; Wu, Hanwen; Li, Guangdi; Chen, Chengrong

2016-11-01

Cover crop species are usually grown to control weeds. After cover crop harvest, crop residue is applied on the ground to improve soil fertility and crop productivity. Little information is available about quantifying the contributions of cover crop application to soil total carbon (C) and nitrogen (N) contents in temperate Australia. Here, we selected eight cover crop treatments, including two legume crops (vetch and field pea), four non-legume crops (rye, wheat, Saia oat, and Indian mustard), a mixture of rye and vetch, and a nil-crop control in temperate Australia to calculate the contributions of cover crops (crop growth + residue decomposition) to soil C and N contents. Cover crops were sown in May 2009 (autumn). After harvest, the crop residue was placed on the soil surface in October 2009. Soil and crop samples were collected in October 2009 after harvest and in May 2010 after 8 months of residue decomposition. We examined cover crop residue biomass, soil and crop total C and N contents, and soil microbial biomass C and N contents. The results showed that cover crop application increased the mean soil total C by 187-253 kg ha -1 and the mean soil total N by 16.3-19.1 kg ha -1 relative to the nil-crop treatment, except for the mixture treatment, which had similar total C and N contents to the nil-crop control. Cover crop application increased the mean soil microbial biomass C by 15.5-20.9 kg ha -1 and the mean soil microbial biomass N by 4.5-10.2 kg ha -1 . We calculated the apparent percentage of soil total C derived from cover crop residue C losses and found that legume crops accounted for 10.6-13.9 %, whereas non-legume crops accounted for 16.4-18.4 % except for the mixture treatment (0.2 %). Overall, short-term cover crop application increased soil total C and N contents and microbial biomass C and N contents, which might help reduce N fertilizer use and improve sustainable agricultural development.

Two Arginine Residues of Streptococcus gordonii Sialic Acid-Binding Adhesin Hsa Are Essential for Interaction to Host Cell Receptors.

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Yumiko Urano-Tashiro

Full Text Available Hsa is a large, serine-rich protein of Streptococcus gordonii DL1 that mediates binding to α2-3-linked sialic acid termini of glycoproteins, including platelet glycoprotein Ibα, and erythrocyte membrane protein glycophorin A, and band 3. The binding of Hsa to platelet glycoprotein Ibα contributes to the pathogenesis of infective endocarditis. This interaction appears to be mediated by a second non-repetitive region (NR2 of Hsa. However, the molecular details of the interaction between the Hsa NR2 region and these glycoproteins are not well understood. In the present study, we identified the amino acid residues of the Hsa NR2 region that are involved in sialic acid recognition. To identify the sialic acid-binding site of Hsa NR2 region, we prepared various mutants of Hsa NR2 fused with glutathione transferase. Fusion proteins harboring Arg340 to Asn (R340N or Arg365 to Asn (R365N substitutions in the NR2 domain exhibited significantly reduced binding to human erythrocytes and platelets. A sugar-binding assay showed that these mutant proteins abolished binding to α2-3-linked sialic acid. Furthermore, we established S. gordonii DL1 derivatives that encoded the corresponding Hsa mutant protein. In whole-cell assays, these mutant strains showed significant reductions in hemagglutination, in platelet aggregation, and in adhesion to human leukocytes. These results indicate that the Arg340 and Arg365 residues of Hsa play an important role in the binding of Hsa to α2-3-linked sialic acid-containing glycoproteins.

Intragenic suppressor of Osiaa23 revealed a conserved tryptophan residue crucial for protein-protein interactions.

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Jun Ni

Full Text Available The Auxin/Indole-3-Acetic Acid (Aux/IAA and Auxin Response Factor (ARF are two important families that play key roles in auxin signal transduction. Both of the families contain a similar carboxyl-terminal domain (Domain III/IV that facilitates interactions between these two families. In spite of the importance of protein-protein interactions among these transcription factors, the mechanisms involved in these interactions are largely unknown. In this study, we isolated six intragenic suppressors of an auxin insensitive mutant, Osiaa23. Among these suppressors, Osiaa23-R5 successfully rescued all the defects of the mutant. Sequence analysis revealed that an amino acid substitution occurred in the Tryptophan (W residue in Domain IV of Osiaa23. Yeast two-hybrid experiments showed that the mutation in Domain IV prevents the protein-protein interactions between Osiaa23 and OsARFs. Phylogenetic analysis revealed that the W residue is conserved in both OsIAAs and OsARFs. Next, we performed site-specific amino acid substitutions within Domain IV of OsARFs, and the conserved W in Domain IV was exchanged by Serine (S. The mutated OsARF(WSs can be released from the inhibition of Osiaa23 and maintain the transcriptional activities. Expression of OsARF(WSs in Osiaa23 mutant rescued different defects of the mutant. Our results suggest a previously unknown importance of Domain IV in both families and provide an indirect way to investigate functions of OsARFs.

Influenza human monoclonal antibody 1F1 interacts with three major antigenic sites and residues mediating human receptor specificity in H1N1 viruses.

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Tshidi Tsibane

Full Text Available Most monoclonal antibodies (mAbs to the influenza A virus hemagglutinin (HA head domain exhibit very limited breadth of inhibitory activity due to antigenic drift in field strains. However, mAb 1F1, isolated from a 1918 influenza pandemic survivor, inhibits select human H1 viruses (1918, 1943, 1947, and 1977 isolates. The crystal structure of 1F1 in complex with the 1918 HA shows that 1F1 contacts residues that are classically defined as belonging to three distinct antigenic sites, Sa, Sb and Ca(2. The 1F1 heavy chain also reaches into the receptor binding site (RBS and interacts with residues that contact sialoglycan receptors and determine HA receptor specificity. The 1F1 epitope is remarkably similar to the previously described murine HC63 H3 epitope, despite significant sequence differences between H1 and H3 HAs. Both antibodies potently inhibit receptor binding, but only HC63 can block the pH-induced conformational changes in HA that drive membrane fusion. Contacts within the RBS suggested that 1F1 may be sensitive to changes that alter HA receptor binding activity. Affinity assays confirmed that sequence changes that switch the HA to avian receptor specificity affect binding of 1F1 and a mAb possessing a closely related heavy chain, 1I20. To characterize 1F1 cross-reactivity, additional escape mutant selection and site-directed mutagenesis were performed. Residues 190 and 227 in the 1F1 epitope were found to be critical for 1F1 reactivity towards 1918, 1943 and 1977 HAs, as well as for 1I20 reactivity towards the 1918 HA. Therefore, 1F1 heavy-chain interactions with conserved RBS residues likely contribute to its ability to inhibit divergent HAs.

Interaction torque contributes to planar reaching at slow speed

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Hoshi Fumihiko

2008-10-01

Full Text Available Abstract Background How the central nervous system (CNS organizes the joint dynamics for multi-joint movement is a complex problem, because of the passive interaction among segmental movements. Previous studies have demonstrated that the CNS predictively compensates for interaction torque (INT which is arising from the movement of the adjacent joints. However, most of these studies have mainly examined quick movements, presumably because the current belief is that the effects of INT are not significant at slow speeds. The functional contribution of INT for multijoint movements performed in various speeds is still unclear. The purpose of this study was to examine the contribution of INT to a planer reaching in a wide range of motion speeds for healthy subjects. Methods Subjects performed reaching movements toward five targets under three different speed conditions. Joint position data were recorded using a 3-D motion analysis device (50 Hz. Torque components, muscle torque (MUS, interaction torque (INT, gravity torque (G, and net torque (NET were calculated by solving the dynamic equations for the shoulder and elbow. NET at a joint which produces the joint kinematics will be an algebraic sum of torque components; NET = MUS - G - INT. Dynamic muscle torque (DMUS = MUS-G was also calculated. Contributions of INT impulse and DMUS impulse to NET impulse were examined. Results The relative contribution of INT to NET was not dependent on speed for both joints at every target. INT was additive (same direction to DMUS at the shoulder joint, while in the elbow DMUS counteracted (opposed to INT. The trajectory of reach was linear and two-joint movements were coordinated with a specific combination at each target, regardless of motion speed. However, DMUS at the elbow was opposed to the direction of elbow movement, and its magnitude varied from trial to trial in order to compensate for the variability of INT. Conclusion Interaction torque was important at

Residual stresses

International Nuclear Information System (INIS)

Macherauch, E.

1978-01-01

Residual stresses are stresses which exist in a material without the influence of external powers and moments. They come into existence when the volume of a material constantly changes its form as a consequence of mechanical, thermal, and/or chemical processes and is hindered by neighbouring volumes. Bodies with residual stress are in mechanical balance. These residual stresses can be manifested by means of all mechanical interventions disturbing this balance. Acoustical, optical, radiological, and magnetical methods involving material changes caused by residual stress can also serve for determining residual stress. Residual stresses have an ambivalent character. In technical practice, they are feared and liked at the same time. They cause trouble because they can be the cause for unexpected behaviour of construction elements. They are feared since they can cause failure, in the worst case with catastrophical consequences. They are appreciated, on the other hand, because, in many cases, they can contribute to improvements of the material behaviour under certain circumstances. But they are especially liked for their giving convenient and (this is most important) mostly uncontrollable explanations. For only in very few cases we have enough knowledge and possibilities for the objective evaluation of residual stresses. (orig.) [de

Near target residues from the peripheral interaction of relativistic heavy ions with bismuth

International Nuclear Information System (INIS)

Aleklett, K.; Morrissey, D.J.; Loveland, W.; Moody, K.; Seaborg, G.T.

1979-01-01

Isotopic distributions for the near target residues Au and Tl were measured radioanalytically for the reaction of 8.0-GeV 20 Ne ions with 209 Bi. The isotopic production cross section for Au and Tl isotopes were calculated by using a macroscopic abrasion-ablation model and a microscopic intranuclear cascade-evaporation model. The importance of the neutron skin in determining the yield of these products from the peripheral interactions was also explored in the framework of the macroscopic model. 3 figures

Spring Chinook Salmon Interactions Indices and Residual/Precocial Monitoring in the Upper Yakima Basin, Annual Report 1998

International Nuclear Information System (INIS)

James, Brenda B.; Pearsons, Todd N.; McMichael, Geoffrey A.

1999-01-01

Select ecological interactions and spring chinook salmon residual/precocial abundance were monitored in 1998 as part of the Yakima/Klickitat Fisheries Project's supplementation monitoring program. Monitoring these variables is part of an effort to help evaluate the factors that contribute to, or limit supplementation success. The ecological interactions that were monitored were prey consumption, competition for food, and competition for space. The abundance of spring chinook salmon life-history forms that have the potential to be influenced by supplementation and that have important ecological and genetic roles were monitored (residuals and precocials). Residual spring chinook salmon do not migrate to the ocean during the normal emigration period and continue to rear in freshwater. Precocials are those salmon that precocially mature in freshwater. The purpose of sampling during 1998 was to collect baseline data one year prior to the release of hatchery spring chinook salmon which occurred during the spring of 1999. All sampling that the authors report on here was conducted in upper Yakima River during summer and fall 1998. The stomach fullness of juvenile spring chinook salmon during the summer and fall averaged 12%. The food competition index suggested that mountain whitefish (0.59), rainbow trout (0.55), and redside shiner (0.55) were competing for food with spring chinook salmon. The space competition index suggested that rainbow trout (0.31) and redside shiner (0.39) were competing for space with spring chinook salmon but mountain whitefish (0.05) were not. Age-0 spring chinook salmon selected a fairly narrow range of microhabitat parameters in the summer and fall relative to what was available. Mean focal depths and velocities for age 0 spring chinook salmon during the summer were 0.5 m ± 0.2 m and 0.26 m/s ± 0.19 m/s, and during the fall 0.5 m ± 0.2 m and 0.24 m/s ± 0.18 m/s. Among potential competitors, age 1+ rainbow trout exhibited the greatest degree

Residual analysis for spatial point processes

DEFF Research Database (Denmark)

Baddeley, A.; Turner, R.; Møller, Jesper

We define residuals for point process models fitted to spatial point pattern data, and propose diagnostic plots based on these residuals. The techniques apply to any Gibbs point process model, which may exhibit spatial heterogeneity, interpoint interaction and dependence on spatial covariates. Ou...... or covariate effects. Q-Q plots of the residuals are effective in diagnosing interpoint interaction. Some existing ad hoc statistics of point patterns (quadrat counts, scan statistic, kernel smoothed intensity, Berman's diagnostic) are recovered as special cases....

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase.

Science.gov (United States)

Nascimento, Érica C M; Oliva, Mónica; Andrés, Juan

2018-05-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

Science.gov (United States)

Nascimento, Érica C. M.; Oliva, Mónica; Andrés, Juan

2018-05-01

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

Hydrogen bond strengths in phosphorylated and sulfated amino acid residues.

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Chaya Rapp

Full Text Available Post-translational modification by the addition of an oxoanion functional group, usually a phosphate group and less commonly a sulfate group, leads to diverse structural and functional consequences in protein systems. Building upon previous studies of the phosphoserine residue (pSer, we address the distinct nature of hydrogen bonding interactions in phosphotyrosine (pTyr and sulfotyrosine (sTyr residues. We derive partial charges for these modified residues and then study them in the context of molecular dynamics simulation of model tripeptides and sulfated protein complexes, potentials of mean force for interacting residue pairs, and a survey of the interactions of modified residues among experimental protein structures. Overall, our findings show that for pTyr, bidentate interactions with Arg are particularly dominant, as has been previously demonstrated for pSer. sTyr interactions with Arg are significantly weaker, even as compared to the same interactions made by the Glu residue. Our work sheds light on the distinct nature of these modified tyrosine residues, and provides a physical-chemical foundation for future studies with the goal of understanding their roles in systems of biological interest.

International symposium on restoration of environments with radioactive residues. Contributed papers

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-07-01

After the use of radioactive materials or the utilization of nuclear energy, some radioactive residues may remain in the environment and give rise to the exposure of persons living or working in that environment. Most commonly, these residues are the result of human activities that have been carried out in the past without proper regard to the internationally accepted radiation protection requirements for practices, or at that time when those requirements were less stringent than today. Of course unforeseen events such as accidents of concentrations of naturally occurring radioactive material can also lead to higher levels of radioactive residues in theenvironment. The purpose of this Symposium is to foster an information exchange on the restoration of environments with radioactive residues. This includes the principles and criteria for guiding decision making and the methodologies for assessing the radiological situation and developing remediation plans for the human habitats affected. The overall aim is to promote an international consensus on the relevant issues in these areas. This document contains 51 presentations delivered during oral and poster sessions. Each of the presentations was separately indexed and provided with an abstract.

International symposium on restoration of environments with radioactive residues. Contributed papers

International Nuclear Information System (INIS)

1999-01-01

After the use of radioactive materials or the utilization of nuclear energy, some radioactive residues may remain in the environment and give rise to the exposure of persons living or working in that environment. Most commonly, these residues are the result of human activities that have been carried out in the past without proper regard to the internationally accepted radiation protection requirements for practices, or at that time when those requirements were less stringent than today. Of course unforeseen events such as accidents of concentrations of naturally occurring radioactive material can also lead to higher levels of radioactive residues in the environment. The purpose of this Symposium is to foster an information exchange on the restoration of environments with radioactive residues. This includes the principles and criteria for guiding decision making and the methodologies for assessing the radiological situation and developing remediation plans for the human habitats affected. The overall aim is to promote an international consensus on the relevant issues in these areas. This document contains 51 presentations delivered during oral and poster sessions. Each of the presentations was separately indexed and provided with an abstract

The importance of residues 195-206 of human blood clotting factor VII in the interaction of factor VII with tissue factor

International Nuclear Information System (INIS)

Wildgoose, P.; Kisiel, W.; Kazim, A.L.

1990-01-01

Previous studies indicated that human and bovine factor VII exhibit 71% amino acid sequence identity. In the present study, competition binding experiments revealed that the interaction of human factor VII with cell-surface human tissue factor was not inhibited by 100-fold molar excess of bovine factor VII. This finding indicated that bovine and human factor VII are not structurally homologous in the region(s) where human factor VII interacts with human tissue factor. On this premise, the authors synthesized three peptides corresponding to regions of human factor VII that exhibited marked structural dissimilarity to bovine factor VII; these regions of dissimilarity included residues 195-206, 263-274, and 314-326. Peptide 195-206 inhibited the interaction of factor VII with cell-surface tissue factor and the activation of factor X by a complex of factor VIIa and tissue factor half-maximally at concentrations of 1-2 mM. A structurally rearranged form of peptide 195-206 containing an aspartimide residue inhibited these reactions half-maximally at concentrations of 250-300 μM. In contrast, neither peptide 263-274 nor peptide 314-326, at 2 mM concentration, significantly affected either factor VIIa interaction with tissue factor or factor VIIa-mediated activation of factor X. The data provide presumptive evidence that residues 195-206 of human factor VII are involved in the interaction of human factor VII with the extracellular domain of human tissue factor apoprotein

A non-catalytic histidine residue influences the function of the metalloprotease of Listeria monocytogenes.

Science.gov (United States)

Forster, Brian M; Bitar, Alan Pavinski; Marquis, Hélène

2014-01-01

Mpl, a thermolysin-like metalloprotease, and PC-PLC, a phospholipase C, are synthesized as proenzymes by the intracellular bacterial pathogen Listeria monocytogenes. During intracellular growth, L. monocytogenes is temporarily confined in a membrane-bound vacuole whose acidification leads to Mpl autolysis and Mpl-mediated cleavage of the PC-PLC N-terminal propeptide. Mpl maturation also leads to the secretion of both Mpl and PC-PLC across the bacterial cell wall. Previously, we identified negatively charged and uncharged amino acid residues within the N terminus of the PC-PLC propeptide that influence the ability of Mpl to mediate the maturation of PC-PLC, suggesting that these residues promote the interaction of the PC-PLC propeptide with Mpl. In the present study, we identified a non-catalytic histidine residue (H226) that influences Mpl secretion across the cell wall and its ability to process PC-PLC. Our results suggest that a positive charge at position 226 is required for Mpl functions other than autolysis. Based on the charge requirement at this position, we hypothesize that this residue contributes to the interaction of Mpl with the PC-PLC propeptide.

Contribution of Eucalyptus Harvest Residues and Nitrogen Fertilization to Carbon Stabilization in Ultisols of Southern Bahia

Directory of Open Access Journals (Sweden)

Fernanda Cristina Caparelli Oliveira

2018-02-01

Full Text Available ABSTRACT: Eucalyptus forests in southern Bahia (BA are planted in soils with a sandy surface layer and humid tropical climate, conditions that lead to soil carbon (C decomposition. Recent studies have shown that nitrogen (N may be important for soil C stabilization. The aim of this study was to evaluate the contribution of Eucalyptus harvest residues and nitrogen fertilization to C stabilization in Ultisols of southern BA. The experiment was conducted in Eucalyptus clonal plantations cultivated in two regions of Eunápolis, BA, Brazil, with different clay content: southern region (140 g kg-1 of clay and western region (310 g kg-1 of clay. Five treatments were evaluated: one control (CTR, without Eucalyptus harvest residues and N fertilization, and four treatments with harvest residues combined with four rates of N fertilization: 0, 25, 50, and 100 kg ha-1. Soil samples were collected from the 0.00-0.10, 0.10-0.20, 0.20-0.40, and 0.40-0.60 m layers at the beginning and the end of the experiment (36 months. The amount of C and N and the C and N isotopic ratio (δ13C and δ15N of particulate organic matter (POM and mineral-associated organic matter (MAOM were determined. In the southern region after 36 months, the C-MAOM stocks in the 0.00-0.10 m layer of the CTR decreased by 33 %. The addition of harvest residue followed by 100 kg ha-1 N increased C-POM and N-POM stocks (0.00-0.10 m compared to the CTR, and the final N-POM stocks and residue-C recovery in the surface soil layer were positively correlated with the increase in N fertilization rates. In the western region, residue maintenance resulted in increased C-MAOM stocks (0.00-0.10 m compared to the CTR, but an increase in N availability reduced this increment. The increase in N fertilization rates did not alter C stocks, but reduced N stocks of POM and MAOM in the upper soil layer. At the end of the experiment, N fertilizer recovery (0.00-0.60 m was similar among the regions evaluated. In

A method for predicting individual residue contributions to enzyme specificity and binding-site energies, and its application to MTH1.

Science.gov (United States)

Stewart, James J P

2016-11-01

A new method for predicting the energy contributions to substrate binding and to specificity has been developed. Conventional global optimization methods do not permit the subtle effects responsible for these properties to be modeled with sufficient precision to allow confidence to be placed in the results, but by making simple alterations to the model, the precisions of the various energies involved can be improved from about ±2 kcal mol -1 to ±0.1 kcal mol -1 . This technique was applied to the oxidized nucleotide pyrophosphohydrolase enzyme MTH1. MTH1 is unusual in that the binding and reaction sites are well separated-an advantage from a computational chemistry perspective, as it allows the energetics involved in docking to be modeled without the need to consider any issues relating to reaction mechanisms. In this study, two types of energy terms were investigated: the noncovalent interactions between the binding site and the substrate, and those responsible for discriminating between the oxidized nucleotide 8-oxo-dGTP and the normal dGTP. Both of these were investigated using the semiempirical method PM7 in the program MOPAC. The contributions of the individual residues to both the binding energy and the specificity of MTH1 were calculated by simulating the effect of mutations. Where comparisons were possible, all calculated results were in agreement with experimental observations. This technique provides fresh insight into the binding mechanism that enzymes use for discriminating between possible substrates.

Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution

Science.gov (United States)

Braberg, Hannes; Moehle, Erica A.; Shales, Michael; Guthrie, Christine; Krogan, Nevan J.

2014-01-01

We have achieved a residue-level resolution of genetic interaction mapping – a technique that measures how the function of one gene is affected by the alteration of a second gene – by analyzing point mutations. Here, we describe how to interpret point mutant genetic interactions, and outline key applications for the approach, including interrogation of protein interaction interfaces and active sites, and examination of post-translational modifications. Genetic interaction analysis has proven effective for characterizing cellular processes; however, to date, systematic high-throughput genetic interaction screens have relied on gene deletions or knockdowns, which limits the resolution of gene function analysis and poses problems for multifunctional genes. Our point mutant approach addresses these issues, and further provides a tool for in vivo structure-function analysis that complements traditional biophysical methods. We also discuss the potential for genetic interaction mapping of point mutations in human cells and its application to personalized medicine. PMID:24842270

EVALUATING AUSTRALIAN FOOTBALL LEAGUE PLAYER CONTRIBUTIONS USING INTERACTIVE NETWORK SIMULATION

Directory of Open Access Journals (Sweden)

Jonathan Sargent

2013-03-01

Full Text Available This paper focuses on the contribution of Australian Football League (AFL players to their team's on-field network by simulating player interactions within a chosen team list and estimating the net effect on final score margin. A Visual Basic computer program was written, firstly, to isolate the effective interactions between players from a particular team in all 2011 season matches and, secondly, to generate a symmetric interaction matrix for each match. Negative binomial distributions were fitted to each player pairing in the Geelong Football Club for the 2011 season, enabling an interactive match simulation model given the 22 chosen players. Dynamic player ratings were calculated from the simulated network using eigenvector centrality, a method that recognises and rewards interactions with more prominent players in the team network. The centrality ratings were recorded after every network simulation and then applied in final score margin predictions so that each player's match contribution-and, hence, an optimal team-could be estimated. The paper ultimately demonstrates that the presence of highly rated players, such as Geelong's Jimmy Bartel, provides the most utility within a simulated team network. It is anticipated that these findings will facilitate optimal AFL team selection and player substitutions, which are key areas of interest to coaches. Network simulations are also attractive for use within betting markets, specifically to provide information on the likelihood of a chosen AFL team list "covering the line".

The H2A-H2B dimeric kinetic intermediate is stabilized by widespread hydrophobic burial with few fully native interactions.

Science.gov (United States)

Guyett, Paul J; Gloss, Lisa M

2012-01-20

The H2A-H2B histone heterodimer folds via monomeric and dimeric kinetic intermediates. Within ∼5 ms, the H2A and H2B polypeptides associate in a nearly diffusion limited reaction to form a dimeric ensemble, denoted I₂ and I₂*, the latter being a subpopulation characterized by a higher content of nonnative structure (NNS). The I₂ ensemble folds to the native heterodimer, N₂, through an observable, first-order kinetic phase. To determine the regions of structure in the I₂ ensemble, we characterized 26 Ala mutants of buried hydrophobic residues, spanning the three helices of the canonical histone folds of H2A and H2B and the H2B C-terminal helix. All but one targeted residue contributed significantly to the stability of I₂, the transition state and N₂; however, only residues in the hydrophobic core of the dimer interface perturbed the I₂* population. Destabilization of I₂* correlated with slower folding rates, implying that NNS is not a kinetic trap but rather accelerates folding. The pattern of Φ values indicated that residues forming intramolecular interactions in the peripheral helices contributed similar stability to I₂ and N₂, but residues involved in intermolecular interactions in the hydrophobic core are only partially folded in I₂. These findings suggest a dimerize-then-rearrange model. Residues throughout the histone fold contribute to the stability of I₂, but after the rapid dimerization reaction, the hydrophobic core of the dimer interface has few fully native interactions. In the transition state leading to N₂, more native-like interactions are developed and nonnative interactions are rearranged. Copyright © 2011 Elsevier Ltd. All rights reserved.

Residue preference mapping of ligand fragments in the Protein Data Bank.

Science.gov (United States)

Wang, Lirong; Xie, Zhaojun; Wipf, Peter; Xie, Xiang-Qun

2011-04-25

The interaction between small molecules and proteins is one of the major concerns for structure-based drug design because the principles of protein-ligand interactions and molecular recognition are not thoroughly understood. Fortunately, the analysis of protein-ligand complexes in the Protein Data Bank (PDB) enables unprecedented possibilities for new insights. Herein, we applied molecule-fragmentation algorithms to split the ligands extracted from PDB crystal structures into small fragments. Subsequently, we have developed a ligand fragment and residue preference mapping (LigFrag-RPM) algorithm to map the profiles of the interactions between these fragments and the 20 proteinogenic amino acid residues. A total of 4032 fragments were generated from 71 798 PDB ligands by a ring cleavage (RC) algorithm. Among these ligand fragments, 315 unique fragments were characterized with the corresponding fragment-residue interaction profiles by counting residues close to these fragments. The interaction profiles revealed that these fragments have specific preferences for certain types of residues. The applications of these interaction profiles were also explored and evaluated in case studies, showing great potential for the study of protein-ligand interactions and drug design. Our studies demonstrated that the fragment-residue interaction profiles generated from the PDB ligand fragments can be used to detect whether these fragments are in their favorable or unfavorable environments. The algorithm for a ligand fragment and residue preference mapping (LigFrag-RPM) developed here also has the potential to guide lead chemistry modifications as well as binding residues predictions.

Conserved residues in the coiled-coil pocket of human immunodeficiency virus type 1 gp41 are essential for viral replication and interhelical interaction

International Nuclear Information System (INIS)

Mo Hongmei; Konstantinidis, Alex K.; Stewart, Kent D.; Dekhtyar, Tatyana; Ng, Teresa; Swift, Kerry; Matayoshi, Edmund D.; Kati, Warren; Kohlbrenner, William; Molla, Akhteruzzaman

2004-01-01

The human immunodeficiency virus type 1 (HIV-1) gp41 plays an important role in mediating the fusion of HIV with host cells. During the fusion process, three N-terminal helices and three C-terminal helices pack in an anti-parallel direction to form a six-helix bundle. X-ray crystallographic analysis of the gp41 core demonstrated that within each coiled-coil interface, there is a deep and large pocket, formed by a cluster of residues in the N-helix coiled-coil. In this report, we systematically analyzed the role of seven conserved residues that are either lining or packing this pocket on the infectivity and interhelical interaction using novel approaches. Our results show that residues L568, V570, W571, and K574 of the N-helix that are lining the side chain and right wall of the pocket are important for establishing a productive infection. Mutations V570A and W571A completely abolished replication, while replication of the L568A and K574A mutants was significantly attenuated relative to wild type. Similarly, residues W628, W631, and I635 of the C-helix that insert into the pocket are essential for infectivity. The impaired infectivity of these seven mutants is in part attributed to the loss in binding affinity of the interhelical interaction. Molecular modeling of the crystal structure of the coiled-coil further shows that alanine substitution of those residues disrupts the hydrophobic interaction between the N- and C-helix. These results suggest that the conserved residues in the coiled-coil domain play a key role in HIV infection and this coiled-coil pocket is a good target for development of inhibitors against HIV. In addition, our data indicate that the novel fluorescence polarization assay described in this study could be valuable in screening for inhibitors that block the interhelical interaction and HIV entry

Conserved Aromatic Residue Confers Cation Selectivity in Claudin-2 and Claudin-10b*

Science.gov (United States)

Li, Jiahua; Zhuo, Min; Pei, Lei; Yu, Alan S. L.

2013-01-01

In tight junctions, both claudin-2 and claudin-10b form paracellular cation-selective pores by the interaction of the first ECL 1 with permeating ions. We hypothesized that a highly conserved aromatic residue near the pore selectivity filter of claudins contributes to cation selectivity by cation-π interaction with the permeating cation. To test this, we generated MDCK I Tet-off cells stably transfected with claudin-2 Tyr67 mutants. The Y67L mutant showed reduced cation selectivity compared with wild-type claudin-2 due to a decrease in Na+ permeability, without affecting the Cl− permeability. The Y67A mutant enlarged the pore size and further decreased the charge selectivity due to an increase in Cl− permeability. The Y67F mutant restored the Na+ permeability, Cl− permeability, and pore size back to wild-type. The accessibility of Y67C to methanethiosulfonate modification indicated that its side chain faces the lumen of the pore. In claudin-10b, the F66L mutant reduced cation selectivity, and the F66A mutant lost pore conductance. We conclude that the conserved aromatic residue near the cation pore domain of claudins contributes to cation selectivity by a dual role of cation-π interaction and a luminal steric effect. Our findings provide new insight into how ion selectivity is achieved in the paracellular pore. PMID:23760508

Combined Role of Two Tryptophane Residues of α-Factor Pheromone

Energy Technology Data Exchange (ETDEWEB)

Hong, Eun Young [Yeungnam Univ., Gyungsan (Korea, Republic of); Hong, Nam Joo [Seoul National Univ., Seoul (Korea, Republic of)

2013-02-15

Amide analogs of tridecapeptide α-factor (WHWLQLKPGQPMYCONH{sub 2}) of Saccharomyces cerevisiae, in which Trp at position 1 and 3 were replaced with other residues, were synthesized to ascertain whether cooperative interactions between two Trp residues occurred upon binding with its receptor. Analogs containing Ala or Aib at position 3 of the peptide [Ala{sup 3}]α-factor amide (2) and [Aib{sup 3}]α-factor amide (5) exhibited greater decreases in bioactivity than analogs with same residue at position one [Ala{sup 1}]α-factor amide (1) and [Aib{sup 1}]α-factor amide (4), reflecting that Trp{sup 3} may plays more important role than Trp{sup 1} for agonist activity. Analogs containing Ala or Aib in both position one and three 3, 6 exhibited complete loss of bioactivity, emphasizing both the essential role and the combined role of two indole rings for triggering cell signaling. In contrast, double substituted analog with D-Trp in both positions 9 exhibited greater activity than single substituted analog with D-Trp 8 or deleted analog 7, reflecting the combined contribution of two tryptophane residues of α-factor ligand to activation of Ste2p through interaction with residue Tyr{sup 266} and importance of the proper parallel orientation of two indole rings for efficient triggering of signal G protein coupled activation. Among ten amide analogs, [Ala{sup 1,3}]α-factor amide (3), [Aib{sup 1,3}]α-factor amide (6), [D-Trp{sup 3}]α-factor amide (8) and [des-Trp{sup 1},Phe{sup 3}]α-factor amide (10) were found to have antagonistic activity. Analogs 3 and 6 showed greater antagonistic activity than analogs 8 and 10.

Combined Role of Two Tryptophane Residues of α-Factor Pheromone

International Nuclear Information System (INIS)

Hong, Eun Young; Hong, Nam Joo

2013-01-01

Amide analogs of tridecapeptide α-factor (WHWLQLKPGQPMYCONH 2 ) of Saccharomyces cerevisiae, in which Trp at position 1 and 3 were replaced with other residues, were synthesized to ascertain whether cooperative interactions between two Trp residues occurred upon binding with its receptor. Analogs containing Ala or Aib at position 3 of the peptide [Ala 3 ]α-factor amide (2) and [Aib 3 ]α-factor amide (5) exhibited greater decreases in bioactivity than analogs with same residue at position one [Ala 1 ]α-factor amide (1) and [Aib 1 ]α-factor amide (4), reflecting that Trp 3 may plays more important role than Trp 1 for agonist activity. Analogs containing Ala or Aib in both position one and three 3, 6 exhibited complete loss of bioactivity, emphasizing both the essential role and the combined role of two indole rings for triggering cell signaling. In contrast, double substituted analog with D-Trp in both positions 9 exhibited greater activity than single substituted analog with D-Trp 8 or deleted analog 7, reflecting the combined contribution of two tryptophane residues of α-factor ligand to activation of Ste2p through interaction with residue Tyr 266 and importance of the proper parallel orientation of two indole rings for efficient triggering of signal G protein coupled activation. Among ten amide analogs, [Ala 1,3 ]α-factor amide (3), [Aib 1,3 ]α-factor amide (6), [D-Trp 3 ]α-factor amide (8) and [des-Trp 1 ,Phe 3 ]α-factor amide (10) were found to have antagonistic activity. Analogs 3 and 6 showed greater antagonistic activity than analogs 8 and 10

A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening.

Science.gov (United States)

Jasper, Julia B; Humbeck, Lina; Brinkjost, Tobias; Koch, Oliver

2018-03-16

Protein ligand interaction fingerprints are a powerful approach for the analysis and assessment of docking poses to improve docking performance in virtual screening. In this study, a novel interaction fingerprint approach (PADIF, protein per atom score contributions derived interaction fingerprint) is presented which was specifically designed for utilising the GOLD scoring functions' atom contributions together with a specific scoring scheme. This allows the incorporation of known protein-ligand complex structures for a target-specific scoring. Unlike many other methods, this approach uses weighting factors reflecting the relative frequency of a specific interaction in the references and penalizes destabilizing interactions. In addition, and for the first time, an exhaustive validation study was performed that assesses the performance of PADIF and two other interaction fingerprints in virtual screening. Here, PADIF shows superior results, and some rules of thumb for a successful use of interaction fingerprints could be identified.

Interactive Contributions of Attribution Biases and Emotional Intensity to Child-Friend Interaction Quality During Preadolescence.

Science.gov (United States)

Chen, Xi; McElwain, Nancy L; Lansford, Jennifer E

2017-12-20

Using data from a subsample of 913 study children and their friends who participated in the NICHD Study of Early Child Care and Youth Development, the interactive contributions of child-reported attribution biases and teacher-reported child emotional intensity (EI) at Grade 4 (M = 9.9 years) to observed child-friend interaction at Grade 6 (M = 11.9 years) were examined. Study children's hostile attribution bias, combined with high EI, predicted more negative child-friend interaction. In contrast, benign attribution bias, combined with high EI, predicted more positive child-friend interaction. The findings are discussed in light of the "fuel" interpretation of EI, in which high-intensity emotions may motivate children to act on their cognitive biases for better or for worse. © 2017 The Authors. Child Development © 2017 Society for Research in Child Development, Inc.

Interaction between chitosan and its related enzymes: A review.

Science.gov (United States)

Shinya, Shoko; Fukamizo, Tamo

2017-11-01

Chitosan-related enzymes including chitosanases, exo-β-glucosaminidases, and enzymes having chitosan-binding modules recognize ligands through electrostatic interactions between the acidic amino acids in proteins and amino groups of chitosan polysaccharides. However, in GH8 chitosanases, several aromatic residues are also involved in substrate recognition through stacking interactions, and these enzymes consequently hydrolyze β-1,4-glucan as well as chitosan. The binding grooves of these chitosanases are extended and opened at both ends of the grooves, so that the enzymes can clamp a long chitosan polysaccharide. The association/dissociation of positively charged glucosamine residues to/from the binding pocket of a GH2 exo-β-glucosaminidase controls the p K a of the catalytic acid, thereby maintaining the high catalytic potency of the enzyme. In contrast to chitosanases, chitosan-binding modules only accommodate a couple of glucosamine residues, predominantly recognizing the non-reducing end glucosamine residue of chitosan by electrostatic interactions and a hydrogen-bonding network. These structural findings on chitosan-related enzymes may contribute to future applications for the efficient conversion of the chitin/chitosan biomass. Copyright © 2017 Elsevier B.V. All rights reserved.

Profile Monitors Based on Residual Gas Interaction

CERN Document Server

Forck, P; Giacomini, T; Peters, A

2005-01-01

The precise determination of transverse beam profiles at high current hadron accelerators has to be performed non-interceptingly. Two methods will be discussed based on the excitation of the residual gas molecules by the beam particles: Firstly, by beam induced fluorescence (BIF) light is emitted from the residual gas molecules and is observed with an image intensified CCD camera. At most laboratories N2 gas is inserted, which has a large cross section for emission in the blue wave length region. Secondly, a larger signal strength is achieved by detecting the ionization products in an Ionization Profile Monitor (IPM). By applying an electric field all ionization products are accelerated toward a spatial resolving Micro-Channel Plate. The signal read-out can either be performed by observing the light from a phosphor screen behind the MCP or electronically by a wire array. Methods to achieve a high spatial resolution and a fast turn-by-turn readout capability are discussed. Even though various approaches at dif...

Effects of the residual proton-neutron interaction in the development of collectivity in nuclei

International Nuclear Information System (INIS)

Casten, R.F.

1990-01-01

The widespread effects of the residual T=0 proton-neutron (p-n) interaction in the evolution of nuclear structure are discussed. Although these effects in inducing single nucleon configuration mixing, and hence in the development of non-spherical nuclear shapes, collectivity, and the associated shape and phase transitions have been known for four decades, it is only in recent years that their deep ramifications have become more fully appreciated. This had led to a unified phenomenological understanding of the role of the p-n interaction in nuclear collectivity and to, for example, the proposal of the N p N n scheme and the associated concept of the P factor, which is a normalized value of N p N n reflecting the average number of p-n interactions per valence nucleon. Simultaneously, experimentally-determined p-n matrix elements for many nuclei have been extracted: they disclose striking anomalies for N=Z nuclei, and intriguing microstructure. These developments and empirical results will be discussed along with microscopic calculations that can be used to interpret them. 18 refs., 13 figs

Quantum oscillation signatures of spin-orbit interactions controlling the residual nodal bilayer-splitting in underdoped high-Tc cuprates

Science.gov (United States)

Harrison, Neil; Shekhter, Arkady

2015-03-01

We investigate the origin of the small residual nodal bilayer-splitting in the underdoped high-Tc superconductor YBa2Cu3O6+x using the results of recently published angle-resolved quantum oscillation data [Sebastian et al., Nature 511, 61 (2014)]. A crucial clue to the origin of the residual bilayer-splitting is found to be provided by the anomalously small Zeeman-splitting of some of the observed cyclotron orbits. We show that such an anomalously Zeeman-splitting (or small effective g-factor) for a subset of orbits can be explained by spin-orbit interactions, which become significant in the nodal regions as a result of the vanishing bilayer coupling. The primary effect of spin-orbit interactions is to cause quasiparticles traversing the nodal region of the Brillouin zone to undergo a spin flip. We suggest that the Rashba-like spin-orbit interactions, naturally present in bilayer systems, have the right symmetry and magnitude to give rise to a network of coupled orbits consistent with experimental observations in underdoped YBa2Cu3O6+x. This work is supported by the DOEm BES proposal LANLF100, while the magnet lab is supported by the NSF and Florida State.

Interaction of elementary damage processes and their contribution to neutron damage of ceramics

International Nuclear Information System (INIS)

Itoh, Noriaki

1989-01-01

Specific features of radiation damage of ceramics as compared with those of metals are discussed. It is pointed out that the electronic excitation gives considerable contribution to radiation damage of ceramics not only by itself but also through interaction with knock-on processes. In the talk first I mention briefly the elementary damage processes; the knock-on process and the processes induced by electronic excitation; the latter is of particularly importance in ceramics because of large energy quantums. Then I discuss possible interactions between these elementary processes; why they may contribute to radiation damage and in what situation they are induced. The types of interactions discussed include those between knock-on processes, between electronic excitation and knock-on processes and between processes induced by electronic excitation. Experimental results which prove directly the significance of such interactions are also described. Importance of such interactions in radiation damage of ceramics and their relevance to other phenomena, such as laser damage, is emphasized. Possible experimental techniques, including those which uses high energy neutron sources, are described. (author)

Relative contribution of residual renal function and different measures of adequacy to survival in hemodialysis patients: an analysis of the Netherlands Cooperative Study on the Adequacy of Dialysis (NECOSAD)-2

NARCIS (Netherlands)

Termorshuizen, Fabian; Dekker, Friedo W.; van Manen, Jeannette G.; Korevaar, Johanna C.; Boeschoten, Elisabeth W.; Krediet, Raymond T.

2004-01-01

A high delivered Kt/V(urea) (dKt/V(urea)) is advocated in the U.S. National Kidney Foundation Dialysis Outcomes Quality Initiative guidelines on hemodialysis (HD) adequacy, irrespective of the presence of residual renal function. The contribution of treatment adequacy and residual renal function to

Effect of Context on the Contribution of Individual Harmonics to Residue Pitch.

Science.gov (United States)

Gockel, Hedwig E; Alsindi, Sami; Hardy, Charles; Carlyon, Robert P

2017-12-01

There is evidence that the contribution of a given harmonic in a complex tone to residue pitch is influenced by the accuracy with which the frequency of that harmonic is encoded. The present study investigated whether listeners adjust the weights assigned to individual harmonics based on acquired knowledge of the reliability of the frequency estimates of those harmonics. In a two-interval forced-choice task, seven listeners indicated which of two 12-harmonic complex tones had the higher overall pitch. In context trials (60 % of all trials), the fundamental frequency (F0) was 200 Hz in one interval and 200 + ΔF0 Hz in the other. In different (blocked) conditions, either the 3rd or the 4th harmonic (plus the 7th, 9th, and 12th harmonics), were replaced by narrowband noises that were identical in the two intervals. Feedback was provided. In randomly interspersed test trials (40 % of all trials), the fundamental frequency was 200 + ΔF0/2 Hz in both intervals; in the second interval, either the third or the fourth harmonic was shifted slightly up or down in frequency with equal probability. There were no narrowband noises. Feedback was not provided. The results showed that substitution of a harmonic by noise in context trials reduced the contribution of that harmonic to pitch judgements in the test trials by a small but significant amount. This is consistent with the notion that listeners give smaller weight to a harmonic or frequency region when they have learned that this frequency region does not provide reliable information for a given task.

Structure-wise discrimination of cytosine, thymine, and uracil by proteins in terms of their nonbonded interactions.

Science.gov (United States)

Usha, S; Selvaraj, S

2014-01-01

The molecular recognition and discrimination of very similar ligand moieties by proteins are important subjects in protein-ligand interaction studies. Specificity in the recognition of molecules is determined by the arrangement of protein and ligand atoms in space. The three pyrimidine bases, viz. cytosine, thymine, and uracil, are structurally similar, but the proteins that bind to them are able to discriminate them and form interactions. Since nonbonded interactions are responsible for molecular recognition processes in biological systems, our work attempts to understand some of the underlying principles of such recognition of pyrimidine molecular structures by proteins. The preferences of the amino acid residues to contact the pyrimidine bases in terms of nonbonded interactions; amino acid residue-ligand atom preferences; main chain and side chain atom contributions of amino acid residues; and solvent-accessible surface area of ligand atoms when forming complexes are analyzed. Our analysis shows that the amino acid residues, tyrosine and phenyl alanine, are highly involved in the pyrimidine interactions. Arginine prefers contacts with the cytosine base. The similarities and differences that exist between the interactions of the amino acid residues with each of the three pyrimidine base atoms in our analysis provide insights that can be exploited in designing specific inhibitors competitive to the ligands.

Some problems of residual activity measurements

International Nuclear Information System (INIS)

Katrik, P.; Mustafin, E.; Strasik, I.; Pavlovic, M.

2013-01-01

As a preparatory work for constructing the Facility for Antiproton and Ion Research (FAIR) at GSI Darmstadt, samples of copper were irradiated by 500 MeV/u 238 U ion beam and investigated by gamma-ray spectroscopy. The nuclides that contribute dominantly to the residual activity have been identified and their contributions have been quantified by two different methods: from the whole-target gamma spectra and by integration of depth-profiles of residual activity of individual nuclides. Results obtained by these two methods are compared and discussed in this paper. (authors)

Amino Acid Interaction (INTAA) web server.

Science.gov (United States)

Galgonek, Jakub; Vymetal, Jirí; Jakubec, David; Vondrášek, Jirí

2017-07-03

Large biomolecules-proteins and nucleic acids-are composed of building blocks which define their identity, properties and binding capabilities. In order to shed light on the energetic side of interactions of amino acids between themselves and with deoxyribonucleotides, we present the Amino Acid Interaction web server (http://bioinfo.uochb.cas.cz/INTAA/). INTAA offers the calculation of the residue Interaction Energy Matrix for any protein structure (deposited in Protein Data Bank or submitted by the user) and a comprehensive analysis of the interfaces in protein-DNA complexes. The Interaction Energy Matrix web application aims to identify key residues within protein structures which contribute significantly to the stability of the protein. The application provides an interactive user interface enhanced by 3D structure viewer for efficient visualization of pairwise and net interaction energies of individual amino acids, side chains and backbones. The protein-DNA interaction analysis part of the web server allows the user to view the relative abundance of various configurations of amino acid-deoxyribonucleotide pairs found at the protein-DNA interface and the interaction energies corresponding to these configurations calculated using a molecular mechanical force field. The effects of the sugar-phosphate moiety and of the dielectric properties of the solvent on the interaction energies can be studied for the various configurations. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

Science.gov (United States)

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

2009-05-01

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

Unique contributions of an arginine side chain to ligand recognition in a glutamate-gated chloride channel

DEFF Research Database (Denmark)

Lynagh, Timothy; Komnatnyy, Vitaly V; Pless, Stephan A

2017-01-01

Glutamate recognition by neurotransmitter receptors often relies on arginine (Arg) residues in the binding site, leading to the assumption that charge-charge interactions underlie ligand recognition. However, assessing the precise chemical contribution of Arg side chains to protein function......-gated chloride channel from the nematode Haemonchus contortus. Our data unveil a surprisingly small contribution of charge at a conserved arginine side chain previously suggested to form a salt bridge with the ligand, glutamate. Instead, our data show that Arg contributes crucially to ligand sensitivity via...

Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions.

Science.gov (United States)

Akiba, Hiroki; Tsumoto, Kouhei

2015-07-01

Antibodies (immunoglobulins) bind specific molecules (i.e. antigens) with high affinity and specificity. In order to understand their mechanisms of recognition, interaction analysis based on thermodynamic and kinetic parameters, as well as structure determination is crucial. In this review, we focus on mutational analysis which gives information about the role of each amino acid residue in antibody-antigen interaction. Taking anti-hen egg lysozyme antibodies and several anti-small molecule antibodies, the energetic contribution of hot-spot and non-hot-spot residues is discussed in terms of thermodynamics. Here, thermodynamics of the contribution from aromatic, charged and hydrogen bond-forming amino acids are discussed, and their different characteristics have been elucidated. The information gives fundamental understanding of the antibody-antigen interaction. Furthermore, the consequences of antibody engineering are analysed from thermodynamic viewpoints: humanization to reduce immunogenicity and rational design to improve affinity. Amino acid residues outside hot-spots in the interface play important roles in these cases, and thus thermodynamic and kinetic parameters give much information about the antigen recognition. Thermodynamic analysis of mutant antibodies thus should lead to advanced strategies to design and select antibodies with high affinity. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels

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McDermott Drew

2009-08-01

Full Text Available Abstract Background Proteins interact through specific binding interfaces that contain many residues in domains. Protein interactions thus occur on three different levels of a concept hierarchy: whole-proteins, domains, and residues. Each level offers a distinct and complementary set of features for computationally predicting interactions, including functional genomic features of whole proteins, evolutionary features of domain families and physical-chemical features of individual residues. The predictions at each level could benefit from using the features at all three levels. However, it is not trivial as the features are provided at different granularity. Results To link up the predictions at the three levels, we propose a multi-level machine-learning framework that allows for explicit information flow between the levels. We demonstrate, using representative yeast interaction networks, that our algorithm is able to utilize complementary feature sets to make more accurate predictions at the three levels than when the three problems are approached independently. To facilitate application of our multi-level learning framework, we discuss three key aspects of multi-level learning and the corresponding design choices that we have made in the implementation of a concrete learning algorithm. 1 Architecture of information flow: we show the greater flexibility of bidirectional flow over independent levels and unidirectional flow; 2 Coupling mechanism of the different levels: We show how this can be accomplished via augmenting the training sets at each level, and discuss the prevention of error propagation between different levels by means of soft coupling; 3 Sparseness of data: We show that the multi-level framework compounds data sparsity issues, and discuss how this can be dealt with by building local models in information-rich parts of the data. Our proof-of-concept learning algorithm demonstrates the advantage of combining levels, and opens up

Calculation of contribution of multiple interactions and efficiency of neutron detectors

International Nuclear Information System (INIS)

Androsenko, A.A.; Androsenko, P.A.; Kazakov, L.E.; Kononov, V.N.; Poletaev, E.D.

1986-01-01

Results of calculation of multiple neutron interactions contribution to efficiency of detectors with 6 Li glass and 10 B plate in the energy range of 0.01-1 MeV are given. The calculation was performed by the Monte-Carlo method using BRAND program complex. It is shown that a correction value for multiple neutron interaction in 6 Li glass of 1 mm thickness constitutes 4.5 % at energy of up to 100 keV and at higher energies has a complex energy dependence reaching 25 % at 440 keV

Elicitin-induced distal systemic resistance in plants is mediated through the protein-protein interactions influenced by selected lysine residues

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Hana eUhlíková

2016-02-01

Full Text Available Elicitins are a family of small proteins with sterol-binding activity that are secreted by Phytophthora and Pythium spp. classified as oomycete PAMPs. Although alfa- and beta-elicitins bind with the same affinity to one high affinity binding site on the plasma membrane, beta-elicitins (possessing 6-7 lysine residues are generally 50- to 100-fold more active at inducing distal HR and systemic resistance than the alfa-isoforms (with only 1-3 lysine residues.To examine the role of lysine residues in elicitin biological activity, we employed site-directed mutagenesis to prepare a series of beta-elicitin cryptogein variants with mutations on specific lysine residues. In contrast to direct infiltration of protein into leaves, application to the stem revealed a rough correlation between protein’s charge and biological activity, resulting in protection against Phytophthora parasitica. A detailed analysis of proteins’ movement in plants showed no substantial differences in distribution through phloem indicating differences in consequent apoplastic or symplastic transport. In this process, an important role of homodimer formation together with the ability to form a heterodimer with potential partner represented by endogenous plants LTPs is suggested. Our work demonstrates a key role of selected lysine residues in these interactions and stresses the importance of processes preceding elicitin recognition responsible for induction of distal systemic resistance.

Complexity in modeling of residual stresses and strains during polymerization of bone cement: effects of conversion, constraint, heat transfer, and viscoelastic property changes.

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Gilbert, Jeremy L

2006-12-15

Aseptic loosening of cemented joint prostheses remains a significant concern in orthopedic biomaterials. One possible contributor to cement loosening is the development of porosity, residual stresses, and local fracture of the cement that may arise from the in-situ polymerization of the cement. In-situ polymerization of acrylic bone cement is a complex set of interacting processes that involve polymerization reactions, heat generation and transfer, full or partial mechanical constraint, evolution of conversion- and temperature-dependent viscoelastic material properties, and thermal and conversion-driven changes in the density of the cement. Interactions between heat transfer and polymerization can lead to polymerization fronts moving through the material. Density changes during polymerization can, in the presence of mechanical constraint, lead to the development of locally high residual strain energy and residual stresses. This study models the interactions during bone cement polymerization and determines how residual stresses develop in cement and incorporates temperature and conversion-dependent viscoelastic behavior. The results show that the presence of polymerization fronts in bone cement result in locally high residual strain energies. A novel heredity integral approach is presented to track residual stresses incorporating conversion and temperature dependent material property changes. Finally, the relative contribution of thermal- and conversion-dependent strains to residual stresses is evaluated and it is found that the conversion-based strains are the major contributor to the overall behavior. This framework provides the basis for understanding the complex development of residual stresses and can be used as the basis for developing more complex models of cement behavior.

Contribution of buried aspartic acid to the stability of the PDZ2 protein

International Nuclear Information System (INIS)

Jayasimha, Pruthvi; Shanmuganathan, Aranganathan; Suladze, Saba; Makhatadze, George I.

2012-01-01

Highlights: ► Buried Asp residues on average form 2.5 to 3 hydrogen bonds and/or 0.8 salt bridges. ► Contribution of buried Asp to stability was estimated using model protein PDZ2. ► The energetic contribution of Asp56 to PDZ2 stability estimated to be 18 kJ · mol −1 . ► Findings are discussed in terms of contribution of Asp residues to protein stability. - Abstract: Statistical analysis of protein structures shows that buried aspartic acid residues on average form 2.5 to 3 hydrogen bonds and/or 0.8 potential ionic interactions with other protein groups. To estimate the energetic contribution of such buried groups to the Gibbs free energy of proteins, we measured the effects of amino acid substitutions of D56 in a model protein PDZ2 on its stability. We used temperature-induced unfolding monitored by DSC and denaturant-induced unfolding monitored by the changes in fluorescence intensity. We find that all substitutions of D56 lead to protein unfolding, thus suggesting that this buried hydrogen bonded aspartic acid has a significant contribution to the stability. To quantify the changes in the Gibbs free energy, one of the variants, D56N was stabilized by addition of the protective osmolyte TMAO. Comparison of the stability of the D56N variant with the wild-type PDZ2 in the presence and absence of TMAO allowed us to estimate the contribution of D56 to the protein stability to be 18 kJ · mol −1 . These findings are discussed in terms of contribution of buried ionizable groups to protein stability.

Forging And Milling Contribution On Residual Stresses For A Textured Biphasic Titanium Alloy

International Nuclear Information System (INIS)

Deleuze, C.; Fabre, A.; Barrallier, L.; Molinas, O.

2011-01-01

Ti-10V-2Fe-3Al is a biphasic titanium alloy (α+β) used in aeronautical applications for its mechanical properties, such as its yield strength of 1200 MPa and it weighs 40% less than steel. This alloy is particularly useful for vital parts with complex geometry, because of its high forging capability. In order to predict the capability for fatigue lifetime, the designers need to know the residual stresses. X-Ray diffraction is the main experimental technique used to determine residual stresses on the surface. In this case, stress levels are primarily influenced by the complex forging and milling process. On this alloy in particular, it may be difficult to characterize stress due to modification of the microstructure close to the surface. Results obtained by x-ray analysis depend on the correct definition of the shape of the diffraction peaks. The more precisely defined the position of the peak, the more accurately the stresses are evaluated. This paper presents a method to detect if residual stresses can be characterized by x-ray diffraction. The characterization of hardness seems to be a relevant technique to quickly analyze the capability of x-ray diffraction to determine residual stresses.

Contribution of microorganisms to non-extractable residue formation during biodegradation of ibuprofen in soil

Energy Technology Data Exchange (ETDEWEB)

Nowak, Karolina M., E-mail: karolina.nowak@ufz.de [UFZ, Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology, Permoserstraße 15, 04318 Leipzig (Germany); Department of Environmental Biology and Chemodynamics, Institute for Environmental Research (Biology V), RWTH Aachen University, Worringerweg 1, 52074 Aachen (Germany); Girardi, Cristobal; Miltner, Anja [UFZ, Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology, Permoserstraße 15, 04318 Leipzig (Germany); Gehre, Matthias [UFZ, Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstraße 15, 04318 Leipzig (Germany); Schäffer, Andreas [Department of Environmental Biology and Chemodynamics, Institute for Environmental Research (Biology V), RWTH Aachen University, Worringerweg 1, 52074 Aachen (Germany); Kästner, Matthias [UFZ, Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology, Permoserstraße 15, 04318 Leipzig (Germany)

2013-02-15

Non-extractable residues (NER) formed during biodegradation of organic contaminants in soil are considered to be mainly composed of parent compounds or their primary metabolites with hazardous potential. However, in the case of biodegradable organic compounds, the soil NER may also contain microbial biomass components, for example fatty acids (FA) and amino acids (AA). After cell death, these biomolecules are subsequently incorporated into non-living soil organic matter (SOM) and are stabilised ultimately forming hardly extractable residues of biogenic origin. We investigated biodegradation of {sup 13}C{sub 6}-ibuprofen, in particular the metabolic incorporation of the {sup 13}C-label into FA and AA and their fate in soil over 90 days. {sup 13}C-FA and {sup 13}C-AA amounts in the living microbial biomass fraction initially increased, then decreased over time and were continuously incorporated into the non-living SOM pool. The {sup 13}C-FA in the non-living SOM remained stable from day 59 whereas the contents of {sup 13}C-AA slightly increased until the end. After 90 days, nearly all NER were biogenic as they were made up almost completely by natural biomass compounds. The presented data demonstrated that the potential environmental risks related to the ibuprofen-derived NER are overestimated. - Highlights: ► Biogenic residue formation during microbial degradation of ibuprofen was studied. ► Nearly all non-extractable residues derived from ibuprofen were biogenic. ► Fatty acids and amino acids formed biogenic non-extractable residues and were stabilised in soil. ► Environmental risks of ibuprofen-derived non-extractable residues are overestimated.

Contribution of microorganisms to non-extractable residue formation during biodegradation of ibuprofen in soil

International Nuclear Information System (INIS)

Nowak, Karolina M.; Girardi, Cristobal; Miltner, Anja; Gehre, Matthias; Schäffer, Andreas; Kästner, Matthias

2013-01-01

Non-extractable residues (NER) formed during biodegradation of organic contaminants in soil are considered to be mainly composed of parent compounds or their primary metabolites with hazardous potential. However, in the case of biodegradable organic compounds, the soil NER may also contain microbial biomass components, for example fatty acids (FA) and amino acids (AA). After cell death, these biomolecules are subsequently incorporated into non-living soil organic matter (SOM) and are stabilised ultimately forming hardly extractable residues of biogenic origin. We investigated biodegradation of 13 C 6 -ibuprofen, in particular the metabolic incorporation of the 13 C-label into FA and AA and their fate in soil over 90 days. 13 C-FA and 13 C-AA amounts in the living microbial biomass fraction initially increased, then decreased over time and were continuously incorporated into the non-living SOM pool. The 13 C-FA in the non-living SOM remained stable from day 59 whereas the contents of 13 C-AA slightly increased until the end. After 90 days, nearly all NER were biogenic as they were made up almost completely by natural biomass compounds. The presented data demonstrated that the potential environmental risks related to the ibuprofen-derived NER are overestimated. - Highlights: ► Biogenic residue formation during microbial degradation of ibuprofen was studied. ► Nearly all non-extractable residues derived from ibuprofen were biogenic. ► Fatty acids and amino acids formed biogenic non-extractable residues and were stabilised in soil. ► Environmental risks of ibuprofen-derived non-extractable residues are overestimated

Shaping Learner Contributions in an EFL Classroom: Implications for L2 Classroom Interactional Competence

Science.gov (United States)

Can Daskin, Nilüfer

2015-01-01

This study investigated the interactional patterns for shaping learner contributions in an EFL classroom with reference to Walsh's classroom interactional competence (CIC). In doing so, an EFL class at an English preparatory school in a Turkish state university was both videotaped and audiotaped in the course of six classroom hours. Conversation…

Ammonia volatilization from crop residues and frozen green manure crops

Science.gov (United States)

de Ruijter, F. J.; Huijsmans, J. F. M.; Rutgers, B.

2010-09-01

Agricultural systems can lose substantial amounts of nitrogen (N). To protect the environment, the European Union (EU) has adopted several directives that set goals to limit N losses. National Emission Ceilings (NEC) are prescribed in the NEC directive for nitrogen oxides and ammonia. Crop residues may contribute to ammonia volatilization, but sufficient information on their contribution to the national ammonia volatilization is lacking. Experiments were carried out with the aim to assess the ammonia volatilization of crop residues left on the soil surface or incorporated into the soil under the conditions met in practice in the Netherlands during late autumn and winter. Ammonia emission from residues of broccoli, leek, sugar beet, cut grass, fodder radish (fresh and frozen) and yellow mustard (frozen) was studied during two winter seasons using volatilization chambers. Residues were either placed on top of soil or mixed with soil. Mixing residues with soil gave insignificant ammonia volatilization, whereas volatilization was 5-16 percent of the N content of residues when placed on top of soil. Ammonia volatilization started after at least 4 days. Total ammonia volatilization was related to C/N-ratio and N concentration of the plant material. After 37 days, cumulative ammonia volatilization was negligible from plant material with N concentration below 2 percent, and was 10 percent of the N content of plant material with 4 percent N. These observations can be explained by decomposition of plant material by micro-organisms. After an initial built up of the microbial population, NH 4+ that is not needed for their own growth is released and can easily emit as NH 3 at the soil surface. The results of the experiments were used to estimate the contribution of crop residues to ammonia volatilization in the Netherlands. Crop residues of arable crops and residues of pasture topping may contribute more than 3 million kg NH 3-N to the national ammonia volatilization of the

Scale-free behaviour of amino acid pair interactions in folded proteins

DEFF Research Database (Denmark)

Petersen, Steffen B.; Neves-Petersen, Maria Teresa; Mortensen, Rasmus J.

2012-01-01

The protein structure is a cumulative result of interactions between amino acid residues interacting with each other through space and/or chemical bonds. Despite the large number of high resolution protein structures, the ‘‘protein structure code’’ has not been fully identified. Our manuscript...... presents a novel approach to protein structure analysis in order to identify rules for spatial packing of amino acid pairs in proteins. We have investigated 8706 high resolution non-redundant protein chains and quantified amino acid pair interactions in terms of solvent accessibility, spatial and sequence...... which amino acid paired residues contributed to the cells with a population above 50, pairs of Ala, Ile, Leu and Val dominate the results. This result is statistically highly significant. We postulate that such pairs form ‘‘structural stability points’’ in the protein structure. Our data shows...

Electrostatic contribution of surface charge residues to the stability of a thermophilic protein: benchmarking experimental and predicted pKa values.

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Chi-Ho Chan

Full Text Available Optimization of the surface charges is a promising strategy for increasing thermostability of proteins. Electrostatic contribution of ionizable groups to the protein stability can be estimated from the differences between the pKa values in the folded and unfolded states of a protein. Using this pKa-shift approach, we experimentally measured the electrostatic contribution of all aspartate and glutamate residues to the stability of a thermophilic ribosomal protein L30e from Thermococcus celer. The pKa values in the unfolded state were found to be similar to model compound pKas. The pKa values in both the folded and unfolded states obtained at 298 and 333 K were similar, suggesting that electrostatic contribution of ionizable groups to the protein stability were insensitive to temperature changes. The experimental pKa values for the L30e protein in the folded state were used as a benchmark to test the robustness of pKa prediction by various computational methods such as H++, MCCE, MEAD, pKD, PropKa, and UHBD. Although the predicted pKa values were affected by crystal contacts that may alter the side-chain conformation of surface charged residues, most computational methods performed well, with correlation coefficients between experimental and calculated pKa values ranging from 0.49 to 0.91 (p<0.01. The changes in protein stability derived from the experimental pKa-shift approach correlate well (r = 0.81 with those obtained from stability measurements of charge-to-alanine substituted variants of the L30e protein. Our results demonstrate that the knowledge of the pKa values in the folded state provides sufficient rationale for the redesign of protein surface charges leading to improved protein stability.

Baryon femtoscopy considering residual correlations as a tool to extract strong interaction potentials

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Szymański Maciej

2015-01-01

Full Text Available In this article, the analysis of baryon-antibaryon femtoscopic correlations is presented. In particular, it is shown that taking into account residual correlations is crucial for the description of pΛ¯$\\bar \\Lambda $ and p̄Λ correlation functions measured by the STAR experiment in Au–Au collisions at the centre-of-mass energy per nucleon pair √sNN = 200 GeV. This approach enables to obtain pΛ¯$\\bar \\Lambda $ (p̄Λ source size consistent with the sizes extracted from correlations in pΛ (p̄Λ¯$\\bar \\Lambda $ and lighter pair systems as well as with model predictions. Moreover, with this analysis it is possible to derive the unknown parameters of the strong interaction potential for baryon-antibaryon pairs under several assumptions.

Interaction of acid mine drainage with Ordinary Portland Cement blended solid residues generated from active treatment of acid mine drainage with coal fly ash.

Science.gov (United States)

Gitari, Wilson M; Petrik, Leslie F; Key, David L; Okujeni, Charles

2011-01-01

Fly ash (FA) has been investigated as a possible treatment agent for Acid mine drainage (AMD) and established to be an alternative, cheap and economically viable agent compared to the conventional alkaline agents. However, this treatment option also leads to generation of solid residues (SR) that require disposal and one of the proposed disposal method is a backfill in coal mine voids. In this study, the interaction of the SR with AMD that is likely to be present in such backfill scenario was simulated by draining columns packed with SR and SR + 6% Ordinary Portland Cement (OPC) unsaturated with simulated AMD over a 6 month period. The evolving geochemistry of the liquid/solid (L/S) system was evaluated in-terms of the mineral phases likely or controlling contaminants attenuation at the different pH regimes generated. Stepwise acidification of the percolates was observed as the drainage progressed. Two pH buffer zones were observed (7.5-9 and 3-4) for SR and (11.2-11.3 and 3.5-4) for SR + 6% OPC. The solid residue cores (SR) appeared to have a significant buffering capacity, maintaining a neutral to slightly alkaline pH in the leachates for an extended period of time (97 days: L/S 4.3) while SR + 6% OPC reduced this neutralization capacity to 22 days (L/S 1.9). Interaction of AMD with SR or SR + 6% OPC generated alkaline conditions that favored precipitation of Fe, Al, Mn-(oxy) hydroxides, Fe and Ca-Al hydroxysulphates that greatly contributed to the contaminants removal. However, precipitation of these phases was restricted to the pH of the leachates remaining at neutral to circum-neutral levels. Backfill of mine voids with SR promises to be a feasible technology for the disposal of the SR but its success will greatly depend on the disposal scenario, AMD generated and the alkalinity generating potential of the SR. A disadvantage would be the possible re-dissolution of the precipitated phases at pH water column. However extrapolation of this concept to a field

Magnetic interactions in strongly correlated systems: Spin and orbital contributions

Energy Technology Data Exchange (ETDEWEB)

Secchi, A., E-mail: a.secchi@science.ru.nl [Radboud University, Institute for Molecules and Materials, 6525 AJ Nijmegen (Netherlands); Lichtenstein, A.I. [Universitat Hamburg, Institut für Theoretische Physik, Jungiusstraße 9, D-20355 Hamburg (Germany); Katsnelson, M.I. [Radboud University, Institute for Molecules and Materials, 6525 AJ Nijmegen (Netherlands)

2015-09-15

We present a technique to map an electronic model with local interactions (a generalized multi-orbital Hubbard model) onto an effective model of interacting classical spins, by requiring that the thermodynamic potentials associated to spin rotations in the two systems are equivalent up to second order in the rotation angles, when the electronic system is in a symmetry-broken phase. This allows to determine the parameters of relativistic and non-relativistic magnetic interactions in the effective spin model in terms of equilibrium Green’s functions of the electronic model. The Hamiltonian of the electronic system includes, in addition to the non-relativistic part, relativistic single-particle terms such as the Zeeman coupling to an external magnetic field, spin–orbit coupling, and arbitrary magnetic anisotropies; the orbital degrees of freedom of the electrons are explicitly taken into account. We determine the complete relativistic exchange tensors, accounting for anisotropic exchange, Dzyaloshinskii–Moriya interactions, as well as additional non-diagonal symmetric terms (which may include dipole–dipole interaction). The expressions of all these magnetic interactions are determined in a unified framework, including previously disregarded features such as the vertices of two-particle Green’s functions and non-local self-energies. We do not assume any smallness in spin–orbit coupling, so our treatment is in this sense exact. Finally, we show how to distinguish and address separately the spin, orbital and spin–orbital contributions to magnetism, providing expressions that can be computed within a tight-binding Dynamical Mean Field Theory.

Identification of the gamma subunit-interacting residues on photoreceptor cGMP phosphodiesterase, PDE6alpha '.

Science.gov (United States)

Granovsky, A E; Artemyev, N O

2000-12-29

Photoreceptor cGMP phosphodiesterase (PDE6) is the effector enzyme in the G protein-mediated visual transduction cascade. In the dark, the activity of PDE6 is shut off by the inhibitory gamma subunit (Pgamma). Chimeric proteins between cone PDE6alpha' and cGMP-binding and cGMP-specific PDE (PDE5) have been constructed and expressed in Sf9 cells to study the mechanism of inhibition of PDE6 catalytic activity by Pgamma. Substitution of the segment PDE5-(773-820) by the corresponding PDE6alpha'-(737-784) sequence in the wild-type PDE5 or in a PDE5/PDE6alpha' chimera containing the catalytic domain of PDE5 results in chimeric enzymes capable of inhibitory interaction with Pgamma. The catalytic properties of the chimeric PDEs remained similar to those of PDE5. Ala-scanning mutational analysis of the Pgamma-binding region, PDE6alpha'-(750-760), revealed PDE6alpha' residues essential for the interaction. The M758A mutation markedly impaired and the Q752A mutation moderately impaired the inhibition of chimeric PDE by Pgamma. The analysis of the catalytic properties of mutant PDEs and a model of the PDE6 catalytic domain suggest that residues Met(758) and Gln(752) directly bind Pgamma. A model of the PDE6 catalytic site shows that PDE6alpha'-(750-760) forms a loop at the entrance to the cGMP-binding pocket. Binding of Pgamma to Met(758) would effectively block access of cGMP to the catalytic cavity, providing a structural basis for the mechanism of PDE6 inhibition.

The relative contribution of waves, tides, and nontidal residuals to extreme total water levels on U.S. West Coast sandy beaches

Science.gov (United States)

Serafin, Katherine A.; Ruggiero, Peter; Stockdon, Hilary F.

2017-01-01

To better understand how individual processes combine to cause flooding and erosion events, we investigate the relative contribution of tides, waves, and nontidal residuals to extreme total water levels (TWLs) at the shoreline of U.S. West Coast sandy beaches. Extreme TWLs, defined as the observed annual maximum event and the simulated 100 year return level event, peak in Washington, and are on average larger in Washington and Oregon than in California. The relative contribution of wave-induced and still water levels (SWL) to the 100 year TWL event is similar to that of the annual maximum event; however, the contribution of storm surge to the SWL doubles across events. Understanding the regional variability of TWLs will lead to a better understanding of how sea level rise, changes in storminess, and possible changes in the frequency of major El Niños may impact future coastal flooding and erosion along the U.S. West Coast and elsewhere.

Interactive Contributions of Cumulative Peer Stress and Executive Function Deficits to Depression in Early Adolescence

Science.gov (United States)

Agoston, Anna M.; Rudolph, Karen D.

2016-01-01

Exposure to peer stress contributes to adolescent depression, yet not all youth experience these effects. Thus, it is important to identify individual differences that shape the consequences of peer stress. This research investigated the interactive contribution of cumulative peer stress during childhood (second-fifth grades) and executive…

Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein’s structural organization

Directory of Open Access Journals (Sweden)

Sengupta Dhriti

2012-06-01

Full Text Available Abstract Background The three-dimensional structure of a protein can be described as a graph where nodes represent residues and the strength of non-covalent interactions between them are edges. These protein contact networks can be separated into long and short-range interactions networks depending on the positions of amino acids in primary structure. Long-range interactions play a distinct role in determining the tertiary structure of a protein while short-range interactions could largely contribute to the secondary structure formations. In addition, physico chemical properties and the linear arrangement of amino acids of the primary structure of a protein determines its three dimensional structure. Here, we present an extensive analysis of protein contact subnetworks based on the London van der Waals interactions of amino acids at different length scales. We further subdivided those networks in hydrophobic, hydrophilic and charged residues networks and have tried to correlate their influence in the overall topology and organization of a protein. Results The largest connected component (LCC of long (LRN-, short (SRN- and all-range (ARN networks within proteins exhibit a transition behaviour when plotted against different interaction strengths of edges among amino acid nodes. While short-range networks having chain like structures exhibit highly cooperative transition; long- and all-range networks, which are more similar to each other, have non-chain like structures and show less cooperativity. Further, the hydrophobic residues subnetworks in long- and all-range networks have similar transition behaviours with all residues all-range networks, but the hydrophilic and charged residues networks don’t. While the nature of transitions of LCC’s sizes is same in SRNs for thermophiles and mesophiles, there exists a clear difference in LRNs. The presence of larger size of interconnected long-range interactions in thermophiles than mesophiles, even at

Assessment of odor activity value coefficient and odor contribution based on binary interaction effects in waste disposal plant

Science.gov (United States)

Wu, Chuandong; Liu, Jiemin; Yan, Luchun; Chen, Haiying; Shao, Huiqi; Meng, Tian

2015-02-01

Odor activity value (OAV) has been widely used for the assessment of odor pollution from various sources. However, little attention has been paid to the extreme OAV variation and potential inaccuracies of odor contribution assessment caused by odor interaction effects. The objective of this study is to assess the odor interaction effect for precise assessment of odor contribution. In this paper, samples were collected from a food waste disposal plant, and analyzed by instrumental and olfactory method to conclude odorants' occurrence and OAV. Then odor activity value coefficient (γ) was first proposed to evaluate the type and the level of binary interaction effects based on determination of OAV variation. By multiplying OAV and γ, odor activity factor (OAF) was used to reflect the real OAV. Correlation between the sum of OAF and odor concentration reached 80.0 ± 5.7%, which was 10 times higher than the sum of OAV used before. Results showed that hydrogen sulfide contributed most (annual average 66.4 ± 15.8%) to odor pollution in the waste disposal plant. However, as odor intensity of samples in summer rising, odor contribution of trimethylamine increased to 48.3 ± 3.7% by the strong synergistic interaction effect, while odor contribution of phenol decreased to 0.1 ± 0.02% for the increasing antagonistic interaction effect.

Reactive control processes contributing to residual switch cost and mixing cost across the adult lifespan.

Science.gov (United States)

Whitson, Lisa R; Karayanidis, Frini; Fulham, Ross; Provost, Alexander; Michie, Patricia T; Heathcote, Andrew; Hsieh, Shulan

2014-01-01

In task-switching paradigms, performance is better when repeating the same task than when alternating between tasks (switch cost) and when repeating a task alone rather than intermixed with another task (mixing cost). These costs remain even after extensive practice and when task cues enable advanced preparation (residual costs). Moreover, residual reaction time mixing cost has been consistently shown to increase with age. Residual switch and mixing costs modulate the amplitude of the stimulus-locked P3b. This mixing effect is disproportionately larger in older adults who also prepare more for and respond more cautiously on these "mixed" repeat trials (Karayanidis et al., 2011). In this paper, we analyze stimulus-locked and response-locked P3 and lateralized readiness potentials to identify whether residual switch and mixing cost arise from the need to control interference at the level of stimulus processing or response processing. Residual mixing cost was associated with control of stimulus-level interference, whereas residual switch cost was also associated with a delay in response selection. In older adults, the disproportionate increase in mixing cost was associated with greater interference at the level of decision-response mapping and response programming for repeat trials in mixed-task blocks. These findings suggest that older adults strategically recruit greater proactive and reactive control to overcome increased susceptibility to post-stimulus interference. This interpretation is consistent with recruitment of compensatory strategies to compensate for reduced repetition benefit rather than an overall decline on cognitive flexibility.

Three- and five-quasiparticle isomers, rotational bands and residual interactions in 175Hf

International Nuclear Information System (INIS)

Dracoulis, G.D.; Walker, P.M.

1980-03-01

Two 3-quasiparticle isomers with spins, parities and half lives of 19/2 + , 1.1 μ and 23/2 - , 1.2 ns have been identified at 1433 and 1766 keV in 175 Hf. A third isomer possibly 35/2 - with a 1.2 μs half-life is found at 3015 keV. The first two are characterised as a 7/2 + (633) neutron coupled to the known 6 + and 8 - 2-proton isomers of the core nuclei. Rotational bands based on the 3-qp isomers are highly perturbed, due to Coriolis mixing, and their structure is reproduced in a band mixing calculation. The energy depression of the 3-quasiparticle states relative to the 2-quasiproton core states is attributed mainly to the residual proton-neutron interaction, and possibly also to blocking effects through neutron admixtures

E2-EPF UCP Possesses E3 Ubiquitin Ligase Activity via Its Cysteine 118 Residue.

Science.gov (United States)

Lim, Jung Hwa; Shin, Hee Won; Chung, Kyung-Sook; Kim, Nam-Soon; Kim, Ju Hee; Jung, Hong-Ryul; Im, Dong-Soo; Jung, Cho-Rok

Here, we show that E2-EPF ubiquitin carrier protein (UCP) elongated E3-independent polyubiquitin chains on the lysine residues of von Hippel-Lindau protein (pVHL) and its own lysine residues both in vitro and in vivo. The initiation of the ubiquitin reaction depended on not only Lys11 linkage but also the Lys6, Lys48 and Lys63 residues of ubiquitin, which were involved in polyubiquitin chain formation on UCP itself. UCP self-association occurred through the UBC domain, which also contributed to the interaction with pVHL. The polyubiquitin chains appeared on the N-terminus of UCP in vivo, which indicated that the N-terminus of UCP contains target lysines for polyubiquitination. The Lys76 residue of UCP was the most critical site for auto-ubiquitination, whereas the polyubiquitin chain formation on pVHL occurred on all three of its lysines (Lys159, Lys171 and Lys196). A UCP mutant in which Cys118 was changed to alanine (UCPC118A) did not form a polyubiquitin chain but did strongly accumulate mono- and di-ubiquitin via auto-ubiquitination. Polyubiquitin chain formation required the coordination of Cys95 and Cys118 between two interacting molecules. The mechanism of the polyubiquitin chain reaction of UCP may involve the transfer of ubiquitin from Cys95 to Cys118 by trans-thiolation, with polyubiquitin chains forming at Cys118 by reversible thioester bonding. The polyubiquitin chains are then moved to the lysine residues of the substrate by irreversible isopeptide bonding. During the elongation of the ubiquitin chain, an active Cys118 residue is required in both parts of UCP, namely, the catalytic enzyme and the substrate. In conclusion, UCP possesses not only E2 ubiquitin conjugating enzyme activity but also E3 ubiquitin ligase activity, and Cys118 is critical for polyubiquitin chain formation.

E2-EPF UCP Possesses E3 Ubiquitin Ligase Activity via Its Cysteine 118 Residue.

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Jung Hwa Lim

Full Text Available Here, we show that E2-EPF ubiquitin carrier protein (UCP elongated E3-independent polyubiquitin chains on the lysine residues of von Hippel-Lindau protein (pVHL and its own lysine residues both in vitro and in vivo. The initiation of the ubiquitin reaction depended on not only Lys11 linkage but also the Lys6, Lys48 and Lys63 residues of ubiquitin, which were involved in polyubiquitin chain formation on UCP itself. UCP self-association occurred through the UBC domain, which also contributed to the interaction with pVHL. The polyubiquitin chains appeared on the N-terminus of UCP in vivo, which indicated that the N-terminus of UCP contains target lysines for polyubiquitination. The Lys76 residue of UCP was the most critical site for auto-ubiquitination, whereas the polyubiquitin chain formation on pVHL occurred on all three of its lysines (Lys159, Lys171 and Lys196. A UCP mutant in which Cys118 was changed to alanine (UCPC118A did not form a polyubiquitin chain but did strongly accumulate mono- and di-ubiquitin via auto-ubiquitination. Polyubiquitin chain formation required the coordination of Cys95 and Cys118 between two interacting molecules. The mechanism of the polyubiquitin chain reaction of UCP may involve the transfer of ubiquitin from Cys95 to Cys118 by trans-thiolation, with polyubiquitin chains forming at Cys118 by reversible thioester bonding. The polyubiquitin chains are then moved to the lysine residues of the substrate by irreversible isopeptide bonding. During the elongation of the ubiquitin chain, an active Cys118 residue is required in both parts of UCP, namely, the catalytic enzyme and the substrate. In conclusion, UCP possesses not only E2 ubiquitin conjugating enzyme activity but also E3 ubiquitin ligase activity, and Cys118 is critical for polyubiquitin chain formation.

Quantum mechanics study of the hydroxyethylamines-BACE-1 active site interaction energies

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Gueto-Tettay, Carlos; Drosos, Juan Carlos; Vivas-Reyes, Ricardo

2011-06-01

The identification of BACE-1, a key enzyme in the production of Amyloid-β (Aβ) peptides, generated by the proteolytic processing of amyloid precursor protein, was a major advance in the field of Alzheimer's disease as this pathology is characterized by the presence of extracellular senile plaques, mainly comprised of Aβ peptides. Hydroxyethylamines have demonstrated a remarkable potential, like candidate drugs, for this disease using BACE-1 as target. Density Functional Theory calculations were employed to estimate interaction energies for the complexes formed between the hydroxyethylamine derivated inhibitors and 24 residues in the BACE-1 active site. The collected data offered not only a general but a particular quantitative description that gives a deep insight of the interactions in the active site, showing at the same time how ligand structural variations affect them. Polar interactions are the major energetic contributors for complex stabilization and those ones with charged aspartate residues are highlighted, as they contribute over 90% of the total attractive interaction energy. Ligand-ARG296 residue interaction reports the most repulsive value and decreasing of the magnitude of this repulsion can be a key feature for the design of novel and more potent BACE-1 inhibitors. Also it was explained why sultam derivated BACE-1 inhibitors are better ones than lactam based. Hydrophobic interactions concentrated at S1 zone and other relevant repulsions and attractions were also evaluated. The comparison of two different theory levels (X3LYP and M062X) allowed to confirm the relevance of the detected interactions as each theory level has its own strength to depict the forces involved, as is the case of M062X which is better describing the hydrophobic interactions. Those facts were also evaluated and confirmed by comparing the quantitative trend, of selected ligand-residue interactions, with MP2 theory level as reference standard method for electrostatic plus

Residues and duality for projective algebraic varieties

CERN Document Server

Kunz, Ernst; Dickenstein, Alicia

2008-01-01

This book, which grew out of lectures by E. Kunz for students with a background in algebra and algebraic geometry, develops local and global duality theory in the special case of (possibly singular) algebraic varieties over algebraically closed base fields. It describes duality and residue theorems in terms of K�hler differential forms and their residues. The properties of residues are introduced via local cohomology. Special emphasis is given to the relation between residues to classical results of algebraic geometry and their generalizations. The contribution by A. Dickenstein gives applications of residues and duality to polynomial solutions of constant coefficient partial differential equations and to problems in interpolation and ideal membership. D. A. Cox explains toric residues and relates them to the earlier text. The book is intended as an introduction to more advanced treatments and further applications of the subject, to which numerous bibliographical hints are given.

Subnanomolar Inhibitor of Cytochrome bc1 Complex Designed via Optimizing Interaction with Conformationally Flexible Residues

Science.gov (United States)

Zhao, Pei-Liang; Wang, Le; Zhu, Xiao-Lei; Huang, Xiaoqin; Zhan, Chang-Guo; Wu, Jia-Wei; Yang, Guang-Fu

2009-01-01

Cytochrome bc1 complex (EC 1.10.2.2, bc1), an essential component of the cellular respiratory chain and the photosynthetic apparatus in photosynthetic bacteria, has been identified as a promising target for new drugs and agricultural fungicides. X-ray diffraction structures of the free bc1 complex and its complexes with various inhibitors revealed that the phenyl group of Phe274 in the binding pocket exhibited significant conformational flexibility upon different inhibitors binding to optimize respective π-π interactions, whereas the side chains of other hydrophobic residues showed conformational stability. Therefore, in the present study, a strategy of optimizing the π-π interaction with conformationally flexible residues was proposed to design and discover new bc1 inhibitors with a higher potency. Eight new compounds were designed and synthesized, among which compound 5c with a Ki value of 570 pM was identified as the most promising drug or fungicide candidate, significantly more potent than the commercially available bc1 inhibitors including azoxystrobin (AZ), kresoxim-methyl (KM), and pyraclostrobin (PY). To our knowledge, this is the first bc1 inhibitor discovered from structure-based design with a potency of subnanomolar Ki value. For all of the compounds synthesized and assayed, the calculated binding free energies correlated reasonably well with the binding free energies derived from the experimental Ki values with a correlation coefficient of r2 = 0.89. The further inhibitory kinetics studies revealed that compound 5c is a non-competitive inhibitor with respect to substrate cytochrome c, but is a competitive inhibitor with respect to substrate ubiquinol. Due to its subnanomolar Ki potency and slow dissociation rate constant (k−0 = 0.00358 s−1), compound 5c could be used as a specific probe for further elucidation of the mechanism of bc1 function and as a new lead compound for future drug discovery. PMID:19928849

Gas-Phase Hydrogen-Deuterium Exchange Labeling of Select Peptide Ion Conformer Types: a Per-Residue Kinetics Analysis.

Science.gov (United States)

Khakinejad, Mahdiar; Kondalaji, Samaneh Ghassabi; Tafreshian, Amirmahdi; Valentine, Stephen J

2015-07-01

The per-residue, gas-phase hydrogen deuterium exchange (HDX) kinetics for individual amino acid residues on selected ion conformer types of the model peptide KKDDDDDIIKIIK have been examined using ion mobility spectrometry (IMS) and HDX-tandem mass spectrometry (MS/MS) techniques. The [M + 4H](4+) ions exhibit two major conformer types with collision cross sections of 418 Å(2) and 446 Å(2); the [M + 3H](3+) ions also yield two different conformer types having collision cross sections of 340 Å(2) and 367 Å(2). Kinetics plots of HDX for individual amino acid residues reveal fast- and slow-exchanging hydrogens. The contributions of each amino acid residue to the overall conformer type rate constant have been estimated. For this peptide, N- and C-terminal K residues exhibit the greatest contributions for all ion conformer types. Interior D and I residues show decreased contributions. Several charge state trends are observed. On average, the D residues of the [M + 3H](3+) ions show faster HDX rate contributions compared with [M + 4H](4+) ions. In contrast the interior I8 and I9 residues show increased accessibility to exchange for the more elongated [M + 4H](4+) ion conformer type. The contribution of each residue to the overall uptake rate showed a good correlation with a residue hydrogen accessibility score model calculated using a distance from charge site and initial incorporation site for nominal structures obtained from molecular dynamic simulations (MDS).

Stacking interactions between carbohydrate and protein quantified by combination of theoretical and experimental methods.

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Michaela Wimmerová

Full Text Available Carbohydrate-receptor interactions are an integral part of biological events. They play an important role in many cellular processes, such as cell-cell adhesion, cell differentiation and in-cell signaling. Carbohydrates can interact with a receptor by using several types of intermolecular interactions. One of the most important is the interaction of a carbohydrate's apolar part with aromatic amino acid residues, known as dispersion interaction or CH/π interaction. In the study presented here, we attempted for the first time to quantify how the CH/π interaction contributes to a more general carbohydrate-protein interaction. We used a combined experimental approach, creating single and double point mutants with high level computational methods, and applied both to Ralstonia solanacearum (RSL lectin complexes with α-L-Me-fucoside. Experimentally measured binding affinities were compared with computed carbohydrate-aromatic amino acid residue interaction energies. Experimental binding affinities for the RSL wild type, phenylalanine and alanine mutants were -8.5, -7.1 and -4.1 kcal x mol(-1, respectively. These affinities agree with the computed dispersion interaction energy between carbohydrate and aromatic amino acid residues for RSL wild type and phenylalanine, with values -8.8, -7.9 kcal x mol(-1, excluding the alanine mutant where the interaction energy was -0.9 kcal x mol(-1. Molecular dynamics simulations show that discrepancy can be caused by creation of a new hydrogen bond between the α-L-Me-fucoside and RSL. Observed results suggest that in this and similar cases the carbohydrate-receptor interaction can be driven mainly by a dispersion interaction.

Lignin biochemistry and soil N determine crop residue decomposition and soil priming

Science.gov (United States)

Cropping history can affect soil properties, including available N, but little is known about the interactive effects of residue biochemistry, temperature and cropping history on residue decomposition. A laboratory incubation examined the role of residue biochemistry and temperature on the decomposi...

The Relationship Between Low-Frequency Motions and Community Structure of Residue Network in Protein Molecules.

Science.gov (United States)

Sun, Weitao

2018-01-01

The global shape of a protein molecule is believed to be dominant in determining low-frequency deformational motions. However, how structure dynamics relies on residue interactions remains largely unknown. The global residue community structure and the local residue interactions are two important coexisting factors imposing significant effects on low-frequency normal modes. In this work, an algorithm for community structure partition is proposed by integrating Miyazawa-Jernigan empirical potential energy as edge weight. A sensitivity parameter is defined to measure the effect of local residue interaction on low-frequency movement. We show that community structure is a more fundamental feature of residue contact networks. Moreover, we surprisingly find that low-frequency normal mode eigenvectors are sensitive to some local critical residue interaction pairs (CRIPs). A fair amount of CRIPs act as bridges and hold distributed structure components into a unified tertiary structure by bonding nearby communities. Community structure analysis and CRIP detection of 116 catalytic proteins reveal that breaking up of a CRIP can cause low-frequency allosteric movement of a residue at the far side of protein structure. The results imply that community structure and CRIP may be the structural basis for low-frequency motions.

Characterization of the interdependency between residues that bind the substrate in a beta-glycosidase.

Science.gov (United States)

Tomassi, M H; Rozenfeld, J H K; Gonçalves, L M; Marana, S R

2010-01-01

The manner by which effects of simultaneous mutations combine to change enzymatic activity is not easily predictable because these effects are not always additive in a linear manner. Hence, the characterization of the effects of simultaneous mutations of amino acid residues that bind the substrate can make a significant contribution to the understanding of the substrate specificity of enzymes. In the beta-glycosidase from Spodoptera frugiperda (Sfbetagly), both residues Q39 and E451 interact with the substrate and this is essential for defining substrate specificity. Double mutants of Sfbetagly (A451E39, S451E39 and S451N39) were prepared by site-directed mutagenesis, expressed in bacteria and purified using affinity chromatography. These enzymes were characterized using p-nitrophenyl beta-galactoside and p-nitrophenyl beta-fucoside as substrates. The k cat/Km ratio for single and double mutants of Sfbetagly containing site-directed mutations at positions Q39 and E451 was used to demonstrate that the effect on the free energy of ESdouble dagger (enzyme-transition state complex) of the double mutations (Gdouble daggerxy) is not the sum of the effects resulting from the single mutations (Gdouble daggerx and Gdouble daggery). This difference in Gdouble dagger indicates that the effects of the single mutations partially overlap. Hence, this common effect counts only once in Gdouble daggerxy. Crystallographic data on beta-glycosidases reveal the presence of a bidentate hydrogen bond involving residues Q39 and E451 and the same hydroxyl group of the substrate. Therefore, both thermodynamic and crystallographic data suggest that residues Q39 and E451 exert a mutual influence on their respective interactions with the substrate.

Compared cycling in a soil-plant system of pea and barley residue nitrogen

DEFF Research Database (Denmark)

Jensen, E.S.

1996-01-01

Field experiments were carried out on a temperate soil to determine the decline rate, the stabilization in soil organic matter and the plant uptake of N from N-15-labelled crop residues. The fate of N from field pea (Pisum sativum L.) and spring barley (Hordeum vulgare L.) residues was followed...... mineralization of N was highly correlated to the concentrations of soluble C and N and the lignin:N ratio of residues. The contribution of residue-derived N to the inorganic N pool was at its maximum 30 DAI (10-55%) and declined to on average 5% after 3 years of decomposition. Residual organic labelled N...... in the top 10 cm soil declined rapidly during the initial 86 DAI for all residue types. Leaching of soluble organic materials may have contributed to this decline. At 216 DAI 72, 59 and 45% of the barley, mature pea and green pea residue N, respectively, were present in organic N-forms in the topsoil. During...

Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity

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Drew Michael GB

2006-03-01

Full Text Available Abstract Background MHC Class I molecules present antigenic peptides to cytotoxic T cells, which forms an integral part of the adaptive immune response. Peptides are bound within a groove formed by the MHC heavy chain. Previous approaches to MHC Class I-peptide binding prediction have largely concentrated on the peptide anchor residues located at the P2 and C-terminus positions. Results A large dataset comprising MHC-peptide structural complexes was created by re-modelling pre-determined x-ray crystallographic structures. Static energetic analysis, following energy minimisation, was performed on the dataset in order to characterise interactions between bound peptides and the MHC Class I molecule, partitioning the interactions within the groove into van der Waals, electrostatic and total non-bonded energy contributions. Conclusion The QSAR techniques of Genetic Function Approximation (GFA and Genetic Partial Least Squares (G/PLS algorithms were used to identify key interactions between the two molecules by comparing the calculated energy values with experimentally-determined BL50 data. Although the peptide termini binding interactions help ensure the stability of the MHC Class I-peptide complex, the central region of the peptide is also important in defining the specificity of the interaction. As thermodynamic studies indicate that peptide association and dissociation may be driven entropically, it may be necessary to incorporate entropic contributions into future calculations.

The presence of modifiable residues in the core peptide part of precursor nisin is not crucial for precursor nisin interactions with NisB- and NisC.

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Rustem Khusainov

Full Text Available Precursor nisin is a model posttranslationally modified precursor lantibiotic that can be structurally divided into a leader peptide sequence and a modifiable core peptide part. The nisin core peptide clearly plays an important role in the precursor nisin-nisin modification enzymes interactions, since it has previously been shown that the construct containing only the nisin leader sequence is not sufficient to pull-down the nisin modification enzymes NisB and NisC. Serines and threonines in the core peptide part are the residues that NisB specifically dehydrates, and cysteines are the residues that NisC stereospecifically couples to the dehydrated amino acids. Here, we demonstrate that increasing the number of negatively charged residues in the core peptide part of precursor nisin, which are absent in wild-type nisin, does not abolish binding of precursor nisin to the modification enzymes NisB and NisC, but dramatically decreases the antimicrobial potency of these nisin mutants. An unnatural precursor nisin variant lacking all serines and threonines in the core peptide part and an unnatural precursor nisin variant lacking all cysteines in the core peptide part still bind the nisin modification enzymes NisB and NisC, suggesting that these residues are not essential for direct interactions with the nisin modification enzymes NisB and NisC. These results are important for lantibiotic engineering studies.

Structure-Activity Relationship in TLR4 Mutations: Atomistic Molecular Dynamics Simulations and Residue Interaction Network Analysis

Science.gov (United States)

Anwar, Muhammad Ayaz; Choi, Sangdun

2017-03-01

Toll-like receptor 4 (TLR4), a vital innate immune receptor present on cell surfaces, initiates a signaling cascade during danger and bacterial intrusion. TLR4 needs to form a stable hexamer complex, which is necessary to dimerize the cytoplasmic domain. However, D299G and T399I polymorphism may abrogate the stability of the complex, leading to compromised TLR4 signaling. Crystallography provides valuable insights into the structural aspects of the TLR4 ectodomain; however, the dynamic behavior of polymorphic TLR4 is still unclear. Here, we employed molecular dynamics simulations (MDS), as well as principal component and residue network analyses, to decipher the structural aspects and signaling propagation associated with mutations in TLR4. The mutated complexes were less cohesive, displayed local and global variation in the secondary structure, and anomalous decay in rotational correlation function. Principal component analysis indicated that the mutated complexes also exhibited distinct low-frequency motions, which may be correlated to the differential behaviors of these TLR4 variants. Moreover, residue interaction networks (RIN) revealed that the mutated TLR4/myeloid differentiation factor (MD) 2 complex may perpetuate abnormal signaling pathways. Cumulatively, the MDS and RIN analyses elucidated the mutant-specific conformational alterations, which may help in deciphering the mechanism of loss-of-function mutations.

Cycling of fertilizer and cotton crop residue nitrogen

International Nuclear Information System (INIS)

Rochester, I.J.; Constable, G.A.; MacLeod, D.A.

1993-01-01

Mineral nitrogen (N), nitrate and ammonium contents were monitored in N-fertilized soils supporting cotton crops to provide information on the nitrification, mineralization and immobilization processes operating in the soil. The relative contributions of fertilizer N, previous cotton crop residue N and indigenous soil N to the mineral N pools and to the current crop's N uptake were calculated. After N fertilizer (urea) application, the soil's mineral N content rose rapidly and subsequently declined at a slower rate. The recovery of 15 N-labelled urea as mineral N declined exponentially with time. Biological immobilization (and possibly denitrification to some extent) were believed to be the major processes reducing post-application soil mineral N content. Progressively less N was mineralized upon incubation of soil sampled through the growing season. Little soil N (either from urea or crop residue) was mineralized at crop maturity. Cycling of N was evident between the soil mineral and organic N pools throughout the cotton growing season. Considerable quantities of fertilizer N were immobilized by the soil micro biomass; immobilized N was remineralized and subsequently taken up by the cotton crop. A large proportion of the crop N was taken up in the latter part of the season when the soil mineral N content was low. It is suggested that much of the N taken up by cotton was derived from microbial sources, rather than crop residues. The application of cotton crop residue (stubble) slightly reduced the mineral N content in the soil by encouraging biological immobilization. 15 N was mineralized very slowly from the labelled crop residue and did not contribute significantly to the supply of N to the current crop. Recovery of labelled fertilizer N and labelled crop residue N by the cotton crop was 28% and 1%, respectively. In comparison, the apparent recovery of fertilizer N was 48%. Indigenous soil N contributed 68% of the N taken up by the cotton crop. 33 refs., 1 tab

Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods

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Pontil Massimiliano

2009-10-01

Full Text Available Abstract Background Alanine scanning mutagenesis is a powerful experimental methodology for investigating the structural and energetic characteristics of protein complexes. Individual amino-acids are systematically mutated to alanine and changes in free energy of binding (ΔΔG measured. Several experiments have shown that protein-protein interactions are critically dependent on just a few residues ("hot spots" at the interface. Hot spots make a dominant contribution to the free energy of binding and if mutated they can disrupt the interaction. As mutagenesis studies require significant experimental efforts, there is a need for accurate and reliable computational methods. Such methods would also add to our understanding of the determinants of affinity and specificity in protein-protein recognition. Results We present a novel computational strategy to identify hot spot residues, given the structure of a complex. We consider the basic energetic terms that contribute to hot spot interactions, i.e. van der Waals potentials, solvation energy, hydrogen bonds and Coulomb electrostatics. We treat them as input features and use machine learning algorithms such as Support Vector Machines and Gaussian Processes to optimally combine and integrate them, based on a set of training examples of alanine mutations. We show that our approach is effective in predicting hot spots and it compares favourably to other available methods. In particular we find the best performances using Transductive Support Vector Machines, a semi-supervised learning scheme. When hot spots are defined as those residues for which ΔΔG ≥ 2 kcal/mol, our method achieves a precision and a recall respectively of 56% and 65%. Conclusion We have developed an hybrid scheme in which energy terms are used as input features of machine learning models. This strategy combines the strengths of machine learning and energy-based methods. Although so far these two types of approaches have mainly been

Causal functional contributions and interactions in the attention network of the brain: an objective multi-perturbation analysis.

Science.gov (United States)

Zavaglia, Melissa; Hilgetag, Claus C

2016-06-01

Spatial attention is a prime example for the distributed network functions of the brain. Lesion studies in animal models have been used to investigate intact attentional mechanisms as well as perspectives for rehabilitation in the injured brain. Here, we systematically analyzed behavioral data from cooling deactivation and permanent lesion experiments in the cat, where unilateral deactivation of the posterior parietal cortex (in the vicinity of the posterior middle suprasylvian cortex, pMS) or the superior colliculus (SC) cause a severe neglect in the contralateral hemifield. Counterintuitively, additional deactivation of structures in the opposite hemisphere reverses the deficit. Using such lesion data, we employed a game-theoretical approach, multi-perturbation Shapley value analysis (MSA), for inferring functional contributions and network interactions of bilateral pMS and SC from behavioral performance in visual attention studies. The approach provides an objective theoretical strategy for lesion inferences and allows a unique quantitative characterization of regional functional contributions and interactions on the basis of multi-perturbations. The quantitative analysis demonstrated that right posterior parietal cortex and superior colliculus made the strongest positive contributions to left-field orienting, while left brain regions had negative contributions, implying that their perturbation may reverse the effects of contralateral lesions or improve normal function. An analysis of functional modulations and interactions among the regions revealed redundant interactions (implying functional overlap) between regions within each hemisphere, and synergistic interactions between bilateral regions. To assess the reliability of the MSA method in the face of variable and incomplete input data, we performed a sensitivity analysis, investigating how much the contribution values of the four regions depended on the performance of specific configurations and on the

Analysis of residual stress relief mechanisms in post-weld heat treatment

International Nuclear Information System (INIS)

Dong, Pingsha; Song, Shaopin; Zhang, Jinmiao

2014-01-01

This paper presents a recent study on weld residual stress relief mechanisms associated with furnace-based uniform post-weld heat treatment (PWHT). Both finite element and analytical methods are used to quantitatively examine how plastic deformation and creep relaxation contribute to residual stress relief process at different stages of PWHT process. The key contribution of this work to an improved understanding of furnace based uniform PWHT can be summarized as follows: (1)Plastic deformation induced stress relief during PWHT can be analytically expressed by the change in material elastic deformation capacity (or elastic deformation limit) measured in terms of material yield strength to Young's modulus ratio, which has a rather limited role in overall residual stress relief during furnace based uniform PWHT. (2)The most dominant stress relief mechanism is creep strain induced stress relaxation, as expected. However, a rapid creep strain development accompanied by a rapid residual stress reduction during heating stage before reaching PWHT temperature is shown to contribute to most of the stress relief seen in overall PWHT process, suggesting PWHT hold time can be significantly reduced as far as residual stress relief is concerned. (3)A simple engineering scheme for estimating residual stress reduction is proposed based on this study by relating material type, PWHT temperature, and component wall thickness. - Highlights: • The paper clarified effects of plastic deformation and creep relaxation on weld residual stress relief during uniform PWHT. • Creep strain development is far more important than plastic strain, mostly completed even before hold time starts. • Plastic strain development is insignificant and be analytically described by a material elastic deformation capacity parameter. • An engineering estimation scheme is proposed for determining residual stress reduction resulted from furnace based PWHT

Conditioned place preference for social interaction in rats: contribution of sensory components.

Science.gov (United States)

Kummer, Kai; Klement, Sabine; Eggart, Vincent; Mayr, Michael J; Saria, Alois; Zernig, Gerald

2011-01-01

A main challenge in the therapy of drug dependent individuals is to help them reactivate interest in non-drug-associated activities. We previously developed a rat experimental model based on the conditioned place preference (CPP) paradigm in which only four 15-min episodes of social interaction with a gender- and weight-matched male Sprague Dawley rat (1) reversed CPP from cocaine to social interaction despite continuing cocaine training and (2) prevented the reinstatement of cocaine CPP. In the present study, we investigated which of the sensory modalities of the composite stimulus "social interaction" contributes most to the rats' preference for it. If touch was limited by steel bars spaced at a distance of 2 cm and running across the whole length of a partitioning, CPP was still acquired, albeit to a lesser degree. If both rats were placed on the same side of a partitioning, rats did not develop CPP for social interaction. Thus, decreasing the available area for social interaction from 750 to 375 cm(2) prevented the acquisition of CPP to social interaction despite the fact that animals could touch each other more intensely than through the bars of the partitioning. When touch was fully restricted by a glass screen dividing the conditioning chambers, and the only sensory modalities left were visual and olfactory cues, place preference shifted to place aversion. Overall, our findings indicate that the major rewarding sensory component of the composite stimulus "social interaction" is touch (taction).

Critical contribution of aromatic rings to specific recognition of polyether rings. The case of ciguatoxin CTX3C-ABC and its specific antibody 1C49.

Science.gov (United States)

Tsumoto, Kouhei; Yokota, Akiko; Tanaka, Yoshikazu; Ui, Mihoko; Tsumuraya, Takeshi; Fujii, Ikuo; Kumagai, Izumi; Nagumo, Yoko; Oguri, Hiroki; Inoue, Masayuki; Hirama, Masahiro

2008-05-02

To address how proteins recognize polyether toxin compounds, we focused on the interaction between the ABC ring compound of ciguatoxin 3C and its specific antibody, 1C49. Surface plasmon resonance analyses indicated that Escherichia coli-expressed variable domain fragments (Fv) of 1C49 had the high affinity constants and slow dissociation constants typical of antigen-antibody interactions. Linear van't Hoff analyses suggested that the interaction is enthalpy-driven. We resolved the crystal structure of 1C49 Fv bound to ABC ring compound of ciguatoxin 3C at a resolution of 1.7A. The binding pocket of the antibody had many aromatic rings and bound the antigen by shape complementarity typical of hapten-antibody interactions. Three hydrogen bonds and many van der Waals interactions were present. We mutated several residues of the antibody to Ala, and we used surface plasmon resonance to analyze the interactions between the mutated antibodies and the antigen. This analysis identified Tyr-91 and Trp-96 in the light chain as hot spots for the interaction, and other residues made incremental contributions by conferring enthalpic advantages and reducing the dissociation rate constant. Systematic mutation of Tyr-91 indicated that CH-pi and pi-pi interactions between the aromatic ring at this site and the antigen made substantial contributions to the association, and van der Waals interactions inhibited dissociation, suggesting that aromaticity and bulkiness are critical for the specific recognition of polyether compounds by proteins.

Reactive control processes contributing to residual switch cost and mixing cost in young and old adults

Directory of Open Access Journals (Sweden)

Lisa Rebecca Whitson

2014-04-01

Full Text Available In task-switching paradigms, performance is better when repeating the same task than when alternating between tasks (switch cost and when repeating a task alone rather than intermixed with another task (mixing cost. These costs remain even after extensive practice and when task cues enable advanced preparation (residual costs. Moreover, residual RT mixing cost has been consistently shown to increase with age. Residual switch and mixing costs modulate the amplitude of the stimulus-locked P3b. This mixing effect is disproportionately larger in older adults who also prepare more for and respond more cautiously on these ‘mixed’ repeat trials (Karayanidis et al., 2011. In this study, we examine stimulus-locked and response-locked P3 and lateralized readiness potentials to identify whether residual switch and mixing cost arise from the need to control interference at the level of stimulus processing or response processing. Residual mixing cost was associated with control of stimulus-level interference, whereas residual switch cost was also associated with a delay in response selection. In older adults, the disproportionate increase in mixing cost was associated with greater interference at the level of decision-response mapping and response programming for repeat trials in mixed-task blocks. We argue that, together with evidence of greater proactive control and more cautious responding for these trials, these findings suggest that older adults strategically recruit greater proactive and reactive control to overcome increased susceptibility to post-stimulus interference. This interpretation is consistent with recruitment of compensatory strategies to compensate for reduced repetition benefit rather than an overall decline on cognitive flexibility.

Slow and pressurized co-pyrolysis of coal and agricultural residues

International Nuclear Information System (INIS)

Aboyade, Akinwale O.; Carrier, Marion; Meyer, Edson L.; Knoetze, Hansie; Görgens, Johann F.

2013-01-01

Highlights: ► Evaluation of co-pyrolysis of coal and biomass in pressurized packed bed reactor. ► Relative influence of coal–biomass mix ratio, temperature and pressure also investigated. ► Results show significant synergy or chemical interactions in the vapor phase. ► Synergistic interactions did not influence distribution of lumped solid liquid and gas products. - Abstract: The distribution of products from the slow heating rate pyrolysis of coal, corn residues (cobs and stover), sugarcane bagasse and their blends were investigated by slow pressurized pyrolysis in a packed bed reactor. A factorial experimental design was implemented to establish the relative significance of coal–biomass mix ratio, temperature and pressure on product distribution. Results showed that the yield and composition of tar and other volatile products were mostly influenced by mix ratio, while temperature and pressure had a low to negligible significance under the range of conditions investigated. Analysis of the composition of condensates and gas products obtained showed that there was significant synergy or chemical interactions in the vapor phase during co-pyrolysis of coal and biomass. However, the interactions did not significantly affect the relative distribution of the lumped solid, liquid and gas products obtained from the blends, beyond what would be expected assuming additive behavior from the contributing fuels.

Mast cell-neural interactions contribute to pain and itch.

Science.gov (United States)

Gupta, Kalpna; Harvima, Ilkka T

2018-03-01

Mast cells are best recognized for their role in allergy and anaphylaxis, but increasing evidence supports their role in neurogenic inflammation leading to pain and itch. Mast cells act as a "power house" by releasing algogenic and pruritogenic mediators, which initiate a reciprocal communication with specific nociceptors on sensory nerve fibers. Consequently, nerve fibers release inflammatory and vasoactive neuropeptides, which in turn activate mast cells in a feedback mechanism, thus promoting a vicious cycle of mast cell and nociceptor activation leading to neurogenic inflammation and pain/pruritus. Mechanisms underlying mast cell differentiation, activation, and intercellular interactions with inflammatory, vascular, and neural systems are deeply influenced by their microenvironment, imparting enormous heterogeneity and complexity in understanding their contribution to pain and pruritus. Neurogenic inflammation is central to both pain and pruritus, but specific mediators released by mast cells to promote this process may vary depending upon their location, stimuli, underlying pathology, gender, and species. Therefore, in this review, we present the contribution of mast cells in pathological conditions, including distressing pruritus exacerbated by psychologic stress and experienced by the majority of patients with psoriasis and atopic dermatitis and in different pain syndromes due to mastocytosis, sickle cell disease, and cancer. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Novel essential residues of Hda for interaction with DnaA in the regulatory inactivation of DnaA: unique roles for Hda AAA Box VI and VII motifs.

Science.gov (United States)

Nakamura, Kenta; Katayama, Tsutomu

2010-04-01

Escherichia coli ATP-DnaA initiates chromosomal replication. For preventing extra-initiations, a complex of ADP-Hda and the DNA-loaded replicase clamp promotes DnaA-ATP hydrolysis, yielding inactive ADP-DnaA. However, the Hda-DnaA interaction mode remains unclear except that the Hda Box VII Arg finger (Arg-153) and DnaA sensor II Arg-334 within each AAA(+) domain are crucial for the DnaA-ATP hydrolysis. Here, we demonstrate that direct and functional interaction of ADP-Hda with DnaA requires the Hda residues Ser-152, Phe-118 and Asn-122 as well as Hda Arg-153 and DnaA Arg-334. Structural analyses suggest intermolecular interactions between Hda Ser-152 and DnaA Arg-334 and between Hda Phe-118 and the DnaA Walker B motif region, in addition to an intramolecular interaction between Hda Asn-122 and Arg-153. These interactions likely sustain a specific association of ADP-Hda and DnaA, promoting DnaA-ATP hydrolysis. Consistently, ATP-DnaA and ADP-DnaA interact with the ADP-Hda-DNA-clamp complex with similar affinities. Hda Phe-118 and Asn-122 are contained in the Box VI region, and their hydrophobic and electrostatic features are basically conserved in the corresponding residues of other AAA(+) proteins, suggesting a conserved role for Box VI. These findings indicate novel interaction mechanisms for Hda-DnaA as well as a potentially fundamental mechanism in AAA(+) protein interactions.

Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions.

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Kevin A James

Full Text Available The ErbB protein tyrosine kinases are among the most important cell signaling families and mutation-induced modulation of their activity is associated with diverse functions in biological networks and human disease. We have combined molecular dynamics simulations of the ErbB kinases with the protein structure network modeling to characterize the reorganization of the residue interaction networks during conformational equilibrium changes in the normal and oncogenic forms. Structural stability and network analyses have identified local communities integrated around high centrality sites that correspond to the regulatory spine residues. This analysis has provided a quantitative insight to the mechanism of mutation-induced "superacceptor" activity in oncogenic EGFR dimers. We have found that kinase activation may be determined by allosteric interactions between modules of structurally stable residues that synchronize the dynamics in the nucleotide binding site and the αC-helix with the collective motions of the integrating αF-helix and the substrate binding site. The results of this study have pointed to a central role of the conserved His-Arg-Asp (HRD motif in the catalytic loop and the Asp-Phe-Gly (DFG motif as key mediators of structural stability and allosteric communications in the ErbB kinases. We have determined that residues that are indispensable for kinase regulation and catalysis often corresponded to the high centrality nodes within the protein structure network and could be distinguished by their unique network signatures. The optimal communication pathways are also controlled by these nodes and may ensure efficient allosteric signaling in the functional kinase state. Structure-based network analysis has quantified subtle effects of ATP binding on conformational dynamics and stability of the EGFR structures. Consistent with the NMR studies, we have found that nucleotide-induced modulation of the residue interaction networks is not

Protonation states of histidine and other key residues in deoxy normal human adult hemoglobin by neutron protein crystallography

International Nuclear Information System (INIS)

Kovalevsky, Andrey; Chatake, Toshiyuki; Shibayama, Naoya; Park, Sam-Yong; Ishikawa, Takuya; Mustyakimov, Marat; Fisher, S. Zoe; Langan, Paul; Morimoto, Yukio

2010-01-01

Using neutron diffraction analysis, the protonation states of 35 of 38 histidine residues were determined for the deoxy form of normal human adult hemoglobin. Distal and buried histidines may contribute to the increased affinity of the deoxy state for hydrogen ions and its decreased affinity for oxygen compared with the oxygenated form. The protonation states of the histidine residues key to the function of deoxy (T-state) human hemoglobin have been investigated using neutron protein crystallography. These residues can reversibly bind protons, thereby regulating the oxygen affinity of hemoglobin. By examining the OMIT F o − F c and 2F o − F c neutron scattering maps, the protonation states of 35 of the 38 His residues were directly determined. The remaining three residues were found to be disordered. Surprisingly, seven pairs of His residues from equivalent α or β chains, αHis20, αHis50, αHis58, αHis89, βHis63, βHis143 and βHis146, have different protonation states. The protonation of distal His residues in the α 1 β 1 heterodimer and the protonation of αHis103 in both subunits demonstrates that these residues may participate in buffering hydrogen ions and may influence the oxygen binding. The observed protonation states of His residues are compared with their ΔpK a between the deoxy and oxy states. Examination of inter-subunit interfaces provided evidence for interactions that are essential for the stability of the deoxy tertiary structure

Characterization of the interdependency between residues that bind the substrate in a β-glycosidase

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M.H. Tomassi

2010-01-01

Full Text Available The manner by which effects of simultaneous mutations combine to change enzymatic activity is not easily predictable because these effects are not always additive in a linear manner. Hence, the characterization of the effects of simultaneous mutations of amino acid residues that bind the substrate can make a significant contribution to the understanding of the substrate specificity of enzymes. In the β-glycosidase from Spodoptera frugiperda (Sfβgly, both residues Q39 and E451 interact with the substrate and this is essential for defining substrate specificity. Double mutants of Sfβgly (A451E39, S451E39 and S451N39 were prepared by site-directed mutagenesis, expressed in bacteria and purified using affinity chromatography. These enzymes were characterized using p-nitrophenyl β-galactoside and p-nitrophenyl β-fucoside as substrates. The k cat/Km ratio for single and double mutants of Sfβgly containing site-directed mutations at positions Q39 and E451 was used to demonstrate that the effect on the free energy of ES‡ (enzyme-transition state complex of the double mutations (∆∆G‡xy is not the sum of the effects resulting from the single mutations (∆∆G‡x and ∆∆G‡y. This difference in ∆∆G‡ indicates that the effects of the single mutations partially overlap. Hence, this common effect counts only once in ∆∆G‡xy. Crystallographic data on β-glycosidases reveal the presence of a bidentate hydrogen bond involving residues Q39 and E451 and the same hydroxyl group of the substrate. Therefore, both thermodynamic and crystallographic data suggest that residues Q39 and E451 exert a mutual influence on their respective interactions with the substrate.

In situ chemical composition measurement of individual cloud residue particles at a mountain site, southern China

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Q. Lin

2017-07-01

Full Text Available To investigate how atmospheric aerosol particles interact with chemical composition of cloud droplets, a ground-based counterflow virtual impactor (GCVI coupled with a real-time single-particle aerosol mass spectrometer (SPAMS was used to assess the chemical composition and mixing state of individual cloud residue particles in the Nanling Mountains (1690 m a. s. l. , southern China, in January 2016. The cloud residues were classified into nine particle types: aged elemental carbon (EC, potassium-rich (K-rich, amine, dust, Pb, Fe, organic carbon (OC, sodium-rich (Na-rich and Other. The largest fraction of the total cloud residues was the aged EC type (49.3 %, followed by the K-rich type (33.9 %. Abundant aged EC cloud residues that mixed internally with inorganic salts were found in air masses from northerly polluted areas. The number fraction (NF of the K-rich cloud residues increased within southwesterly air masses from fire activities in Southeast Asia. When air masses changed from northerly polluted areas to southwesterly ocean and livestock areas, the amine particles increased from 0.2 to 15.1 % of the total cloud residues. The dust, Fe, Pb, Na-rich and OC particle types had a low contribution (0.5–4.1 % to the total cloud residues. Higher fraction of nitrate (88–89 % was found in the dust and Na-rich cloud residues relative to sulfate (41–42 % and ammonium (15–23 %. Higher intensity of nitrate was found in the cloud residues relative to the ambient particles. Compared with nonactivated particles, nitrate intensity decreased in all cloud residues except for dust type. To our knowledge, this study is the first report on in situ observation of the chemical composition and mixing state of individual cloud residue particles in China.

A feature-based approach to modeling protein-protein interaction hot spots.

Science.gov (United States)

Cho, Kyu-il; Kim, Dongsup; Lee, Doheon

2009-05-01

Identifying features that effectively represent the energetic contribution of an individual interface residue to the interactions between proteins remains problematic. Here, we present several new features and show that they are more effective than conventional features. By combining the proposed features with conventional features, we develop a predictive model for interaction hot spots. Initially, 54 multifaceted features, composed of different levels of information including structure, sequence and molecular interaction information, are quantified. Then, to identify the best subset of features for predicting hot spots, feature selection is performed using a decision tree. Based on the selected features, a predictive model for hot spots is created using support vector machine (SVM) and tested on an independent test set. Our model shows better overall predictive accuracy than previous methods such as the alanine scanning methods Robetta and FOLDEF, and the knowledge-based method KFC. Subsequent analysis yields several findings about hot spots. As expected, hot spots have a larger relative surface area burial and are more hydrophobic than other residues. Unexpectedly, however, residue conservation displays a rather complicated tendency depending on the types of protein complexes, indicating that this feature is not good for identifying hot spots. Of the selected features, the weighted atomic packing density, relative surface area burial and weighted hydrophobicity are the top 3, with the weighted atomic packing density proving to be the most effective feature for predicting hot spots. Notably, we find that hot spots are closely related to pi-related interactions, especially pi . . . pi interactions.

A feature-based approach to modeling protein–protein interaction hot spots

Science.gov (United States)

Cho, Kyu-il; Kim, Dongsup; Lee, Doheon

2009-01-01

Identifying features that effectively represent the energetic contribution of an individual interface residue to the interactions between proteins remains problematic. Here, we present several new features and show that they are more effective than conventional features. By combining the proposed features with conventional features, we develop a predictive model for interaction hot spots. Initially, 54 multifaceted features, composed of different levels of information including structure, sequence and molecular interaction information, are quantified. Then, to identify the best subset of features for predicting hot spots, feature selection is performed using a decision tree. Based on the selected features, a predictive model for hot spots is created using support vector machine (SVM) and tested on an independent test set. Our model shows better overall predictive accuracy than previous methods such as the alanine scanning methods Robetta and FOLDEF, and the knowledge-based method KFC. Subsequent analysis yields several findings about hot spots. As expected, hot spots have a larger relative surface area burial and are more hydrophobic than other residues. Unexpectedly, however, residue conservation displays a rather complicated tendency depending on the types of protein complexes, indicating that this feature is not good for identifying hot spots. Of the selected features, the weighted atomic packing density, relative surface area burial and weighted hydrophobicity are the top 3, with the weighted atomic packing density proving to be the most effective feature for predicting hot spots. Notably, we find that hot spots are closely related to π–related interactions, especially π · · · π interactions. PMID:19273533

Ion-ion interactions in the denatured state contribute to the stabilization of CutA1 proteins.

Science.gov (United States)

Yutani, Katsuhide; Matsuura, Yoshinori; Naitow, Hisashi; Joti, Yasumasa

2018-05-16

In order to elucidate features of the denatured state ensembles that exist in equilibrium with the native state under physiological conditions, we performed 1.4-μs molecular dynamics (MD) simulations at 400 K and 450 K using the monomer subunits of three CutA1 mutants from Escherichia coli: an SH-free mutant (Ec0SH) with denaturation temperature (T d ) = 85.6 °C, a hydrophobic mutant (Ec0VV) with T d  = 113.3 °C, and an ionic mutant (Ec0VV_6) with T d  = 136.8 °C. The occupancy of salt bridges by the six substituted charged residues in Ec0VV_6 was 140.1% at 300 K and 89.5% at 450 K, indicating that even in the denatured state, salt bridge occupancy was high, approximately 60% of that at 300 K. From these results, we can infer that proteins from hyperthermophiles with a high ratio of charged residues are stabilized by a decrease in conformational entropy due to ion-ion interactions in the denatured state. The mechanism must be comparable to the stabilization conferred by disulfide bonds within a protein. This suggests that introduction of charged residues, to promote formation of salt bridges in the denatured state, would be a simple way to rationally design stability-enhanced mutants.

Influence of pH on pesticide sorption by soil containing wheat residue-derived char

International Nuclear Information System (INIS)

Sheng Guangyao; Yang Yaning; Huang Minsheng; Yang Kai

2005-01-01

Field burning of crop residues incorporates resulting chars into soil and may thus influence the environmental fate of pesticides in the soil. This study evaluated the influence of pH on the sorption of diuron, bromoxynil, and ametryne by a soil in the presence and absence of a wheat residue-derived char. The sorption was measured at pHs ∼3.0 and ∼7.0. Wheat char was found to be a highly effective sorbent for the pesticides, and its presence (1% by weight) in soil contributed >70% to the pesticide sorption (with one exception). The sorption of diuron was not influenced by pH, due to its electroneutrality. Bromoxynil becomes dissociated at high pHs to form anionic species. Its sorption by soil and wheat char was lower at pH ∼7.0 than at pH ∼3.0, probably due to reduced partition of the anionic species of bromoxynil into soil organic matter and its weak interaction with the carbon surface of the char. Ametryne in its molecular form at pH ∼7.0 was sorbed by char-amended soil via partitioning into soil organic matter and interaction with the carbon surface of the char. Protonated ametryne at pH ∼3.0 was substantially sorbed by soil primarily via electrostatic forces. Sorption of protonated ametryne by wheat char was also significant, likely due not only to the interaction with the carbon surface but also to interactions with hydrated silica and surface functional groups of the char. Sorption of ametryne by char-amended soil at pH ∼3.0 was thus influenced by both the soil and the char. Environmental conditions may thus significantly influence the sorption and behavior of pesticides in agricultural soils containing crop residue-derived chars. - Wheat char was effective for adsorption of pesticides in soil, with efficacy varying with pH and particular pesticides

Influence of pH on pesticide sorption by soil containing wheat residue-derived char

Energy Technology Data Exchange (ETDEWEB)

Sheng Guangyao [Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701 (United States)]. E-mail: gsheng@uark.edu; Yang Yaning [Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701 (United States); Huang Minsheng [Department of Environmental Science and Technology, East China Normal University, Shanghai 200062 (China); Yang Kai [Department of Environmental Science and Technology, East China Normal University, Shanghai 200062 (China)

2005-04-01

Field burning of crop residues incorporates resulting chars into soil and may thus influence the environmental fate of pesticides in the soil. This study evaluated the influence of pH on the sorption of diuron, bromoxynil, and ametryne by a soil in the presence and absence of a wheat residue-derived char. The sorption was measured at pHs {approx}3.0 and {approx}7.0. Wheat char was found to be a highly effective sorbent for the pesticides, and its presence (1% by weight) in soil contributed >70% to the pesticide sorption (with one exception). The sorption of diuron was not influenced by pH, due to its electroneutrality. Bromoxynil becomes dissociated at high pHs to form anionic species. Its sorption by soil and wheat char was lower at pH {approx}7.0 than at pH {approx}3.0, probably due to reduced partition of the anionic species of bromoxynil into soil organic matter and its weak interaction with the carbon surface of the char. Ametryne in its molecular form at pH {approx}7.0 was sorbed by char-amended soil via partitioning into soil organic matter and interaction with the carbon surface of the char. Protonated ametryne at pH {approx}3.0 was substantially sorbed by soil primarily via electrostatic forces. Sorption of protonated ametryne by wheat char was also significant, likely due not only to the interaction with the carbon surface but also to interactions with hydrated silica and surface functional groups of the char. Sorption of ametryne by char-amended soil at pH {approx}3.0 was thus influenced by both the soil and the char. Environmental conditions may thus significantly influence the sorption and behavior of pesticides in agricultural soils containing crop residue-derived chars. - Wheat char was effective for adsorption of pesticides in soil, with efficacy varying with pH and particular pesticides.

Investigating the properties of residues. Characterization of pellets from fermentation residues; Den Eigenschaften der Reststoffe auf der Spur. Untersuchung widmet sich der Charakterisierung von Pellets aus Gaerresten

Energy Technology Data Exchange (ETDEWEB)

Kratzeisen, Martin; Mueller, Joachim [Hohenheim Univ., Stuttgart (Germany). Inst. fuer Agrartechnik; Starcevic, Nikica [Hohenheim Univ., Stuttgart (Germany). Inst. fuer Agrartechnik; Strabag Umweltanlagen GmbH, Muenchen (Germany). Projekt Produktentwicklung/Schlammbehandlung

2009-09-15

Fermentation residues are by-products of the biogas process. Farmers use them as fertilizers, but as the size of biogas plants grows, so does the residues volume. It is now too much for local use, and transport to other sites is expensive. Fuel pellets production may be an alternative. Pellets from fermentation residues are not accepted as yet because too little is known about their characteristics. The contribution describes an investigation that intends to identify the fuel characteristics of pellets from fermentation residues. (orig.)

On the relationship between residue structural environment and sequence conservation in proteins.

Science.gov (United States)

Liu, Jen-Wei; Lin, Jau-Ji; Cheng, Chih-Wen; Lin, Yu-Feng; Hwang, Jenn-Kang; Huang, Tsun-Tsao

2017-09-01

Residues that are crucial to protein function or structure are usually evolutionarily conserved. To identify the important residues in protein, sequence conservation is estimated, and current methods rely upon the unbiased collection of homologous sequences. Surprisingly, our previous studies have shown that the sequence conservation is closely correlated with the weighted contact number (WCN), a measure of packing density for residue's structural environment, calculated only based on the C α positions of a protein structure. Moreover, studies have shown that sequence conservation is correlated with environment-related structural properties calculated based on different protein substructures, such as a protein's all atoms, backbone atoms, side-chain atoms, or side-chain centroid. To know whether the C α atomic positions are adequate to show the relationship between residue environment and sequence conservation or not, here we compared C α atoms with other substructures in their contributions to the sequence conservation. Our results show that C α positions are substantially equivalent to the other substructures in calculations of various measures of residue environment. As a result, the overlapping contributions between C α atoms and the other substructures are high, yielding similar structure-conservation relationship. Take the WCN as an example, the average overlapping contribution to sequence conservation is 87% between C α and all-atom substructures. These results indicate that only C α atoms of a protein structure could reflect sequence conservation at the residue level. © 2017 Wiley Periodicals, Inc.

Tidal residual current and its role in the mean flow on the Changjiang Bank

Science.gov (United States)

Xuan, Jiliang; Yang, Zhaoqing; Huang, Daji; Wang, Taiping; Zhou, Feng

2016-02-01

The tidal residual current may play an important role in the mean flow in the Changjiang Bank region, in addition to other residual currents, such as the Taiwan Warm Current, the Yellow Sea Coastal Current, and the Yellow Sea Warm Current. In this paper, a detailed structure of the tidal residual current, in particular the meso-scale eddies, in the Changjiang Bank region is observed from model simulations, and its role in the mean flow is quantified using the well-validated Finite Volume Coastal Ocean Model. The tidal residual current in the Changjiang Bank region consists of two components: an anticyclonic regional-scale tidal residual circulation around the edge of the Changjiang Bank and some cyclonic meso-scale tidal residual eddies across the Changjiang Bank. The meso-scale tidal residual eddies occur across the Changjiang Bank and contribute to the regional-scale tidal residual circulation offshore at the northwest boundary and on the northeast edge of the Changjiang Bank, southeastward along the 50 m isobath. Tidal rectification is the major mechanism causing the tidal residual current to flow along the isobaths. Both components of the tidal residual current have significant effects on the mean flow. A comparison between the tidal residual current and the mean flow indicates that the contribution of the tidal residual current to the mean flow is greater than 50%.

Tidal residual current and its role in the mean flow on the Changjiang Bank

Energy Technology Data Exchange (ETDEWEB)

Xuan, Jiliang; Yang, Zhaoqing; Huang, Daji; Wang, Taiping; Zhou, Feng

2016-02-01

Tidal residual current may play an important role in the mean flow in the Changjiang Bank region, in addition to other residual currents, such as the Taiwan Warm Current, the Yellow Sea Coastal Current, and the Yellow Sea Warm Current. In this paper, a detailed structure of the tidal residual current, in particular the meso-scale eddies, in the Changjiang Bank region is observed from model simulations, and its role in the mean flow is quantified using the well-validated Finite Volume Coastal Ocean Model). The tidal residual current in the Changjiang Bank region consists of two components: an anticyclonic regional-scale tidal residual circulation around the edge of the Changjiang Bank and some cyclonic meso-scale tidal residual eddies across the Changjiang Bank. The meso-scale tidal residual eddies occur across the Changjiang Bank and contribute to the regional-scale tidal residual circulation offshore at the northwest boundary and at the northeast edge of the Changjiang Bank, southeastward along the 50 m isobath. Tidal rectification is the major mechanism causing the tidal residual current to flow along the isobaths. Both components of the tidal residual current have significant effects on the mean flow. A comparison between the tidal residual current and the mean flow indicates that the contribution of the tidal residual current to the mean flow is greater than 50%.

Impact of sugarcane field residue and mill bagasse on seed germination

Science.gov (United States)

Research indicates that sugarcane field residue and sugarcane mill bagasse may be allelopathic. Allelopathy is the chemical interaction between plants, which may result in the inhibition of plant growth and development. Previous research in Louisiana indicated that sugarcane field residue may inhibi...

Generic GPCR residue numbers - aligning topology maps while minding the gaps

DEFF Research Database (Denmark)

Isberg, Vignir; de Graaf, Chris; Bortolato, Andrea

2015-01-01

Generic residue numbers facilitate comparisons of, for example, mutational effects, ligand interactions, and structural motifs. The numbering scheme by Ballesteros and Weinstein for residues within the class A GPCRs (G protein-coupled receptors) has more than 1100 citations, and the recent crysta...

Residual stress analysis in reactor pressure vessel attachments

International Nuclear Information System (INIS)

Dexter, R.J.; Pont, D.

1991-08-01

Residual stresses in cladding and welded attachments could contribute to the problem of stress-corrosion cracking in boiling-water reactors (BWR). As part of a larger program aimed at quantifying residual stress in BWR components, models that would be applicable for predicting residual stress in BWR components are reviewed and documented. The review includes simple methods of estimating residual stresses as well as advanced finite-element software. In general, simple methods are capable of predicting peak magnitudes of residual stresses but are incapable of adequately characterizing the distribution of residual stresses. Ten groups of researchers using finite-element software are reviewed in detail. For each group, the assumptions of the model, possible simplifications, material property data, and specific applications are discussed. The most accurate results are obtained when a metallurgical simulation is performed, transformation plasticity effects are included, and the heating and cooling parts of the welding thermal cycle are simulated. Two models are identified which can provide these features. The present state of these models and the material property data available in the literature are adequate to quantify residual stress in BWR components

Eviromental Economic and Technological Residues Management Demands: An Optimization Tool.

Directory of Open Access Journals (Sweden)

Marisa Soares Borges

2012-12-01

Full Text Available Industrial residues management is a very demanding task since many different goals must be achieved. The combination of different approaches used by people from different stuff is very challenging activity that can misuse the residues potential value and applicability. An interactive WEB base tool, to integrate different sectors and overcome residues management difficulties will be presented. The system must be loaded with all data concerning the residue life cycle, and through data integration and modeling routine will give the best alternative as output. As wider and complete the system data becomes, by information loading from differen t segment, more efficient the residues management becomes. The user friendly tool will encourage the participation of industries, labs and research institutions to obtain qualified information about industrial residues inventory, raw materials recovery, characteristics, treatment and alternative uses, to achieve residues management sustainability.

Interactive effects of rice residue and water stress on growth and metabolism of wheat seedlings

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Nimisha Amist

2014-08-01

Full Text Available In the present study effects of rice residue with and without water stress were studied on Triticum aestivum L. cv. Shatabadi. The mixture of residue and garden soil in 1:1 ratio was considered as 50% (R1 and only decomposed residue as 100% (R2. Garden soil was taken as control. Twenty five seeds were sown in each experimental trays filled with soil mixture according to the treatments. Trays were arranged in two groups. After 15 days one set was subjected to water stress (WS by withholding water supply for 3 days. Morphological and biochemical parameters of 18 days old seedlings were recorded. Seedling height decreased in all treatments. A gradual decrease in relative water content, pigment and protein contents of wheat seedlings were observed. Sugar and proline contents increased in treatments. An increase in malondialdehyde (MDA content and antioxidative enzyme activities was recorded. Elevation in catalase activity was observed in all treatments except in plants with water deficit. Ascorbate peroxidase (APX and guaiacol peroxidase (GPX activities increased when residue mixed with soil but decreased in seedlings under the combined influence of the residue and water stress. Higher amount of MDA and lower activities of APX and GPX reflected the oxidative damage in seedlings under combined treatments. Rice residue inhibited growth of wheat seedlings. Water stress intensified the effects of residue.

Professional Interaction, Relevant Practical Experience, and Intellectual Contributions at Nondoctoral AACSB-Accredited Accounting Programs

Science.gov (United States)

Arlinghaus, Barry P.

2008-01-01

In this article, the author discusses a survey of faculty members at nondoctoral AACSB-accredited accounting programs in the United States. The purpose of the survey was to determine the environment for professional interaction and relevant experience in light of institutional demands for intellectual contributions. The findings show that the…

A tool for calculating binding-site residues on proteins from PDB structures

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Hu Jing

2009-08-01

Full Text Available Abstract Background In the research on protein functional sites, researchers often need to identify binding-site residues on a protein. A commonly used strategy is to find a complex structure from the Protein Data Bank (PDB that consists of the protein of interest and its interacting partner(s and calculate binding-site residues based on the complex structure. However, since a protein may participate in multiple interactions, the binding-site residues calculated based on one complex structure usually do not reveal all binding sites on a protein. Thus, this requires researchers to find all PDB complexes that contain the protein of interest and combine the binding-site information gleaned from them. This process is very time-consuming. Especially, combing binding-site information obtained from different PDB structures requires tedious work to align protein sequences. The process becomes overwhelmingly difficult when researchers have a large set of proteins to analyze, which is usually the case in practice. Results In this study, we have developed a tool for calculating binding-site residues on proteins, TCBRP http://yanbioinformatics.cs.usu.edu:8080/ppbindingsubmit. For an input protein, TCBRP can quickly find all binding-site residues on the protein by automatically combining the information obtained from all PDB structures that consist of the protein of interest. Additionally, TCBRP presents the binding-site residues in different categories according to the interaction type. TCBRP also allows researchers to set the definition of binding-site residues. Conclusion The developed tool is very useful for the research on protein binding site analysis and prediction.

Residual nilpotence and residual solubility of groups

International Nuclear Information System (INIS)

Mikhailov, R V

2005-01-01

The properties of the residual nilpotence and the residual solubility of groups are studied. The main objects under investigation are the class of residually nilpotent groups such that each central extension of these groups is also residually nilpotent and the class of residually soluble groups such that each Abelian extension of these groups is residually soluble. Various examples of groups not belonging to these classes are constructed by homological methods and methods of the theory of modules over group rings. Several applications of the theory under consideration are presented and problems concerning the residual nilpotence of one-relator groups are considered.

Residual symptoms and functioning in depression, does the type of residual symptom matter? A post-hoc analysis

Directory of Open Access Journals (Sweden)

Romera Irene

2013-02-01

Full Text Available Abstract Background The degrees to which residual symptoms in major depressive disorder (MDD adversely affect patient functioning is not known. This post-hoc analysis explored the association between different residual symptoms and patient functioning. Methods Patients with MDD who responded (≥50% on the 17-item Hamilton Rating Scale for Depression; HAMD-17 after 3 months of treatment (624/930 were included. Residual core mood-symptoms (HAMD-17 core symptom subscale ≥1, residual insomnia-symptoms (HAMD-17 sleep subscale ≥1, residual anxiety-symptoms (HAMD-17-anxiety subscale ≥1, residual somatic-symptoms (HAMD-17 Item 13 ≥1, pain (Visual Analogue Scale ≥30, and functioning were assessed after 3 months treatment. A stepwise logistic regression model with normal functioning (Social and Occupational Functioning Assessment Scale ≥80 as the dependent variable was used. Results After 3 months, 59.5% of patients (371/624 achieved normal functioning and 66.0% (412/624 were in remission. Residual symptom prevalence was: core mood symptoms 72%; insomnia 63%; anxiety 78%; and somatic symptoms 41%. Pain reported in 18%. Factors associated with normal functioning were absence of core mood symptoms (odds ratio [OR] 8.7; 95% confidence interval [CI], 4.6–16.7, absence of insomnia symptoms (OR 1.8; 95% CI, 1.2–2.7, episode length (4–24 weeks vs. ≥24 weeks [OR 2.0; 95% CI, 1.1–3.6] and better baseline functioning (OR 1.0; 95% CI, 1.0–1.1. A significant interaction between residual anxiety symptoms and pain was found (p = 0.0080. Conclusions Different residual symptoms are associated to different degrees with patient functioning. To achieve normal functioning, specific residual symptoms domains might be targeted for treatment.

Inverse gene-for-gene interactions contribute additively to tan spot susceptibility in wheat.

Science.gov (United States)

Liu, Zhaohui; Zurn, Jason D; Kariyawasam, Gayan; Faris, Justin D; Shi, Gongjun; Hansen, Jana; Rasmussen, Jack B; Acevedo, Maricelis

2017-06-01

Tan spot susceptibility is conferred by multiple interactions of necrotrophic effector and host sensitivity genes. Tan spot of wheat, caused by Pyrenophora tritici-repentis, is an important disease in almost all wheat-growing areas of the world. The disease system is known to involve at least three fungal-produced necrotrophic effectors (NEs) that interact with the corresponding host sensitivity (S) genes in an inverse gene-for-gene manner to induce disease. However, it is unknown if the effects of these NE-S gene interactions contribute additively to the development of tan spot. In this work, we conducted disease evaluations using different races and quantitative trait loci (QTL) analysis in a wheat recombinant inbred line (RIL) population derived from a cross between two susceptible genotypes, LMPG-6 and PI 626573. The two parental lines each harbored a single known NE sensitivity gene with LMPG-6 having the Ptr ToxC sensitivity gene Tsc1 and PI 626573 having the Ptr ToxA sensitivity gene Tsn1. Transgressive segregation was observed in the population for all races. QTL mapping revealed that both loci (Tsn1 and Tsc1) were significantly associated with susceptibility to race 1 isolates, which produce both Ptr ToxA and Ptr ToxC, and the two genes contributed additively to tan spot susceptibility. For isolates of races 2 and 3, which produce only Ptr ToxA and Ptr ToxC, only Tsn1 and Tsc1 were associated with tan spot susceptibility, respectively. This work clearly demonstrates that tan spot susceptibility in this population is due primarily to two NE-S interactions. Breeders should remove both sensitivity genes from wheat lines to obtain high levels of tan spot resistance.

Two Salt Bridges Differentially Contribute to the Maintenance of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Channel Function*

Science.gov (United States)

Cui, Guiying; Freeman, Cody S.; Knotts, Taylor; Prince, Chengyu Z.; Kuang, Christopher; McCarty, Nael A.

2013-01-01

Previous studies have identified two salt bridges in human CFTR chloride ion channels, Arg352-Asp993 and Arg347-Asp924, that are required for normal channel function. In the present study, we determined how the two salt bridges cooperate to maintain the open pore architecture of CFTR. Our data suggest that Arg347 not only interacts with Asp924 but also interacts with Asp993. The tripartite interaction Arg347-Asp924-Asp993 mainly contributes to maintaining a stable s2 open subconductance state. The Arg352-Asp993 salt bridge, in contrast, is involved in stabilizing both the s2 and full (f) open conductance states, with the main contribution being to the f state. The s1 subconductance state does not require either salt bridge. In confirmation of the role of Arg352 and Asp993, channels bearing cysteines at these sites could be latched into a full open state using the bifunctional cross-linker 1,2-ethanediyl bismethanethiosulfonate, but only when applied in the open state. Channels remained latched open even after washout of ATP. The results suggest that these interacting residues contribute differently to stabilizing the open pore in different phases of the gating cycle. PMID:23709221

Environmental dredging residual generation and management.

Science.gov (United States)

Patmont, Clay; LaRosa, Paul; Narayanan, Raghav; Forrest, Casey

2018-05-01

The presence and magnitude of sediment contamination remaining in a completed dredge area can often dictate the success of an environmental dredging project. The need to better understand and manage this remaining contamination, referred to as "postdredging residuals," has increasingly been recognized by practitioners and investigators. Based on recent dredging projects with robust characterization programs, it is now understood that the residual contamination layer in the postdredging sediment comprises a mixture of contaminated sediments that originate from throughout the dredge cut. This mixture of contaminated sediments initially exhibits fluid mud properties that can contribute to sediment transport and contamination risk outside of the dredge area. This article reviews robust dredging residual evaluations recently performed in the United States and Canada, including the Hudson River, Lower Fox River, Ashtabula River, and Esquimalt Harbour, along with other projects. These data better inform the understanding of residuals generation, leading to improved models of dredging residual formation to inform remedy evaluation, selection, design, and implementation. Data from these projects confirm that the magnitude of dredging residuals is largely determined by site conditions, primarily in situ sediment fluidity or liquidity as measured by dry bulk density. While the generation of dredging residuals cannot be avoided, residuals can be successfully and efficiently managed through careful development and implementation of site-specific management plans. Integr Environ Assess Manag 2018;14:335-343. © 2018 The Authors. Integrated Environmental Assessment and Management Published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC). © 2018 The Authors. Integrated Environmental Assessment and Management Published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Residual Resistance Data from Cavity Production Projects at Jefferson Lab

International Nuclear Information System (INIS)

Ciovati, Gianluigi; Geng, Rongli; Mammosser, John; Saunders, Jeffrey

2010-01-01

A fundamental limitation towards achieving high quality factors in superconducting radio-frequency cavities is the so-called residual resistance. Understanding and controlling the residual resistance has important implications towards improving the efficiency and reduce the operating cost of continuous wave superconducting linear accelerators. In this contribution we will report on the residual resistance values obtained from measurements of the quality factor of a large set of cavities, with resonant frequency between 805 MHz and 1.5 GHz, all of them processed and tested at Jefferson Lab. Surface treatments included both buffered chemical polishing and electropolishing. The results indicate an approximate value of the residual resistance of about 7-10 n Omega.

Comment on contact contributions to the magnetic hyperfine interaction of rare-earth impurities in iron

International Nuclear Information System (INIS)

Bernas, H.

1977-01-01

The influence of the strong d character of the Fe conduction band on the hyperfine interaction of dilute rare earth impurities is emphasized, and the contact contributions are estimated. Apparent inconsistencies between hyperfine field measurements for Eu and Gd in Fe are noted

Highly specific salt bridges govern bacteriophage P22 icosahedral capsid assembly: identification of the site in coat protein responsible for interaction with scaffolding protein.

Science.gov (United States)

Cortines, Juliana R; Motwani, Tina; Vyas, Aashay A; Teschke, Carolyn M

2014-05-01

Icosahedral virus assembly requires a series of concerted and highly specific protein-protein interactions to produce a proper capsid. In bacteriophage P22, only coat protein (gp5) and scaffolding protein (gp8) are needed to assemble a procapsid-like particle, both in vivo and in vitro. In scaffolding protein's coat binding domain, residue R293 is required for procapsid assembly, while residue K296 is important but not essential. Here, we investigate the interaction of scaffolding protein with acidic residues in the N-arm of coat protein, since this interaction has been shown to be electrostatic. Through site-directed mutagenesis of genes 5 and 8, we show that changing coat protein N-arm residue 14 from aspartic acid to alanine causes a lethal phenotype. Coat protein residue D14 is shown by cross-linking to interact with scaffolding protein residue R293 and, thus, is intimately involved in proper procapsid assembly. To a lesser extent, coat protein N-arm residue E18 is also implicated in the interaction with scaffolding protein and is involved in capsid size determination, since a cysteine mutation at this site generated petite capsids. The final acidic residue in the N-arm that was tested, E15, is shown to only weakly interact with scaffolding protein's coat binding domain. This work supports growing evidence that surface charge density may be the driving force of virus capsid protein interactions. Bacteriophage P22 infects Salmonella enterica serovar Typhimurium and is a model for icosahedral viral capsid assembly. In this system, coat protein interacts with an internal scaffolding protein, triggering the assembly of an intermediate called a procapsid. Previously, we determined that there is a single amino acid in scaffolding protein required for P22 procapsid assembly, although others modulate affinity. Here, we identify partners in coat protein. We show experimentally that relatively weak interactions between coat and scaffolding proteins are capable of driving

Effect of mungbean residue and nitrogen levels on barley

International Nuclear Information System (INIS)

Jan, A.; Muhammad, Z.; Daur, I.; Khan, I.A.

2011-01-01

A field experiment was conducted to evaluate response of barley to mungbean residue (0, 10, 20 and 30 Mg ha/sup -1/), nitrogen levels (0, 25, 50 and 75 kg ha/sup -1/) and their interaction. Emergence m/sup -2/ (50), plant height (109 cm), leaf area tiller-1 (106 cm/sup 2/), lodging score (5.55), termites attack (3.4%), grains spike-1 (67), biological yield (12.80 Mg ha/sup -1/) and grain yield (2.32 Mg ha/sup -1/) were significantly (p=0.05) higher for 30 Mg ha/sup -1/ mungbean residue compared to other levels. Similarly plant height (110 cm), lodging score (5.29) and biological yield (13.75 Mg ha/sup -1/) were higher at 75 kg ha/sup -1/ N compared to other levels of N. Productive tillers m/sup -2/, grains spike/sup -1/, 1000 grain weight, grain yield and harvest index were optimum at 50 kg ha-1 N as compared to 75 kg ha/sup -1/ N that encouraged lodging. Interaction between residue and nitrogen indicated that 10 Mg residue and 50 kg N ha/sup -1/ is recommended to achieve maximum net return under comparable conditions. (author)

A charged residue at the subunit interface of PCNA promotes trimer formation by destabilizing alternate subunit interactions

International Nuclear Information System (INIS)

Freudenthal, Bret D.; Gakhar, Lokesh; Ramaswamy, S.; Washington, M. Todd

2009-01-01

Eukaryotic proliferating cell nuclear antigen (PCNA), an essential accessory factor in DNA replication and repair, is a ring-shaped homotrimer. A novel nontrimeric structure of E113G-mutant PCNA protein is reported, which shows that this protein forms alternate subunit interactions. It is concluded that the charged side chain of Glu113 promotes normal trimer formation by destabilizing these alternate subunit interactions. Eukaryotic proliferating cell nuclear antigen (PCNA) is an essential replication accessory factor that interacts with a variety of proteins involved in DNA replication and repair. Each monomer of PCNA has an N-terminal domain A and a C-terminal domain B. In the structure of the wild-type PCNA protein, domain A of one monomer interacts with domain B of a neighboring monomer to form a ring-shaped trimer. Glu113 is a conserved residue at the subunit interface in domain A. Two distinct X-ray crystal structures have been determined of a mutant form of PCNA with a substitution at this position (E113G) that has previously been studied because of its effect on translesion synthesis. The first structure was the expected ring-shaped trimer. The second structure was an unanticipated nontrimeric form of the protein. In this nontrimeric form, domain A of one PCNA monomer interacts with domain A of a neighboring monomer, while domain B of this monomer interacts with domain B of a different neighboring monomer. The B–B interface is stabilized by an antiparallel β-sheet and appears to be structurally similar to the A–B interface observed in the trimeric form of PCNA. The A–A interface, in contrast, is primarily stabilized by hydrophobic interactions. Because the E113G substitution is located on this hydrophobic surface, the A–A interface should be less favorable in the case of the wild-type protein. This suggests that the side chain of Glu113 promotes trimer formation by destabilizing these possible alternate subunit interactions

Activities Contributing a Great Deal to the Students' Interactive Skills in Foreign Language Classes

Science.gov (United States)

Asatryan, Susanna

2016-01-01

While teaching speaking it is desired to provide a rich environment in class for meaningful communication to take place. With this aim, various speaking activities can contribute a great deal to students in developing their interactive skills necessary for life. These activities make students active in the learning process and at the same time…

The interactive effect of fungicide residues and yeast assimilable nitrogen on fermentation kinetics and hydrogen sulfide production during cider fermentation.

Science.gov (United States)

Boudreau, Thomas F; Peck, Gregory M; O'Keefe, Sean F; Stewart, Amanda C

2017-01-01

Fungicide residues on fruit may adversely affect yeast during cider fermentation, leading to sluggish or stuck fermentation or the production of hydrogen sulfide (H 2 S), which is an undesirable aroma compound. This phenomenon has been studied in grape fermentation but not in apple fermentation. Low nitrogen availability, which is characteristic of apples, may further exacerbate the effects of fungicides on yeast during fermentation. The present study explored the effects of three fungicides: elemental sulfur (S 0 ) (known to result in increased H 2 S in wine); fenbuconazole (used in orchards but not vineyards); and fludioxonil (used in post-harvest storage of apples). Only S 0 led to increased H 2 S production. Fenbuconazole (≥0.2 mg L -1 ) resulted in a decreased fermentation rate and increased residual sugar. An interactive effect of yeast assimilable nitrogen (YAN) concentration and fenbuconazole was observed such that increasing the YAN concentration alleviated the negative effects of fenbuconazole on fermentation kinetics. Cidermakers should be aware that residual fenbuconazole (as low as 0.2 mg L -1 ) in apple juice may lead to stuck fermentation, especially when the YAN concentration is below 250 mg L -1 . These results indicate that fermentation problems attributed to low YAN may be caused or exacerbated by additional factors such as fungicide residues, which have a greater impact on fermentation performance under low YAN conditions. © 2016 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. © 2016 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Tyrosine residues modification studied by MALDI-TOF mass spectrometry

International Nuclear Information System (INIS)

Santrucek, Jiri; Strohalm, Martin; Kadlcik, Vojtech; Hynek, Radovan; Kodicek, Milan

2004-01-01

Amino acid residue-specific reactivity in proteins is of great current interest in structural biology as it provides information about solvent accessibility and reactivity of the residue and, consequently, about protein structure and possible interactions. In the work presented tyrosine residues of three model proteins with known spatial structure are modified with two tyrosine-specific reagents: tetranitromethane and iodine. Modified proteins were specifically digested by proteases and the mass of resulting peptide fragments was determined using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Our results show that there are only small differences in the extent of tyrosine residues modification by tetranitromethane and iodine. However, data dealing with accessibility of reactive residues obtained by chemical modifications are not completely identical with those obtained by nuclear magnetic resonance and X-ray crystallography. These interesting discrepancies can be caused by local molecular dynamics and/or by specific chemical structure of the residues surrounding

Allelopathic impact of HoCP 96-540 field residue on seed germination

Science.gov (United States)

Research indicates that sugarcane field residue and sugarcane mill bagasse may be allelopathic. Allelopathy is the chemical interaction between plants, which may result in the inhibition of plant growth and development. Previous research in Louisiana indicated that sugarcane field residue may inhibi...

Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation

DEFF Research Database (Denmark)

Oliveira, Rodrigo Gouveia; Pedersen, Anders Gorm

2007-01-01

ABSTRACT: BACKGROUND: Some amino acid residues functionally interact with each other. This interaction will result in an evolutionary co-variation between these residues - coevolution. Our goal is to find these coevolving residues. RESULTS: We present six new methods for detecting coevolving...... residues. Among other things, we suggest measures that are variants of Mutual Information, and measures that use a multidimensional representation of each residue in order to capture the physico-chemical similarities between amino acids. We created a benchmarking system, in silico, able to evaluate...

Residues essential for Panton-Valentine leukocidin S component binding to its cell receptor suggest both plasticity and adaptability in its interaction surface.

Directory of Open Access Journals (Sweden)

Benoit-Joseph Laventie

Full Text Available Panton-Valentine leukocidin (PVL, a bicomponent staphylococcal leukotoxin, is involved in the poor prognosis of necrotizing pneumonia. The present study aimed to elucidate the binding mechanism of PVL and in particular its cell-binding domain. The class S component of PVL, LukS-PV, is known to ensure cell targeting and exhibits the highest affinity for the neutrophil membrane (Kd∼10(-10 M compared to the class F component of PVL, LukF-PV (Kd∼10(-9 M. Alanine scanning mutagenesis was used to identify the residues involved in LukS-PV binding to the neutrophil surface. Nineteen single alanine mutations were performed in the rim domain previously described as implicated in cell membrane interactions. Positions were chosen in order to replace polar or exposed charged residues and according to conservation between leukotoxin class S components. Characterization studies enabled to identify a cluster of residues essential for LukS-PV binding, localized on two loops of the rim domain. The mutations R73A, Y184A, T244A, H245A and Y250A led to dramatically reduced binding affinities for both human leukocytes and undifferentiated U937 cells expressing the C5a receptor. The three-dimensional structure of five of the mutants was determined using X-ray crystallography. Structure analysis identified residues Y184 and Y250 as crucial in providing structural flexibility in the receptor-binding domain of LukS-PV.

Different finite element techniques to predict welding residual stresses in aluminum alloy plates

International Nuclear Information System (INIS)

Moein, Hadi; Sattari-Far, Iradj

2014-01-01

This study is a 3D thermomechanical finite element (FE) analysis of a single-pass and butt-welded work-hardened aluminum (Al) 5456 plates. It aims to validate the use of FE welding simulations to predict residual stress states in assessing the integrity of welded components. The predicted final residual stresses in the plate from the FE simulations are verified through comparison with experimental measurements. Three techniques are used to simulate the welding process. In the first two approaches, welding deposition is applied by using element birth and interaction techniques. In the third approach, the entire weld zone is simultaneously deposited. Results show a value at approximately the yield strength for longitudinal residual stresses of the welded center of the butt-welded Al alloy plates with a thickness of 2 mm. Considering the application of a comprehensive heat source, along with heat loss modeling and the temperature dependent properties of the material, the approach without deposition predicts a reasonable distribution of residual stresses. However, the element birth and interaction techniques, compared with the no-deposit technique, provide more accurate results in calculating residual stresses. Furthermore, the element interaction technique, compared with the element birth technique, exhibits higher efficiency and flexibility in modeling the deposition of welded metals as well as less modeling cost.

Three C-terminal residues from the sulphonylurea receptor contribute to the functional coupling between the KATP channel subunits SUR2A and Kir6.2

Science.gov (United States)

Dupuis, Julien P; Revilloud, Jean; Moreau, Christophe J; Vivaudou, Michel

2008-01-01

Cardiac ATP-sensitive potassium (KATP) channels are metabolic sensors formed by the association of the inward rectifier potassium channel Kir6.2 and the sulphonylurea receptor SUR2A. SUR2A adjusts channel gating as a function of intracellular ATP and ADP and is the target of pharmaceutical openers and blockers which, respectively, up- and down-regulate Kir6.2. In an effort to understand how effector binding to SUR2A translates into Kir6.2 gating modulation, we examined the role of a 65-residue SUR2A fragment linking transmembrane domain TMD2 and nucleotide-binding domain NBD2 that has been shown to interact with Kir6.2. This fragment of SUR2A was replaced by the equivalent residues of its close homologue, the multidrug resistance protein MRP1. The chimeric construct was expressed in Xenopus oocytes and characterized using the patch-clamp technique. We found that activation by MgADP and synthetic openers was greatly attenuated although apparent affinities were unchanged. Further chimeragenetic and mutagenetic studies showed that mutation of three residues, E1305, I1310 and L1313 (rat numbering), was sufficient to confer this defective phenotype. The same mutations had no effects on channel block by the sulphonylurea glibenclamide or by ATP, suggesting a role for these residues in activatory – but not inhibitory – transduction processes. These results indicate that, within the KATP channel complex, the proximal C-terminal of SUR2A is a critical link between ligand binding to SUR2A and Kir6.2 up-regulation. PMID:18450778

Ionic interaction of myosin loop 2 with residues located beyond the N-terminal part of actin probed by chemical cross-linking.

Science.gov (United States)

Pliszka, Barbara; Martin, Brian M; Karczewska, Emilia

2008-02-01

To probe ionic contacts of skeletal muscle myosin with negatively charged residues located beyond the N-terminal part of actin, myosin subfragment 1 (S1) and actin split by ECP32 protease (ECP-actin) were cross-linked with 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). We have found that unmodified S1 can be cross-linked not only to the N-terminal part, but also to the C-terminal 36 kDa fragment of ECP-actin. Subsequent experiments performed on S1 cleaved by elastase or trypsin indicate that the cross-linking site in S1 is located within loop 2. This site is composed of Lys-636 and Lys-637 and can interact with negatively charged residues of the 36 kDa actin fragment, most probably with Glu-99 and Glu-100. Cross-links are formed both in the absence and presence of MgATP.P(i) analog, although the addition of nucleotide decreases the efficiency of the cross-linking reaction.

Radioactivity of combustion residues from coal-fired power stations

International Nuclear Information System (INIS)

Vom Berg, W.; Puch, K.H.

1996-01-01

Each year in Germany, about 18 mill. t of combustion residues are produced from the combustion of bituminous coal and lignite. They are utilized to a great extent in the construction industry and in mining. During the combustion of coal, the radio-nuclides remain predominantly in the ash. The radionuclide concentration in lignite ash is within the range of that in natural soil. The combustion residues of bituminous coal contain radio-nuclides of a similar order of magnitude as also can occur in natural rock. The utilization of combustion residues in construction materials makes a negligible contribution to radiation exposure through retention in buildings. (orig.) [de

Nitrogen Transfer from Cover Crop Residues to Onion Grown under Minimum Tillage in Southern Brazil

Directory of Open Access Journals (Sweden)

Leoncio de Paula Koucher

2017-08-01

Full Text Available ABSTRACT Nitrogen derived from cover crop residues may contribute to the nutrition of onion grown under minimum tillage (MT and cultivated in rotation. The aim of this study was to evaluate the N transferred from different cover crop residues to the onion crop cultivated under MT in southern Brazil. In June 2014, oilseed radish, black oat, and oilseed radish + black oat residues labeled with 15N were deposited on the soil surface before transplanting onions. During the growth season and at harvest, young expanded onion leaves, complete plants, and samples from different soil layers were collected and analyzed for recovery of 15N-labeled residue. Oilseed radish decomposed faster than other residues and 4 % of residue N was recovered in leaves and bulbs at harvest, but in general, N in plant organs was derived from sources other than the cover crop residues. In addition, leaf N was in the proper range for all treatments and was adequately mobilized to the bases for bulbing. The N derived from decomposing residues contributed little to onion development and the use of these plants should be chosen based on their advantages for physical and biological soil quality.

Long-term stabilization of crop residues and soil organic carbon affected by residue quality and initial soil pH.

Science.gov (United States)

Wang, Xiaojuan; Butterly, Clayton R; Baldock, Jeff A; Tang, Caixian

2017-06-01

Residues differing in quality and carbon (C) chemistry are presumed to contribute differently to soil pH change and long-term soil organic carbon (SOC) pools. This study examined the liming effect of different crop residues (canola, chickpea and wheat) down the soil profile (0-30cm) in two sandy soils differing in initial pH as well as the long-term stability of SOC at the amended layer (0-10cm) using mid-infrared (MIR) and solid-state 13 C nuclear magnetic resonance (NMR) spectroscopy. A field column experiment was conducted for 48months. Chickpea- and canola-residue amendments increased soil pH at 0-10cm in the Podzol by up to 0.47 and 0.36units, and in the Cambisol by 0.31 and 0.18units, respectively, at 48months when compared with the non-residue-amended control. The decomposition of crop residues was greatly retarded in the Podzol with lower initial soil pH during the first 9months. The MIR-predicted particulate organic C (POC) acted as the major C sink for residue-derived C in the Podzol. In contrast, depletion of POC and recovery of residue C in MIR-predicted humic organic C (HOC) were detected in the Cambisol within 3months. Residue types showed little impact on total SOC and its chemical composition in the Cambisol at 48months, in contrast to the Podzol. The final HOC and resistant organic C (ROC) pools in the Podzol amended with canola and chickpea residues were about 25% lower than the control. This apparent priming effect might be related to the greater liming effect of these two residues in the Podzol. Copyright © 2017 Elsevier B.V. All rights reserved.

Combining crystallographic information and an aspherical-atom data bank in the evaluation of the electrostatic interaction energy in an enzyme–substrate complex: influenza neuraminidase inhibition

Energy Technology Data Exchange (ETDEWEB)

Dominiak, Paulina M., E-mail: pdomin@chem.uw.edu.pl [Department of Chemistry, State University of New York at Buffalo, NY 14260 (United States); Department of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszawa (Poland); Volkov, Anatoliy; Dominiak, Adam P. [Department of Chemistry, State University of New York at Buffalo, NY 14260 (United States); Jarzembska, Katarzyna N. [Department of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszawa (Poland); Coppens, Philip, E-mail: pdomin@chem.uw.edu.pl [Department of Chemistry, State University of New York at Buffalo, NY 14260 (United States)

2009-05-01

The electrostatic component of the enzyme/inhibitor interaction of a wide range influenza neuraminidases and inhibitors has been analyzed using transferable aspherical-atom densities from a recently compiled databank. Results are subdivided into the contributions of individual active-site residues and different functional groups of the inhibitors, and the effect of the Arg292→Lys mutation is considered. Although electrostatic interactions contribute only a part of the interaction energies between macromolecules, unlike dispersion forces they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In the reported study, a wide range of complexes of influenza neuraminidases with inhibitor molecules (sialic acid derivatives and others) have been analyzed using charge densities from a transferable aspherical-atom data bank. The strongest interactions of the residues are with the acidic group at the C2 position of the inhibitor (∼−300 kJ mol{sup −1} for —COO{sup −} in non-aromatic inhibitors, ∼−120–210 kJ mol{sup −1} for —COO{sup −} in aromatic inhibitors and ∼−450 kJ mol{sup −1} for —PO{sub 3}{sup 2−}) and with the amino and guanidine groups at C4 (∼−250 kJ mol{sup −1}). Other groups contribute less than ∼100 kJ mol{sup −1}. Residues Glu119, Asp151, Glu227, Glu276 and Arg371 show the largest variation in electrostatic energies of interaction with different groups of inhibitors, which points to their important role in the inhibitor recognition. The Arg292→Lys mutation reduces the electrostatic interactions of the enzyme with the acidic group at C2 for all inhibitors that have been studied (SIA, DAN, 4AM, ZMR, G20, G28, G39 and BCZ), but enhances the interactions with the glycerol group at C6 for inhibitors that contain it. This is in agreement with the lower level

Spring Chinook Salmon Interactions Indices and Residual/Precocial Monitoring in the Upper Yakima Basin; Yakima/Klickitat Fisheries Project Monitoring and Evaluation, 2001-2002 Annual Report.

Energy Technology Data Exchange (ETDEWEB)

Pearsons, Todd N.; James, Brenda B.; Johnson, Christopher L. (Washington Department of Fish and Wildlife, Olympia, WA)

2003-05-01

This report examines some of the factors that can influence the success of supplementation, which is currently being tested in the Yakima Basin using upper Yakima stock of spring chinook salmon. Supplementation success in the Yakima Basin is defined relative to four topic areas: natural production, genetics, ecological interactions, and harvest (Busack et al. 1997). The success of spring chinook salmon supplementation in the Yakima Basin is dependent, in part, upon fish culture practices and favorable physical and biological conditions in the natural environment (Busack et al. 1997). Shortfalls in either of these two topics (i.e., failure in culturing many fish that have high long-term fitness or environmental conditions that constrain spring chinook salmon production) will cause supplementation success to be limited. For example, inadvertent selection or propagation of spring chinook that residualize or precocially mature may hinder supplementation success. Spring chinook salmon that residualize (do not migrate during the normal migration period) may have lower survival rates than migrants and, additionally, may interact with wild fish and cause unacceptable impacts to non-target taxa. Large numbers of precocials (nonanadromous spawners) may increase competition for females and significantly skew ratios of offspring sired by nonanadromous males, which could result in more nonanadromous spring chinook in future generations. Conditions in the natural environment may also limit the success of spring chinook supplementation. For example, intra or interspecific competition may constrain spring chinook salmon production. Spring chinook salmon juveniles may compete with each other for food or space or compete with other species that have similar ecological requirements. Monitoring of spring chinook salmon residuals, precocials, prey abundance, carrying capacity, and competition will help researchers interpret why supplementation is working or not working (Busack et al

Dynamics of an Active-Site Flap Contributes to Catalysis in a JAMM Family Metallo Deubiquitinase.

Science.gov (United States)

Bueno, Amy N; Shrestha, Rashmi K; Ronau, Judith A; Babar, Aditya; Sheedlo, Michael J; Fuchs, Julian E; Paul, Lake N; Das, Chittaranjan

2015-10-06

The endosome-associated deubiquitinase (DUB) AMSH is a member of the JAMM family of zinc-dependent metallo isopeptidases with high selectivity for Lys63-linked polyubiquitin chains, which play a key role in endosomal-lysosomal sorting of activated cell surface receptors. The catalytic domain of the enzyme features a flexible flap near the active site that opens and closes during its catalytic cycle. Structural analysis of its homologues, AMSH-LP (AMSH-like protein) and the fission yeast counterpart, Sst2, suggests that a conserved Phe residue in the flap may be critical for substrate binding and/or catalysis. To gain insight into the contribution of this flap in substrate recognition and catalysis, we generated mutants of Sst2 and characterized them using a combination of enzyme kinetics, X-ray crystallography, molecular dynamics simulations, and isothermal titration calorimetry (ITC). Our analysis shows that the Phe residue in the flap contributes key interactions during the rate-limiting step but not to substrate binding, since mutants of Phe403 exhibit a defect only in kcat but not in KM. Moreover, ITC studies show Phe403 mutants have similar KD for ubiquitin compared to the wild-type enzyme. The X-ray structures of both Phe403Ala and the Phe403Trp, in both the free and ubiquitin bound form, reveal no appreciable structural change that might impair substrate or alter product binding. We observed that the side chain of the Trp residue is oriented identically with respect to the isopeptide moiety of the substrate as the Phe residue in the wild-type enzyme, so the loss of activity seen in this mutant cannot be explained by the absence of a group with the ability to provide van der Waals interactions that facilitate the hyrdolysis of the Lys63-linked diubiquitin. Molecular dynamics simulations indicate that the flap in the Trp mutant is quite flexible, allowing almost free rotation of the indole side chain. Therefore, it is possible that these different dynamic

Computer Simulations Reveal Multiple Functions for Aromatic Residues in Cellulase Enzymes (Fact Sheet)

Energy Technology Data Exchange (ETDEWEB)

2012-07-01

NREL researchers use high-performance computing to demonstrate fundamental roles of aromatic residues in cellulase enzyme tunnels. National Renewable Energy Laboratory (NREL) computer simulations of a key industrial enzyme, the Trichoderma reesei Family 6 cellulase (Cel6A), predict that aromatic residues near the enzyme's active site and at the entrance and exit tunnel perform different functions in substrate binding and catalysis, depending on their location in the enzyme. These results suggest that nature employs aromatic-carbohydrate interactions with a wide variety of binding affinities for diverse functions. Outcomes also suggest that protein engineering strategies in which mutations are made around the binding sites may require tailoring specific to the enzyme family. Cellulase enzymes ubiquitously exhibit tunnels or clefts lined with aromatic residues for processing carbohydrate polymers to monomers, but the molecular-level role of these aromatic residues remains unknown. In silico mutation of the aromatic residues near the catalytic site of Cel6A has little impact on the binding affinity, but simulation suggests that these residues play a major role in the glucopyranose ring distortion necessary for cleaving glycosidic bonds to produce fermentable sugars. Removal of aromatic residues at the entrance and exit of the cellulase tunnel, however, dramatically impacts the binding affinity. This suggests that these residues play a role in acquiring cellulose chains from the cellulose crystal and stabilizing the reaction product, respectively. These results illustrate that the role of aromatic-carbohydrate interactions varies dramatically depending on the position in the enzyme tunnel. As aromatic-carbohydrate interactions are present in all carbohydrate-active enzymes, the results have implications for understanding protein structure-function relationships in carbohydrate metabolism and recognition, carbon turnover in nature, and protein engineering

Quadratic residues and non-residues selected topics

CERN Document Server

Wright, Steve

2016-01-01

This book offers an account of the classical theory of quadratic residues and non-residues with the goal of using that theory as a lens through which to view the development of some of the fundamental methods employed in modern elementary, algebraic, and analytic number theory. The first three chapters present some basic facts and the history of quadratic residues and non-residues and discuss various proofs of the Law of Quadratic Reciprosity in depth, with an emphasis on the six proofs that Gauss published. The remaining seven chapters explore some interesting applications of the Law of Quadratic Reciprocity, prove some results concerning the distribution and arithmetic structure of quadratic residues and non-residues, provide a detailed proof of Dirichlet’s Class-Number Formula, and discuss the question of whether quadratic residues are randomly distributed. The text is a valuable resource for graduate and advanced undergraduate students as well as for mathematicians interested in number theory.

Anionic Sites, Fucose Residues and Class I Human Leukocyte Antigen Fate During Interaction of Toxoplasma gondii with Endothelial Cells

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Stumbo Ana Carolina

2002-01-01

Full Text Available Toxoplasma gondii invades and proliferates in human umbilical vein endothelial cells where it resides in a parasitophorous vacuole. In order to analyze which components of the endothelial cell plasma membrane are internalized and become part of the parasitophorous vacuole membrane, the culture of endothelial cells was labeled with cationized ferritin or UEA I lectin or anti Class I human leukocytte antigen (HLA before or after infection with T. gondii. The results showed no cationized ferritin and UEA I lectin in any parasitophorous vacuole membrane, however, the Class I HLA molecule labeling was observed in some endocytic vacuoles containing parasite until 1 h of interaction with T. gondii. After 24 h parasite-host cell interaction, the labeling was absent on the vacuolar membrane, but presents only in small vesicles near parasitophorous vacuole. These results suggest the anionic site and fucose residues are excluded at the time of parasitophorous vacuole formation while Class I HLA molecules are present only on a minority of Toxoplasma-containig vacuoles.

SRTC Contribution to EMSP 81898 Annual Report 2003

International Nuclear Information System (INIS)

Lam, Poh-Sang

2004-01-01

The following describes the SRTC contributions to EMSP 81898 with emphasis on the specific applications to the SRS high level radioactive waste tanks. In particular, the crack growth criteria, constraint effects, and the weld residual stress effects are covered. The write-up consists of two parts: (1) Crack Growth Simulation, and (2) Stress Corrosion Cracking in Weld Residual Stress

Contribution of long-range interactions to the secondary structure of an unfolded globin.

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Fedyukina, Daria V; Rajagopalan, Senapathy; Sekhar, Ashok; Fulmer, Eric C; Eun, Ye-Jin; Cavagnero, Silvia

2010-09-08

This work explores the effect of long-range tertiary contacts on the distribution of residual secondary structure in the unfolded state of an alpha-helical protein. N-terminal fragments of increasing length, in conjunction with multidimensional nuclear magnetic resonance, were employed. A protein representative of the ubiquitous globin fold was chosen as the model system. We found that, while most of the detectable alpha-helical population in the unfolded ensemble does not depend on the presence of the C-terminal region (corresponding to the native G and H helices), specific N-to-C long-range contacts between the H and A-B-C regions enhance the helical secondary structure content of the N terminus (A-B-C regions). The simple approach introduced here, based on the evaluation of N-terminal polypeptide fragments of increasing length, is of general applicability to identify the influence of long-range interactions in unfolded proteins. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Social inequalities in health: measuring the contribution of housing deprivation and social interactions for Spain.

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Urbanos-Garrido, Rosa M

2012-12-14

Social factors have been proved to be main determinants of individuals' health. Recent studies have also analyzed the contribution of some of those factors, such as education and job status, to socioeconomic inequalities in health. The aim of this paper is to provide new evidence about the factors driving socioeconomic inequalities in health for the Spanish population by including housing deprivation and social interactions as health determinants. Cross-sectional study based on the Spanish sample of European Statistics on Income and Living Conditions (EU-SILC) for 2006. The concentration index measuring income-related inequality in health is decomposed into the contribution of each determinant. Several models are estimated to test the influence of different regressors for three proxies of ill-health. Health inequality favouring the better-off is observed in the distribution of self-assessed health, presence of chronic diseases and presence of limiting conditions. Inequality is mainly explained, besides age, by social factors such as labour status and financial deprivation. Housing deprivation contributes to pro-rich inequality in a percentage ranging from 7.17% to 13.85%, and social interactions from 6.16% to 10.19%. The contribution of some groups of determinants significantly differs depending on the ill-health variable used. Health inequalities can be mostly reduced or shaped by policy, as they are mainly explained by social determinants such as labour status, education and other socioeconomic conditions. The major role played on health inequality by variables taking part in social exclusion points to the need to focus on the most vulnerable groups.

Geometrical contributions to the exchange constants: Free electrons with spin-orbit interaction

Science.gov (United States)

Freimuth, Frank; Blügel, Stefan; Mokrousov, Yuriy

2017-05-01

Using thermal quantum field theory, we derive an expression for the exchange constant that resembles Fukuyama's formula for orbital magnetic susceptibility (OMS). Guided by this formal analogy between the exchange constant and OMS, we identify a contribution to the exchange constant that arises from the geometrical properties of the band structure in mixed phase space. We compute the exchange constants for free electrons and show that the geometrical contribution is generally important. Our formalism allows us to study the exchange constants in the presence of spin-orbit interaction. Thereby, we find sizable differences between the exchange constants of helical and cycloidal spin spirals. Furthermore, we discuss how to calculate the exchange constants based on a gauge-field approach in the case of the Rashba model with an additional exchange splitting, and we show that the exchange constants obtained from this gauge-field approach are in perfect agreement with those obtained from the quantum field theoretical method.

Identification of Key Residues for Enzymatic Carboxylate Reduction

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Holly Stolterfoht

2018-02-01

Full Text Available Carboxylate reductases (CARs, E.C. 1.2.1.30 generate aldehydes from their corresponding carboxylic acid with high selectivity. Little is known about the structure of CARs and their catalytically important amino acid residues. The identification of key residues for carboxylate reduction provides a starting point to gain deeper understanding of enzymatic carboxylate reduction. A multiple sequence alignment of CARs with confirmed activity recently identified in our lab and from the literature revealed a fingerprint of conserved amino acids. We studied the function of conserved residues by multiple sequence alignments and mutational replacements of these residues. In this study, single-site alanine variants of Neurospora crassa CAR were investigated to determine the contribution of conserved residues to the function, expressability or stability of the enzyme. The effect of amino acid replacements was investigated by analyzing enzymatic activity of the variants in vivo and in vitro. Supported by molecular modeling, we interpreted that five of these residues are essential for catalytic activity, or substrate and co-substrate binding. We identified amino acid residues having significant impact on CAR activity. Replacement of His 237, Glu 433, Ser 595, Tyr 844, and Lys 848 by Ala abolish CAR activity, indicating their key role in acid reduction. These results may assist in the functional annotation of CAR coding genes in genomic databases. While some other conserved residues decreased activity or had no significant impact, four residues increased the specific activity of NcCAR variants when replaced by alanine. Finally, we showed that NcCAR wild-type and mutants efficiently reduce aliphatic acids.

Structural contributions to the third-law entropy of uranyl phases

International Nuclear Information System (INIS)

Chen, F.; Ewing, R.C.

1999-01-01

Entropies that are used in geochemical calculations are usually based on calorimetric measurements. However, because of the contributions of neglected residual entropies which cannot be determined by calorimetric measurements, the true third-law entropies for many phases may be quite different from those derived from thermal data. The residual entropies are caused by site-mixing, structural disorder and magnetic spin disorder and may result in a considerable contribution to the third-law entropy of solid phases. Magnetic spin-configurational entropy is not expected to be significant in uranyl phases. However, because most uranyl phases are based on sheet or chain structures and usually contain several molecular water groups, site-mixing, vacancies, as well as disorder in the orientation of hydrogen bonds and the polar H 2 O molecules may occur. Calculations of the ideal site-mixing configurational entropy for some uranyl phases indicate that the residual contributions that arise from substitution and vacancies to the third-law entropies of uranyl phases may be large. A brief examination of the crystal chemistry of water molecules in uranyl phases suggests that considerable residual entropy may be caused by the disorder of hydrogen bonds associated with interstitial H 2 O groups

Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

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Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

2016-02-01

Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation. © 2015 Wiley Periodicals, Inc.

Mapping and quantification of organic agro-industrial residues in East Africa

Energy Technology Data Exchange (ETDEWEB)

Jungersen, G. [Dansk Teknologisk Inst. (Denmark); Kivaisi, A.; Rubindamayugi, M. [Univ. of Dar es Salaam (Tanzania, United Republic of)

1998-05-01

The East-African agro-industries generate very large quantities of organic residues from production and processing of different crops. These residues form a major contribution to the pollution of air, soil and water ways, but, at the same time they constitute a large potential for production of bioenergy through anaerobic digestion as well as potential substrate for other biological fermentation processes. The utilization of these resources for production of valuable products would contribute significantly to: Improvement of the local energy supply, through production of bio-energy; Improvement of the economy of the East African agro-industry; Reduction of the environmental impact from the agro-industrial sector. Except for production of cane sugar, most agro-industrial residues are generated from cash crops, which are produced and processed in the developing countries and where the final products mainly are used for export. In the East-African Region the most important of these crops are: Sisal, coffee, Cashew nuts and Pineapple. In addition significant quantities of organic residues are generated from other food processing activities like breweries, consumption of bananas etc. The total potential methane production of the residues available for use in biomethanization systems in East Africa is 189.61 million m{sup 3} of methane per year. Converted to diesel oil equivalents and including the residues only feasible for combustion systems, the total bioenergy potential of agro-industrial residues in Eastern Africa is 279,176 TOE. If this potential was fully utilized for production of electricity, it would correspond to installed effects of 37,68 and 31 MW in Tanzania, Kenya and Uganda, respectively, equivalent to 10%, 11% and 18% of the currently installed effect is these countries. Residues from sisal and coffee processing constitute the main part of the bioenergy potential, on average approximately 75%, while the remaining 25% of the potential are formed by the

Carbon Nanotubes Facilitate Oxidation of Cysteine Residues of Proteins.

Science.gov (United States)

Hirano, Atsushi; Kameda, Tomoshi; Wada, Momoyo; Tanaka, Takeshi; Kataura, Hiromichi

2017-10-19

The adsorption of proteins onto nanoparticles such as carbon nanotubes (CNTs) governs the early stages of nanoparticle uptake into biological systems. Previous studies regarding these adsorption processes have primarily focused on the physical interactions between proteins and nanoparticles. In this study, using reduced lysozyme and intact human serum albumin in aqueous solutions, we demonstrated that CNTs interact chemically with proteins. The CNTs induce the oxidation of cysteine residues of the proteins, which is accounted for by charge transfer from the sulfhydryl groups of the cysteine residues to the CNTs. The redox reaction simultaneously suppresses the intermolecular association of proteins via disulfide bonds. These results suggest that CNTs can affect the folding and oxidation degree of proteins in biological systems such as blood and cytosol.

Thermogravimetric investigation of the co-combustion between the pyrolysis oil distillation residue and lignite.

Science.gov (United States)

Li, Hao; Xia, Shuqian; Ma, Peisheng

2016-10-01

Co-combustion of lignite with distillation residue derived from rice straw pyrolysis oil was investigated by non-isothermal thermogravimetric analysis (TGA). The addition of distillation residue improved the reactivity and combustion efficiency of lignite, such as increasing the weight loss rate at peak temperature and decreasing the burnout temperature and the total burnout. With increasing distillation residue content in the blended fuels, the synergistic interactions between distillation residue and lignite firstly increased and then decreased during co-combustion stage. Results of XRF, FTIR, (13)C NMR and SEM analysis indicated that chemical structure, mineral components and morphology of samples have great influence on the synergistic interactions. The combustion mechanisms and kinetic parameters were calculated by the Coats Redfern model, suggesting that the lowest apparent activation energy (120.19kJ/mol) for the blended fuels was obtained by blending 60wt.% distillation residue during main co-combustion stage. Copyright © 2016 Elsevier Ltd. All rights reserved.

A PM7 dynamic residue-ligand interactions energy landscape of the BACE1 inhibitory pathway by hydroxyethylamine compounds. Part I: The flap closure process.

Science.gov (United States)

Gueto-Tettay, Carlos; Martinez-Consuegra, Alejandro; Zuchniarz, Joshua; Gueto-Tettay, Luis Roberto; Drosos-Ramírez, Juan Carlos

2017-09-01

BACE1 is an enzyme of scientific interest because it participates in the progression of Alzheimer's disease. Hydroxyethylamines (HEAs) are a family of compounds which exhibit inhibitory activity toward BACE1 at a nanomolar level, favorable pharmacokinetic properties and oral bioavailability. The first step in the inhibition of BACE1 by HEAs consists of their entrance into the protease active site and the resultant conformational change in the protein, from Apo to closed form. These two conformations differ in the position of an antiparallel loop (called the flap) which covers the entrance to the catalytic site. For BACE1, closure of this flap is vital to its catalytic activity and to inhibition of the enzyme due to the new interactions thereby formed with the ligand. In the present study a dynamic energy landscape of residue-ligand interaction energies (ReLIE) measured for 112 amino acids in the BACE1 active site and its immediate vicinity during the closure of the flap induced by 8 HEAs of different inhibitory power is presented. A total of 6.272 million ReLIE calculations, based on the PM7 semiempirical method, provided a deep and quantitative view of the first step in the inhibition of the aspartyl protease. The information suggests that residues Asp93, Asp289, Thr292, Thr293, Asn294 and Arg296 are anchor points for the ligand, accounting for approximately 45% of the total protein-ligand interaction. Additionally, flap closure improved the BACE1-HEA interaction by around 25%. Furthermore, the inhibitory activity of HEAs could be related to the capacity of these ligands to form said anchor point interactions and maintain them over time: the lack of some of these anchor interactions delayed flap closure or impeded it completely, or even caused the flap to reopen. The methodology employed here could be used as a tool to evaluate future structural modifications which lead to improvements in the favorability and stability of BACE1-HEA ReLIEs, aiding in the design of

Residual flow patterns and morphological changes along a macro- and meso-tidal coastline

Science.gov (United States)

Leonardi, Nicoletta; Plater, Andrew James

2017-11-01

The hydrodynamic and residual transport patterns arising from oscillating tidal motion have important consequences for the transport of sediments, and for the evolution of the shoreline, especially under macro- and meso-tidal conditions. For many locations there are significant uncertainties about residual currents and sediment transport characteristics, and their possible influence on the morphological evolution of the coastline and on the character of the bed. Herein we use the coastline of SE England as a test case to investigate possible changes in residual currents, and residual transport patterns from neap to spring tide, the reciprocal interaction between residuals and the character of the bed, and the morphological evolution of the coastline at a century timescale. We found that in the long term the morphology of the system evolves toward a dynamic equilibrium configuration characterized by smaller, and spatially constant residual transport patterns. While the spatial distribution of residual currents maintains a similar trend during both neap and spring tide, during spring tide and for large areas residual currents switch between northerly and southerly directions, and their magnitude is doubled. Residual eddies develop in regions characterized by the presence of sand bars due to the interaction of the tide with the varying topography. Residual transport patterns are also computed for various sediment fractions, and based on the hydrodynamics and sediment availability at the bottom. We found that the distribution of sediments on the bed is significantly correlated with the intensity of residuals. Finally, the majority of long-term morphological changes tend to develop or augment sand banks features, with an increase in elevation and steepening of the bank contours.

Spring Chinook Salmon Interactions Indices and Residual/Precocious Male Monitoring in the Upper Yakima Basin; Yakima/Klickitat Fisheries Project Monitoring and Evaluation, 2004-2005 Annual Report.

Energy Technology Data Exchange (ETDEWEB)

Pearsons, Todd N.; Johnson, Christopher L. (Washington Department of Fish and Wildlife, Olympia, WA); James, Brenda B. (Cascade Aquatics, Ellensburg, WA)

2005-05-01

This report examines some of the factors that can influence the success of supplementation, which is currently being tested in the Yakima Basin using upper Yakima stock of spring chinook salmon. Supplementation success in the Yakima Basin is defined relative to four topic areas: natural production, genetics, ecological interactions, and harvest (Busack et al. 1997). The success of spring chinook salmon supplementation in the Yakima Basin is dependent, in part, upon fish culture practices and favorable physical and biological conditions in the natural environment (Busack et al. 1997; James et al. 1999; Pearsons et al., 2003; Pearsons et al. 2004). Shortfalls in either of these two topics (i.e., failure in culturing many fish that have high long-term fitness or environmental conditions that constrain spring chinook salmon production) will cause supplementation success to be limited. For example, inadvertent selection or propagation of spring chinook that residualize or precocially mature may hinder supplementation success. Spring chinook salmon that residualize (do not migrate during the normal migration period) may have lower survival rates than migrants and, additionally, may interact with wild fish and cause unacceptable impacts to non-target taxa. Large numbers of precocials (nonanadromous spawners) may increase competition for females and significantly skew ratios of offspring sired by nonanadromous males, which could result in more nonanadromous spring chinook in future generations. Conditions in the natural environment may also limit the success of spring chinook supplementation. For example, intra or interspecific competition may constrain spring chinook salmon production. Spring chinook salmon juveniles may compete with each other for food or space or compete with other species that have similar ecological requirements. Monitoring of spring chinook salmon residuals, precocials, prey abundance, carrying capacity, and competition will help researchers

The Energetics of Streptococcal Enolase Octamer Formation: The Quantitative Contributions of the Last Eight Amino Acids at the Carboxy-Terminus.

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Jack A Kornblatt

Full Text Available The enolase produced by Streptococcus pyogenes is a homo-octamer whose overall shape resembles that of a donut. The octamer is best described as a tetramer of dimers. As such, it contains two types of interfaces. The first is common to almost all enolases as most enolases that have been studied are dimers. The second is unique to the octamers and includes residues near the carboxy-terminus. The primary sequence of the enolase contains 435 residues with an added 19 as an N-terminal hexahistine tag. We have systematically truncated the carboxy-terminus, individually removing the first 8 residues. This gave rise to a series of eight structures containing respectively, 435, 434, 433, 432, 431, 430, 429 and 427 residues. The truncations cause the protein to gradually dissociate from octamers to enzymatically inactive monomers with very small amounts of intermediate tetramers and dimers. We have evaluated the contributions of the missing residues to the monomer/octamer equilibrium using a combination of analytical ultracentrifugation and activity assays. For the dissociation reaction, octamer 8 monomer truncation of all eight C-terminal residues resulted in a diminution in the standard Gibbs energy of dissociation of about 59 kJ/mole of octamer relative to the full length protein. Considering that this change is spread over eight subunits, this translates to a change in standard Gibbs interaction energy of less than 8 kJ/mole of monomer distributed over the eight monomers. The resulting proteins, containing 434, 433, 432, 431, 430, 429 and 427 residues per monomer, showed intermediate free energies of dissociation. Finally, three other mutations were introduced into our reference protein to establish how they influenced the equilibrium. The main importance of this work is it shows that for homo-multimeric proteins a small change in the standard Gibbs interaction energy between subunits can have major physiological effects.

Interaction of singlet oxygen with bovine serum albumin and the role of the protein nano-compartmentalization.

Science.gov (United States)

Giménez, Rodrigo E; Vargová, Veronika; Rey, Valentina; Turbay, M Beatriz Espeche; Abatedaga, Inés; Morán Vieyra, Faustino E; Paz Zanini, Verónica I; Mecchia Ortiz, Juan H; Katz, Néstor E; Ostatná, Veronika; Borsarelli, Claudio D

2016-05-01

Singlet molecular oxygen ((1)O2) contributes to protein damage triggering biophysical and biochemical changes that can be related with aging and oxidative stress. Serum albumins, such as bovine serum albumin (BSA), are abundant proteins in blood plasma with different biological functions. This paper presents a kinetic and spectroscopic study of the (1)O2-mediated oxidation of BSA using the tris(2,2'-bipyridine)ruthenium(II) cation [Ru(bpy)3](2+) as sensitizer. BSA quenches efficiently (1)O2 with a total (chemical+physical interaction) rate constant kt(BSA)=7.3(±0.4)×10(8)M(-1)s(-1), where the chemical pathway represented 37% of the interaction. This efficient quenching by BSA indicates the participation of several reactive residues. MALDI-TOF MS analysis of intact BSA confirmed that after oxidation by (1)O2, the mass protein increased the equivalent of 13 oxygen atoms. Time-resolved emission spectra analysis of BSA established that Trp residues were oxidized to N'-formylkynurenine, being the solvent-accessible W134 preferentially oxidized by (1)O2 as compared with the buried W213. MS confirmed oxidation of at least two Tyr residues to form dihydroxyphenylalanine, with a global reactivity towards (1)O2 six-times lower than for Trp residues. Despite the lack of MS evidences, kinetic and chemical analysis also suggested that residues other than Trp and Tyr, e.g. Met, must react with (1)O2. Modeling of the 3D-structure of BSA indicated that the oxidation pattern involves a random distribution of (1)O2 into BSA; allowing also the interaction of (1)O2 with buried residues by its diffusion from the bulk solvent through interconnected internal hydrophilic and hydrophobic grooves. Copyright © 2016 Elsevier Inc. All rights reserved.

Radio reduction of the vitamin K in ethanolic solution: Contribution to radical oxidation study of a glutamic residue

International Nuclear Information System (INIS)

Fackir, L.

1995-01-01

The biological action of vitamin K may involve mono electronic exchanges. Therefore, in this work we achieved a radiolytical study on one land, of mono electronic reduction of vitamin K hydroquinone symbolized by KHsubn pp. We also studied the vitamin K2 model of glutamic residue( B - Glu ) by radiolytic mean. The study of radical mechanisms of vitamin K1 reduction in ethanolic solution showed that vitamin K1 is a good sensor of free radicals alpha - hydroxyethyles ( R sup . ) issued from the radiolysis of vitamin K1 ethanolic solutions, saturated with N sub2 O. The final product is hydroquinone K sub 1 H sub 2. It has been demonstrated that mono electronic reduction can be also initiated by solvated electrons. The mono electronic oxidation of K H sub p has been studied in ethanolic solution.The results showed that K H sub p is a good sensor of peroxyl radicals model (RO sub2) sup . issues from ethanol. The oxidation leads to the formation a dimeric from of the quinone K. All these results showed that the free radicals R sup . centred on carbon are efficient reducing agents of vitamin K1, and that the peroxyl radicals R Osub2 centred on oxygen are possible oxidants of KH sub p. At the end and for modeling the eventual interaction of semi quinonic radical with glutamic acid. We have irradiated mixture of vitamin K1 and a compound having a glutamic residue, the concentration ratio (B-Glu) sub 0/ (K sub 1) sub 0 varying for 0,03 to 1. The obtained results showed that the yield of vitamin K sub 1 disappearance is superior to G (R sup .)/R for low concentration of B-Glu. 80 figs., 5 tabs., 105 refs. (F. M.)

Vacuum fluctuations and radiation reaction contributions to the resonance dipole-dipole interaction between two atoms near a reflecting boundary

Science.gov (United States)

Zhou, Wenting; Rizzuto, Lucia; Passante, Roberto

2018-04-01

We investigate the resonance dipole-dipole interaction energy between two identical atoms, one in the ground state and the other in the excited state, interacting with the electromagnetic field in the presence of a perfectly reflecting plane boundary. The atoms are prepared in a correlated (symmetric or antisymmetric) Bell-type state. Following a procedure due to Dalibard et al. [J. Dalibard et al., J. Phys. (Paris) 43, 1617 (1982);, 10.1051/jphys:0198200430110161700 J. Phys. (Paris) 45, 637 (1984), 10.1051/jphys:01984004504063700], we separate the contributions of vacuum fluctuations and radiation reaction (source) field to the resonance interaction energy between the two atoms and show that only the source field contributes to the interatomic interaction, while vacuum field fluctuations do not. By considering specific geometric configurations of the two-atom system with respect to the mirror and specific choices of dipole orientations, we show that the presence of the mirror significantly affects the resonance interaction energy and that different features appear with respect to the case of atoms in free space, for example, a change in the spatial dependence of the interaction. Our findings also suggest that the presence of a boundary can be exploited to tailor and control the resonance interaction between two atoms, as well as the related energy transfer process. The possibility of observing these phenomena is also discussed.

Engineering Aromatic-Aromatic Interactions To Nucleate Folding in Intrinsically Disordered Regions of Proteins.

Science.gov (United States)

Balakrishnan, Swati; Sarma, Siddhartha P

2017-08-22

Aromatic interactions are an important force in protein folding as they combine the stability of a hydrophobic interaction with the selectivity of a hydrogen bond. Much of our understanding of aromatic interactions comes from "bioinformatics" based analyses of protein structures and from the contribution of these interactions to stabilizing secondary structure motifs in model peptides. In this study, the structural consequences of aromatic interactions on protein folding have been explored in engineered mutants of the molten globule protein apo-cytochrome b 5 . Structural changes from disorder to order due to aromatic interactions in two variants of the protein, viz., WF-cytb5 and FF-cytb5, result in significant long-range secondary and tertiary structure. The results show that 54 and 52% of the residues in WF-cytb5 and FF-cytb5, respectively, occupy ordered regions versus 26% in apo-cytochrome b 5 . The interactions between the aromatic groups are offset-stacked and edge-to-face for the Trp-Phe and Phe-Phe mutants, respectively. Urea denaturation studies indicate that both mutants have a C m higher than that of apo-cytochrome b 5 and are more stable to chaotropic agents than apo-cytochrome b 5 . The introduction of these aromatic residues also results in "trimer" interactions with existing aromatic groups, reaffirming the selectivity of the aromatic interactions. These studies provide insights into the aromatic interactions that drive disorder-to-order transitions in intrinsically disordered regions of proteins and will aid in de novo protein design beyond small peptide scaffolds.

Prediction of Active Site and Distal Residues in E. coli DNA Polymerase III alpha Polymerase Activity.

Science.gov (United States)

Parasuram, Ramya; Coulther, Timothy A; Hollander, Judith M; Keston-Smith, Elise; Ondrechen, Mary Jo; Beuning, Penny J

2018-02-20

The process of DNA replication is carried out with high efficiency and accuracy by DNA polymerases. The replicative polymerase in E. coli is DNA Pol III, which is a complex of 10 different subunits that coordinates simultaneous replication on the leading and lagging strands. The 1160-residue Pol III alpha subunit is responsible for the polymerase activity and copies DNA accurately, making one error per 10 5 nucleotide incorporations. The goal of this research is to determine the residues that contribute to the activity of the polymerase subunit. Homology modeling and the computational methods of THEMATICS and POOL were used to predict functionally important amino acid residues through their computed chemical properties. Site-directed mutagenesis and biochemical assays were used to validate these predictions. Primer extension, steady-state single-nucleotide incorporation kinetics, and thermal denaturation assays were performed to understand the contribution of these residues to the function of the polymerase. This work shows that the top 15 residues predicted by POOL, a set that includes the three previously known catalytic aspartate residues, seven remote residues, plus five previously unexplored first-layer residues, are important for function. Six previously unidentified residues, R362, D405, K553, Y686, E688, and H760, are each essential to Pol III activity; three additional residues, Y340, R390, and K758, play important roles in activity.

Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution.

Directory of Open Access Journals (Sweden)

Daniel Y Little

Full Text Available The structure and function of a protein is dependent on coordinated interactions between its residues. The selective pressures associated with a mutation at one site should therefore depend on the amino acid identity of interacting sites. Mutual information has previously been applied to multiple sequence alignments as a means of detecting coevolutionary interactions. Here, we introduce a refinement of the mutual information method that: 1 removes a significant, non-coevolutionary bias and 2 accounts for heteroscedasticity. Using a large, non-overlapping database of protein alignments, we demonstrate that predicted coevolving residue-pairs tend to lie in close physical proximity. We introduce coevolution potentials as a novel measure of the propensity for the 20 amino acids to pair amongst predicted coevolutionary interactions. Ionic, hydrogen, and disulfide bond-forming pairs exhibited the highest potentials. Finally, we demonstrate that pairs of catalytic residues have a significantly increased likelihood to be identified as coevolving. These correlations to distinct protein features verify the accuracy of our algorithm and are consistent with a model of coevolution in which selective pressures towards preserving residue interactions act to shape the mutational landscape of a protein by restricting the set of admissible neutral mutations.

Tyrosine Residues Regulate Multiple Nuclear Functions of P54nrb.

Science.gov (United States)

Lee, Ahn R; Hung, Wayne; Xie, Ning; Liu, Liangliang; He, Leye; Dong, Xuesen

2017-04-01

The non-POU-domain-containing octamer binding protein (NONO; also known as p54nrb) has various nuclear functions ranging from transcription, RNA splicing, DNA synthesis and repair. Although tyrosine phosphorylation has been proposed to account for the multi-functional properties of p54nrb, direct evidence on p54nrb as a phosphotyrosine protein remains unclear. To investigate the tyrosine phosphorylation status of p54nrb, we performed site-directed mutagenesis on the five tyrosine residues of p54nrb, replacing the tyrosine residues with phenylalanine or alanine, and immunoblotted for tyrosine phosphorylation. We then preceded with luciferase reporter assays, RNA splicing minigene assays, co-immunoprecipitation, and confocal microscopy to study the function of p54nrb tyrosine residues on transcription, RNA splicing, protein-protein interaction, and cellular localization. We found that p54nrb was not phosphorylated at tyrosine residues. Rather, it has non-specific binding affinity to anti-phosphotyrosine antibodies. However, replacement of tyrosine with phenylalanine altered p54nrb activities in transcription co-repression and RNA splicing in gene context-dependent fashions by means of differential regulation of p54nrb protein association with its interacting partners and co-regulators of transcription and splicing. These results demonstrate that tyrosine residues, regardless of phosphorylation status, are important for p54nrb function. J. Cell. Physiol. 232: 852-861, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The Yin and Yang of SagS: Distinct Residues in the HmsP Domain of SagS Independently Regulate Biofilm Formation and Biofilm Drug Tolerance

Science.gov (United States)

Dingemans, Jozef; Poudyal, Bandita

2018-01-01

ABSTRACT The formation of inherently drug-tolerant biofilms by the opportunistic pathogen Pseudomonas aeruginosa requires the sensor-regulator hybrid SagS, with ΔsagS biofilms being unstructured and exhibiting increased antimicrobial susceptibility. Recent findings indicated SagS to function as a switch to control biofilm formation and drug tolerance independently. Moreover, findings suggested the periplasmic sensory HmsP domain of SagS is likely to be the control point in the regulation of biofilm formation and biofilm cells transitioning to a drug-tolerant state. We thus asked whether specific amino acid residues present in the HmsP domain contribute to the switch function of SagS. HmsP domain residues were therefore subjected to alanine replacement mutagenesis to identify substitutions that block the sensory function(s) of SagS, which is apparent by attached cells being unable to develop mature biofilms and/or prevent transition to an antimicrobial-resistant state. Mutant analyses revealed 32 residues that only contribute to blocking one sensory function. Moreover, amino acid residues affecting attachment and subsequent biofilm formation but not biofilm tolerance also impaired histidine kinase signaling via BfiS. In contrast, residues affecting biofilm drug tolerance but not attachment and subsequent biofilm formation negatively impacted BrlR transcription factor levels. Structure prediction suggested the two sets of residues affecting sensory functions are located in distinct areas that were previously described as being involved in ligand binding interactions. Taken together, these studies identify the molecular basis for the dual regulatory function of SagS. IMPORTANCE The membrane-bound sensory protein SagS plays a pivotal role in P. aeruginosa biofilm formation and biofilm cells gaining their heightened resistance to antimicrobial agents, with SagS being the control point at which both pathways diverge. Here, we demonstrate for the first time that the two

Weak-interaction rates in stellar conditions

Science.gov (United States)

Sarriguren, Pedro

2018-05-01

Weak-interaction rates, including β-decay and electron captures, are studied in several mass regions at various densities and temperatures of astrophysical interest. In particular, we study odd-A nuclei in the pf-shell region, which are involved in presupernova formations. Weak rates are relevant to understand the late stages of the stellar evolution, as well as the nucleosynthesis of heavy nuclei. The nuclear structure involved in the weak processes is studied within a quasiparticle proton-neutron random-phase approximation with residual interactions in both particle-hole and particle-particle channels on top of a deformed Skyrme Hartree-Fock mean field with pairing correlations. First, the energy distributions of the Gamow-Teller strength are discussed and compared with the available experimental information, measured under terrestrial conditions from charge-exchange reactions. Then, the sensitivity of the weak-interaction rates to both astrophysical densities and temperatures is studied. Special attention is paid to the relative contribution to these rates of thermally populated excited states in the decaying nucleus and to the electron captures from the degenerate electron plasma.

Protein structure based prediction of catalytic residues.

Science.gov (United States)

Fajardo, J Eduardo; Fiser, Andras

2013-02-22

Worldwide structural genomics projects continue to release new protein structures at an unprecedented pace, so far nearly 6000, but only about 60% of these proteins have any sort of functional annotation. We explored a range of features that can be used for the prediction of functional residues given a known three-dimensional structure. These features include various centrality measures of nodes in graphs of interacting residues: closeness, betweenness and page-rank centrality. We also analyzed the distance of functional amino acids to the general center of mass (GCM) of the structure, relative solvent accessibility (RSA), and the use of relative entropy as a measure of sequence conservation. From the selected features, neural networks were trained to identify catalytic residues. We found that using distance to the GCM together with amino acid type provide a good discriminant function, when combined independently with sequence conservation. Using an independent test set of 29 annotated protein structures, the method returned 411 of the initial 9262 residues as the most likely to be involved in function. The output 411 residues contain 70 of the annotated 111 catalytic residues. This represents an approximately 14-fold enrichment of catalytic residues on the entire input set (corresponding to a sensitivity of 63% and a precision of 17%), a performance competitive with that of other state-of-the-art methods. We found that several of the graph based measures utilize the same underlying feature of protein structures, which can be simply and more effectively captured with the distance to GCM definition. This also has the added the advantage of simplicity and easy implementation. Meanwhile sequence conservation remains by far the most influential feature in identifying functional residues. We also found that due the rapid changes in size and composition of sequence databases, conservation calculations must be recalibrated for specific reference databases.

Robust cross-links in molluscan adhesive gels: testing for contributions from hydrophobic and electrostatic interactions.

Science.gov (United States)

Smith, A M; Robinson, T M; Salt, M D; Hamilton, K S; Silvia, B E; Blasiak, R

2009-02-01

The cross-linking interactions that provide cohesive strength to molluscan adhesive gels were investigated. Metal-based interactions have been shown to play an important role in the glue of the slug Arion subfuscus (Draparnaud), but other types of interactions may also contribute to the glue's strength and their role has not been investigated. This study shows that treatments that normally disrupt hydrophobic or electrostatic interactions have little to no effect on the slug glue. High salt concentrations and non-ionic detergent do not affect the solubility of the proteins in the glue or the ability of the glue proteins to stiffen gels. In contrast, metal chelation markedly disrupts the gel. Experiments with gel filtration chromatography identify a 40 kDa protein that is a central component of the cross-links in the glue. This 40 kDa protein forms robust macromolecular aggregations that are stable even in the presence of high concentrations of salt, non-ionic detergent, urea or metal chelators. Metal chelation during glue secretion, however, may block some of these cross-links. Such robust, non-specific interactions in an aqueous environment are highly unusual for hydrogels and reflect an intriguing cross-linking mechanism.

Contribution of the Tyr-1 in Plantaricin149a to Disrupt Phospholipid Model Membranes

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Georgina Tonarelli

2013-06-01

Full Text Available Plantaricin149a (Pln149a is a cationic antimicrobial peptide, which was suggested to cause membrane destabilization via the carpet mechanism. The mode of action proposed to this antimicrobial peptide describes the induction of an amphipathic α-helix from Ala7 to Lys20, while the N-terminus residues remain in a coil conformation after binding. To better investigate this assumption, the purpose of this study was to determine the contributions of the Tyr1 in Pln149a in the binding to model membranes to promote its destabilization. The Tyr to Ser substitution increased the dissociation constant (KD of the antimicrobial peptide from the liposomes (approximately three-fold higher, and decreased the enthalpy of binding to anionic vesicles from −17.2 kcal/mol to −10.2 kcal/mol. The peptide adsorption/incorporation into the negatively charged lipid vesicles was less effective with the Tyr1 substitution and peptide Pln149a perturbed the liposome integrity more than the analog, Pln149S. Taken together, the peptide-lipid interactions that govern the Pln149a antimicrobial activity are found not only in the amphipathic helix, but also in the N-terminus residues, which take part in enthalpic contributions due to the allocation at a lipid-aqueous interface.

Molecular Dynamics Simulation of Barnase: Contribution of Noncovalent Intramolecular Interaction to Thermostability

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Zhiguo Chen

2013-01-01

Full Text Available Bacillus amyloliquefaciens ribonuclease Barnase (RNase Ba is a 12 kD (kilodalton small extracellular ribonuclease. It has broad application prospects in agriculture, clinical medicine, pharmaceutical, and so forth. In this work, the thermal stability of Barnase has been studied using molecular dynamics simulation at different temperatures. The present study focuses on the contribution of noncovalent intramolecular interaction to protein stability and how they affect the thermal stability of the enzyme. Profiles of root mean square deviation and root mean square fluctuation identify thermostable and thermosensitive regions of Barnase. Analyses of trajectories in terms of secondary structure content, intramolecular hydrogen bonds and salt bridge interactions indicate distinct differences in different temperature simulations. In the simulations, Four three-member salt bridge networks (Asp8-Arg110-Asp12, Arg83-Asp75-Arg87, Lys66-Asp93-Arg69, and Asp54-Lys27-Glu73 have been identified as critical salt bridges for thermostability which are maintained stably at higher temperature enhancing stability of three hydrophobic cores. The study may help enlighten our knowledge of protein structural properties, noncovalent interactions which can stabilize secondary peptide structures or promote folding, and also help understand their actions better. Such an understanding is required for designing efficient enzymes with characteristics for particular applications at desired working temperatures.

Three-particle one-hole multiple scattering contribution to the nuclear effective interaction in mass-18 nuclei

International Nuclear Information System (INIS)

Bando, H.; Krenciglowa, E.M.; Ando, K.

1979-01-01

Within the systematic framework of the double partition approach, the three-particle one-hole multiple scattering and Q-box formalisms are combined to give the valence-linked and connected energy-independent effective interaction. All low-lying [2p+3p1h] contributions to the mass-18 effective interaction are evaluated using an essentially exact energy-dependent reaction matrix based on the Reid SC potential. The low-lying one-body field of the core nucleus is treated consistently with the underlying reaction matrix G through particle- and hole-line self-energy insertions. Center-of-mass motion, folded diagrams and starting energy dependence are properly taken into account throughout. The low-lying [2p+3p1h] correlations are strongly damped by self-energy insertions. By incorporating only the folded diagram contributions with origins in the low-lying space, the net effect of all low-lying [2p+3p1h] correlations is to give back the bare-G plus second-order core-polarization spectra which are found to be in respectable agreement with the experimental spectra. However, including the full folded diagram contribution, which has additional contributions from the high-lying space through the energy dependence of G, leads to final spectra which deviate sizably from experiment. The present results are conclusive in the sense that the treatment is essentially exact for low-lying [2p+3p1h] correlations which originate from the high-lying two-particle correlations through the reaction matrix G. (Auth.)

Residual stresses in weld-clad reactor pressure vessel steel

International Nuclear Information System (INIS)

Bertram, W.

1975-01-01

Cladding of low alloy nuclear reactor pressure vessel steel with austenitic stainless steel introduces in heavy section components high residual stresses which may cause microcrack formation in stress relief heat treatment. In this investigation an attempt is made to contribute to the solution of the stress relief cracking problem by determining quantitatively the magnitude and distribution of the residual stresses after cladding and after subsequent stress relief heat treatment. The distribution of residual stresses was determined on the basis of a combined experimental-mathematical procedure. Heavy section plate specimens of low alloy steel as base material were given an austenitic monolayer-cladding using the techniques of strip electrode and plasma hot wire cladding, respectively. A number of plates was stress relief heat treated. Starting from the cladded surface the thickness of the plates was reduced by subsequent removal of layers of material. The elastic strain reaction to the removal of each layer was measured by strain gauges. From the data obtained the biaxial residual stress distribution was computed as a function of thickness using relations which are derived for this particular case. In summary, lower residual stresses are caused by reduced thickness of the components. As the heat input, is decreased at identical base material thickness, the residual stresses are lowered also. The height of the tensile residual stress peak, however, remains approximataly constant. In stress relief annealed condition the residual stresses in the cladding are in tension; in the base material the residual stresses are negligibly small

Interaction of Myosin Phosphatase Target Subunit (MYPT1) with Myosin Phosphatase-RhoA Interacting Protein (MRIP): A Role of Glutamic Acids in the Interaction.

Science.gov (United States)

Lee, Eunhee; Stafford, Walter F

2015-01-01

Scaffold proteins bind to and functionally link protein members of signaling pathways. Interaction of the scaffold proteins, myosin phosphatase target subunit (MYPT1) and myosin phosphatase-RhoA interacting protein (MRIP), causes co-localization of myosin phosphatase and RhoA to actomyosin. To examine biophysical properties of interaction of MYPT1 with MRIP, we employed analytical ultracentrifugation and surface plasmon resonance. In regard to MRIP, its residues 724-837 are sufficient for the MYPT1/MRIP interaction. Moreover, MRIP binds to MYPT1 as either a monomer or a dimer. With respect to MYPT1, its leucine repeat region, LR (residues 991-1030) is sufficient to account for the MYPT1/MRIP interaction. Furthermore, point mutations that replace glutamic acids 998-1000 within LR reduced the binding affinity toward MRIP. This suggests that the glutamic acids of MYPT1 play an important role in the interaction.

BLAST-based structural annotation of protein residues using Protein Data Bank.

Science.gov (United States)

Singh, Harinder; Raghava, Gajendra P S

2016-01-25

In the era of next-generation sequencing where thousands of genomes have been already sequenced; size of protein databases is growing with exponential rate. Structural annotation of these proteins is one of the biggest challenges for the computational biologist. Although, it is easy to perform BLAST search against Protein Data Bank (PDB) but it is difficult for a biologist to annotate protein residues from BLAST search. A web-server StarPDB has been developed for structural annotation of a protein based on its similarity with known protein structures. It uses standard BLAST software for performing similarity search of a query protein against protein structures in PDB. This server integrates wide range modules for assigning different types of annotation that includes, Secondary-structure, Accessible surface area, Tight-turns, DNA-RNA and Ligand modules. Secondary structure module allows users to predict regular secondary structure states to each residue in a protein. Accessible surface area predict the exposed or buried residues in a protein. Tight-turns module is designed to predict tight turns like beta-turns in a protein. DNA-RNA module developed for predicting DNA and RNA interacting residues in a protein. Similarly, Ligand module of server allows one to predicted ligands, metal and nucleotides ligand interacting residues in a protein. In summary, this manuscript presents a web server for comprehensive annotation of a protein based on similarity search. It integrates number of visualization tools that facilitate users to understand structure and function of protein residues. This web server is available freely for scientific community from URL http://crdd.osdd.net/raghava/starpdb .

The Ising model for prediction of disordered residues from protein sequence alone

International Nuclear Information System (INIS)

Lobanov, Michail Yu; Galzitskaya, Oxana V

2011-01-01

Intrinsically disordered regions serve as molecular recognition elements, which play an important role in the control of many cellular processes and signaling pathways. It is useful to be able to predict positions of disordered residues and disordered regions in protein chains using protein sequence alone. A new method (IsUnstruct) based on the Ising model for prediction of disordered residues from protein sequence alone has been developed. According to this model, each residue can be in one of two states: ordered or disordered. The model is an approximation of the Ising model in which the interaction term between neighbors has been replaced by a penalty for changing between states (the energy of border). The IsUnstruct has been compared with other available methods and found to perform well. The method correctly finds 77% of disordered residues as well as 87% of ordered residues in the CASP8 database, and 72% of disordered residues as well as 85% of ordered residues in the DisProt database

Low-energy structure studies of odd-odd deformed nuclei and the coriolis and residual interactions

Energy Technology Data Exchange (ETDEWEB)

Dewberry, R.A.

1980-08-01

The nuclear level structure of /sup 176/Lu, /sup 170/Tm, /sup 166/Ho, and /sup 160/Tb have been studied by means of the /sup 177/Hf(t,..cap alpha..)/sup 176/Lu, /sup 171/Yb(t,..cap alpha..)/sup 170/Tm, /sup 167/Er(t,..cap alpha..)/sup 166/Ho, and /sup 161/Dy(t,..cap alpha..)/sup 160/Tb reactions and with the use of previously published (d,p) spectroscopy and gamma transitions from the (n,..gamma..) reactions. The (t,..cap alpha..) reactions have been performed and analyzed with 17 MeV tritons and the Los Alamos Q3D spectrometer. Eighty-one new rotational states in excited proton configurations or vibrational excited states are proposed. An independent parameterization of the Coriolis interaction is presented, which leads to satisfactory results in reproducing experimental single-particle transfer reaction cross-sections by theoretical calculations. The anomalous population of the excited neutron configurations (404 reduces to -624 up arrow) in /sup 176/Lu and (411 reduces to +- 512 up arrow) in /sup 170/Tm, and the anomalously low (t,..cap alpha..) cross-sections of the (411 up arrow +- 633 up arrow) configuration in /sup 166/Ho are observed. Qualitative explanation of the anomalies is presented in terms of the mixing of states which satisfy the requirement delta/sub I'/,/sub I/delta/sub K'/,/sub K/. Off-diagonal H/sub INT/ matrix elements are calculated, which show that the residual interaction cannot be used to account for the magnitude of the cross-sections observed.

Water absorption in PEEK and PEI matrices. Contribution to the understanding of water-polar group interactions

Science.gov (United States)

Courvoisier, E.; Bicaba, Y.; Colin, X.

2016-05-01

The water absorption in two aromatic linear polymers (PEEK and PEI) was studied between 10% and 90% RH at 30, 50 and 70°C. It was found that these polymers display classical Henry and Fick's behaviors. Moreover, they have very close values of equilibrium water concentration C∞ and water diffusivity D presumably because their respective polar groups establish molecular interactions of the same nature with water. This assumption was checked from a literature compilation of values of C∞ and D for a large variety of linear and tridimensional polymers containing a single type of polar group. It was then evidenced that almost all types of carbonyl group (in particular, those belonging to imides, amides and ketones) have the same molar contribution to water absorption, except those belonging to esters which are much less hydrophilic. Furthermore, hydroxyl and sulfone groups are much more hydrophilic than carbonyl groups so that their molar contribution is located on another master curve. On this basis, semi-empirical structure/water transport property relationships were proposed. It was found that C∞ increases exponentially with the concentration of polar groups (presumably because water is doubly bonded), but also with the intensity of their molecular interactions with water. In contrast, D is inversely proportional to C∞, which means that polar group-water interactions slow down the rate of water diffusion.

Liquefaction behaviors of bamboo residues in a glycerol-based solvent using microwave energy

Science.gov (United States)

Jiulong Xie; Chung-Yun Hse; Todd F. Shupe; Jinqiu Qi; Hui Pan

2014-01-01

Liquefaction of bamboo was performed in glycerol–methanol as co-solvent using microwave energy and was evaluated by characterizing the liquefied residues. High efficiency conversion of bamboo was achieved under mild reaction conditions. Liquefaction temperature and time interacted to affect the liquefaction reaction. Fourier transform infrared analyzes of the residues...

Beam, vacuum and walls, a 3-body interaction

International Nuclear Information System (INIS)

Arianer, J.

2002-11-01

The interactions between beams of accelerated particles, residual gas and walls involve complex physical processes. In most cases these interactions affect the quality of the vacuum and the value of the pressure. This course reviews all these interactions in a pedagogical and practical way that may be useful for any user of devices involving beams of particles. This document is made up of 6 chapters: 1) basic notions (Maxwell-Boltzmann distribution, kinematics of charged particles, collisions, excitation and ionization), 2) properties of beams (emittance, local effects, and synchrotron radiation), 3) interactions between residual gas and particle beams (Bremsstrahlung radiation, energy loss due to ionization, charge shift of ion beams, photo-absorption and photo-ionization, and slowing-down in a plasma), 4) surface properties (crystal structure, and interaction between surface and the residual gas), 5) interaction between the beam and walls (reflection and diffraction of electrons, secondary emission of electrons, desorption induced by electron and ion impacts, photon production, ion-wall interaction, sputtering, ion penetration, surface ionization and thermal-ionization), and 6) radiation-wall interaction (diffusion, damping, photo-electric effect, desorption induced by photons, pair production and laser-surface interaction). (A.C.)

Decomposition of sugar cane crop residues under different nitrogen rates

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Douglas Costa Potrich

2014-09-01

Full Text Available The deposition of organic residues through mechanical harvesting of cane sugar is a growing practice in sugarcane production system. The maintenance of these residues on the soil surface depends mainly on environmental conditions. Nitrogen fertilization on dry residues tend to retard decomposition of these, providing benefits such as increased SOM. Thus, the object of this research was to evaluate the effect of different doses of nitrogen on sugar cane crop residues, as its decomposition and contribution to carbon sequestration in soil. The experiment was conducted in Dourados-MS and consisted of a randomized complete block design. Dried residues were placed in litter bags and the treatments were arranged in a split plot, being the four nitrogen rates (0, 50, 100 and 150 kg ha-1 N the plots, and the seven sampling times (0, 30, 60, 90, 120, 150 and 180 the spit plots. Decomposition rates of residues, total organic carbon and labile carbon on soil were analysed. The application of increasing N doses resulted in an increase in their decomposition rates. Despite this, note also the mineral N application as a strategy to get higher levels of labile carbon in soil.

Quantification of Drive-Response Relationships Between Residues During Protein Folding.

Science.gov (United States)

Qi, Yifei; Im, Wonpil

2013-08-13

Mutual correlation and cooperativity are commonly used to describe residue-residue interactions in protein folding/function. However, these metrics do not provide any information on the causality relationships between residues. Such drive-response relationships are poorly studied in protein folding/function and difficult to measure experimentally due to technical limitations. In this study, using the information theory transfer entropy (TE) that provides a direct measurement of causality between two times series, we have quantified the drive-response relationships between residues in the folding/unfolding processes of four small proteins generated by molecular dynamics simulations. Instead of using a time-averaged single TE value, the time-dependent TE is measured with the Q-scores based on residue-residue contacts and with the statistical significance analysis along the folding/unfolding processes. The TE analysis is able to identify the driving and responding residues that are different from the highly correlated residues revealed by the mutual information analysis. In general, the driving residues have more regular secondary structures, are more buried, and show greater effects on the protein stability as well as folding and unfolding rates. In addition, the dominant driving and responding residues from the TE analysis on the whole trajectory agree with those on a single folding event, demonstrating that the drive-response relationships are preserved in the non-equilibrium process. Our study provides detailed insights into the protein folding process and has potential applications in protein engineering and interpretation of time-dependent residue-based experimental observables for protein function.

The effect of delignification process with alkaline peroxide on lactic acid production from furfural residues

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Yong Tang

2012-11-01

Full Text Available Furfural residues produced from the furfural industry were investigated as a substrate for lactic acid production by simultaneous saccharification and fermentation (SSF. Alkaline peroxide was used for delignification of furfural residues to improve the final lactic acid concentration. The residue was treated with 1.3% to 1.7% hydrogen peroxide at 80 °C for 1 h with a substrate concentration of 3.33%. SSF of furfural residues with different delignification degrees were carried out to evaluate the effect of delignification degree on lactic acid production. Using corn hydrolysates/ furfural residues as substrates, SSF with different media were carried out to investigate the effect of lignin on the interaction between enzymes and lactic acid bacteria. Lactic acid bacteria had a negative effect on cellulase, thus resulting in the reduction of enzyme activity. Lignin and nutrients slowed down the decreasing trend of enzyme activity. A higher delignification resulted in a slower fermentation rate and lower yield due to degradation products of lignin and the effect of lignin on the interaction between enzymes and lactic acid bacteria. For the purpose of lactic acid production, a moderate delignification (furfural residues with the lignin content of 14.8% was optimum.

Identification of key amino acid residues in the hTGR5-nomilin interaction and construction of its binding model.

Science.gov (United States)

Sasaki, Takashi; Mita, Moeko; Ikari, Naho; Kuboyama, Ayane; Hashimoto, Shuzo; Kaneko, Tatsuya; Ishiguro, Masaji; Shimizu, Makoto; Inoue, Jun; Sato, Ryuichiro

2017-01-01

TGR5, a member of the G protein-coupled receptor (GPCR) family, is activated by bile acids. Because TGR5 promotes energy expenditure and improves glucose homeostasis, it is recognized as a key target in treating metabolic diseases. We previously showed that nomilin, a citrus limonoid, activates TGR5 and confers anti-obesity and anti-hyperglycemic effects in mice. Information on the TGR5-nomilin interaction regarding molecular structure, however, has not been reported. In the present study, we found that human TGR5 (hTGR5) shows higher nomilin responsiveness than does mouse TGR5 (mTGR5). Using mouse-human chimeric TGR5, we also found that three amino acid residues (Q77ECL1, R80ECL1, and Y893.29) are important in the hTGR5-nomilin interaction. Based on these results, an hTGR5-nomilin binding model was constructed using in silico docking simulation, demonstrating that four hydrophilic hydrogen-bonding interactions occur between nomilin and hTGR5. The binding mode of hTGR5-nomilin is vastly different from those of other TGR5 agonists previously reported, suggesting that TGR5 forms various binding patterns depending on the type of agonist. Our study promotes a better understanding of the structure of TGR5, and it may be useful in developing and screening new TGR5 agonists.

Drug and chemical residues in domestic animals.

Science.gov (United States)

Mussman, H C

1975-02-01

Given the large number of chemical substances that may find their way into the food supply, a system is needed to monitor their presence. The U. S. Department of Agriculture's Meat and Poultry Inspection Program routinely tests for chemical residues in animals coming to slaughter. Pesticides, heavy metals, growth promotants (hormones and hormonelike agents), and antibiotics are included. Samples are taken statistically so that inferences as to national incidence of residues can be drawn. When a problem is identified, a more selective sampling is designed to help follow up on the initial regulatory action. In testing for pesticides, only DDT and dieldrin are found with any frequency and their levels are decreasing; violative residues of any chlorinated hydrocarbon are generally a result of an industrial accident rather than agricultural usage. Analyses for heavy metals have revealed detectable levels of mercury, lead, and others, but none at levels that are considered a health hazard. Of the hormone or hormonelike substances, only diethylstilbestrol has been a residue problem and its future is uncertain. The most extensive monitoring for veterinary drugs is on the antimicrobials, including sulfonamides, streptomycin, and the tetracycline group of antibiotics that constitute the bulk of the violations; their simultaneous use prophylactically and therapeutically has contributed to the problem in certain cases. A strong, well-designed user education program on proper application of pesticides, chemicals, and veterinary drugs appears to be one method of reducing the incidence of unwanted residues.

Determination of properties of clean coal technology post-process residue

Directory of Open Access Journals (Sweden)

Agnieszka Klupa

2016-01-01

Full Text Available This article presents the possibilities of using modern measuring devices to determine the properties of process residues (Polish acronym: UPP. UPP was taken from the combustion process from a power plant in Silesia. Determining the properties of UPP is the basis for making decisions about its practical application, for example, as a raw material to obtain useful products such as: pozzolan, cenosphere or zeolite, for which there is demand. The development of advanced technology and science has given rise to modern and precise research tools that contribute to the development of appropriate methods to assess the properties of post-process residue. For this study the following were used: scanning electron microscope with EDS microanalysis and an analyzer for particle size-, shape- and number- analysis. The study conducted confirms the effectiveness of SEM analysis to determine the properties of post-process residue from Clean Coal Technologies (CCT. The results obtained are an introduction to further research on the determination of properties of CCT post-process residue. Research to determine the properties of CCT post-process residue only began relatively recently.

Residues and world-sheet instantons

International Nuclear Information System (INIS)

Beasley, Chris; Witten, Edward

2003-01-01

We reconsider the question of which Calabi-Yau compactifications of the heterotic string are stable under world-sheet instanton corrections to the effective space-time superpotential. For instance, compactifications described by (0; 2) linear sigma models are believed to be stable, suggesting a remarkable cancellation among the instanton effects in these theories. Here, we show that this cancellation follows directly from a residue theorem, whose proof relies only upon the right-moving world-sheet supersymmetries and suitable compactness properties of the (0; 2) linear sigma model. Our residue theorem also extends to a new class of 'half-linear' sigma models. Using these half-linear models, we show that heterotic compactifications on the quintic hypersurface in CP 4 for which the gauge bundle pulls back from a bundle on CP 4 are stable. Finally, we apply similar ideas to compute the superpotential contributions from families of membrane instantons in M-theory compactifications on manifolds of G 2 holonomy. (author)

Binding properties of SUMO-interacting motifs (SIMs) in yeast.

Science.gov (United States)

Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

2015-03-01

Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

Dispersion Interactions between Urea and Nucleobases Contribute to the Destabilization of RNA by Urea in Aqueous Solution

Science.gov (United States)

Kasavajhala, Koushik; Bikkina, Swetha; Patil, Indrajit; MacKerell, Alexander D.; Priyakumar, U. Deva

2015-01-01

Urea has long been used to investigate protein folding and, more recently, RNA folding. Studies have proposed that urea denatures RNA by participating in stacking interactions and hydrogen bonds with nucleic acid bases. In this study, the ability of urea to form unconventional stacking interactions with RNA bases is investigated using ab initio calculations (RI-MP2 and CCSD(T) methods with the aug-cc-pVDZ basis set). A total of 29 stable nucleobase-urea stacked complexes are identified in which the intermolecular interaction energies (up to −14 kcal/mol) are dominated by dispersion effects. Natural bond orbital (NBO) and atoms in molecules (AIM) calculations further confirm strong interactions between urea and nucleobases. Calculations on model systems with multiple urea and water molecules interacting with a guanine base lead to a hypothesis that urea molecules along with water are able to form cage-like structures capable of trapping nucleic acid bases in extrahelical states by forming both hydrogen bonded and dispersion interactions, thereby contributing to the unfolding of RNA in the presence of urea in aqueous solution. PMID:25668757

Residual stresses

International Nuclear Information System (INIS)

Sahotra, I.M.

2006-01-01

The principal effect of unloading a material strained into the plastic range is to create a permanent set (plastic deformation), which if restricted somehow, gives rise to a system of self-balancing within the same member or reaction balanced by other members of the structure., known as residual stresses. These stresses stay there as locked-in stresses, in the body or a part of it in the absence of any external loading. Residual stresses are induced during hot-rolling and welding differential cooling, cold-forming and extruding: cold straightening and spot heating, fabrication and forced fitting of components constraining the structure to a particular geometry. The areas which cool more quickly develop residual compressive stresses, while the slower cooling areas develop residual tensile stresses, and a self-balancing or reaction balanced system of residual stresses is formed. The phenomenon of residual stresses is the most challenging in its application in surface modification techniques determining endurance mechanism against fracture and fatigue failures. This paper discusses the mechanism of residual stresses, that how the residual stresses are fanned and what their behavior is under the action of external forces. Such as in the case of a circular bar under limit torque, rectangular beam under limt moment, reclaiming of shafts welds and peening etc. (author)

Aromatic residues located close to the active center are essential for the catalytic reaction of flap endonuclease-1 from hyperthermophilic archaeon Pyrococcus horikoshii.

Science.gov (United States)

Matsui, Eriko; Abe, Junko; Yokoyama, Hideshi; Matsui, Ikuo

2004-04-16

Flap endonuclease-1 (FEN-1) possessing 5'-flap endonuclease and 5'-->3' exonuclease activity plays important roles in DNA replication and repair. In this study, the kinetic parameters of mutants at highly conserved aromatic residues, Tyr33, Phe35, Phe79, and Phe278-Phe279, in the vicinity of the catalytic centers of FEN-1 were examined. The substitution of these aromatic residues with alanine led to a large reduction in kcat values, although these mutants retained Km values similar to that of the wild-type enzyme. Notably, the kcat of Y33A and F79A decreased 333-fold and 71-fold, respectively, compared with that of the wild-type enzyme. The aromatic residues Tyr33 and Phe79, and the aromatic cluster Phe278-Phe279 mainly contributed to the recognition of the substrates without the 3' projection of the upstream strand (the nick, 5'-recess-end, single-flap, and pseudo-Y substrates) for the both exo- and endo-activities, but played minor roles in recognizing the substrates with the 3' projection (the double flap substrate and the nick substrate with the 3' projection). The replacement of Tyr33, Phe79, and Phe278-Phe279, with non-charged aromatic residues, but not with aliphatic hydrophobic residues, recovered the kcat values almost fully for the substrates without the 3' projection of the upstream strand, suggesting that the aromatic groups of Tyr33, Phe79, and Phe278-Phe279 might be involved in the catalytic reaction, probably via multiple stacking interactions with nucleotide bases. The stacking interactions of Tyr33 and Phe79 might play important roles in fixing the template strand and the downstream strand, respectively, in close proximity to the active center to achieve the productive transient state leading to the hydrolysis.

The earthworm gastrointestinal effect on the release of organic bound residues in soils

Science.gov (United States)

Du, J. H.

2018-03-01

Earthworm activities promote the release of bound residues and the digestive activities of earthworms contribute to the process. Earthworm digestive effects on bound residues can be divided into physical and chemical effects. Physical effects include gastrointestinal abrasion and mixing. The abrasion of soil and litter residues in earthworm gizzards and intestine can grind the food into fine particles, which increase the contact surface with microbial and promote the desorption of bound residues. Chemical effects are attributed to the secreted surfactant substances and digestive enzymes. The surfactants, especially at levels that lead to micellization, can enhance the desorption process of the organic contaminants that sored in the soil. The enzymes in earthworm digestive tracts can decompose the humus in soil, which may promote the release of organic residues that bind with humus.

Functional contributions and interactions between the human hippocampus and subregions of the striatum during arbitrary associative learning and memory

Science.gov (United States)

Mattfeld, Aaron T.; Stark, Craig E. L.

2015-01-01

The hippocampus and striatum are thought to have different functional roles in learning and memory. It is unknown under what experimental conditions their contributions are dissimilar or converge, and the extent to which they interact over the course of learning. In order to evaluate both the functional contributions of as well as the interactions between the human hippocampus and striatum, the present study used high-resolution functional magnetic resonance imaging (fMRI) and variations of a conditional visuomotor associative learning task that either taxed arbitrary associative learning (Experiment 1) or stimulus-response learning (Experiment 2). In the first experiment we observed changes in activity in the hippocampus and anterior caudate that reflect differences between the two regions consistent with distinct computational principles. In the second experiment we observed activity in the putamen that reflected content specific representations during the learning of arbitrary conditional visuomotor associations. In both experiments the hippocampus and ventral striatum demonstrated dynamic functional coupling during the learning of new arbitrary associations, but not during retrieval of well-learned arbitrary associations using control variants of the tasks that did not preferentially tax one system versus the other. These findings suggest that both the hippocampus and subregions of the dorsal striatum contribute uniquely to the learning of arbitrary associations while the hippocampus and ventral striatum interact over the course of learning. PMID:25560298

Estimating the spatial scale of herbicide and soil interactions by nested sampling, hierarchical analysis of variance and residual maximum likelihood

Energy Technology Data Exchange (ETDEWEB)

Price, Oliver R., E-mail: oliver.price@unilever.co [Warwick-HRI, University of Warwick, Wellesbourne, Warwick, CV32 6EF (United Kingdom); University of Reading, Soil Science Department, Whiteknights, Reading, RG6 6UR (United Kingdom); Oliver, Margaret A. [University of Reading, Soil Science Department, Whiteknights, Reading, RG6 6UR (United Kingdom); Walker, Allan [Warwick-HRI, University of Warwick, Wellesbourne, Warwick, CV32 6EF (United Kingdom); Wood, Martin [University of Reading, Soil Science Department, Whiteknights, Reading, RG6 6UR (United Kingdom)

2009-05-15

An unbalanced nested sampling design was used to investigate the spatial scale of soil and herbicide interactions at the field scale. A hierarchical analysis of variance based on residual maximum likelihood (REML) was used to analyse the data and provide a first estimate of the variogram. Soil samples were taken at 108 locations at a range of separating distances in a 9 ha field to explore small and medium scale spatial variation. Soil organic matter content, pH, particle size distribution, microbial biomass and the degradation and sorption of the herbicide, isoproturon, were determined for each soil sample. A large proportion of the spatial variation in isoproturon degradation and sorption occurred at sampling intervals less than 60 m, however, the sampling design did not resolve the variation present at scales greater than this. A sampling interval of 20-25 m should ensure that the main spatial structures are identified for isoproturon degradation rate and sorption without too great a loss of information in this field. - Estimating the spatial scale of herbicide and soil interactions by nested sampling.

Estimating the spatial scale of herbicide and soil interactions by nested sampling, hierarchical analysis of variance and residual maximum likelihood

International Nuclear Information System (INIS)

Price, Oliver R.; Oliver, Margaret A.; Walker, Allan; Wood, Martin

2009-01-01

An unbalanced nested sampling design was used to investigate the spatial scale of soil and herbicide interactions at the field scale. A hierarchical analysis of variance based on residual maximum likelihood (REML) was used to analyse the data and provide a first estimate of the variogram. Soil samples were taken at 108 locations at a range of separating distances in a 9 ha field to explore small and medium scale spatial variation. Soil organic matter content, pH, particle size distribution, microbial biomass and the degradation and sorption of the herbicide, isoproturon, were determined for each soil sample. A large proportion of the spatial variation in isoproturon degradation and sorption occurred at sampling intervals less than 60 m, however, the sampling design did not resolve the variation present at scales greater than this. A sampling interval of 20-25 m should ensure that the main spatial structures are identified for isoproturon degradation rate and sorption without too great a loss of information in this field. - Estimating the spatial scale of herbicide and soil interactions by nested sampling.

Roles of the β 146 histidyl residue in the molecular basis of the Bohr Effect of hemoglobin: A proton nuclear magnetic resonance study

International Nuclear Information System (INIS)

Busch, M.R.; Mace, J.E.; Ho, N.T.; Ho, Chien

1991-01-01

Assessment of the roles of the carboxyl-terminal β146 histidyl residues in the alkaline Bohr effect in human and normal adult hemoglobin by high-resolution proton nuclear magnetic resonance spectroscopy requires assignment of the resonances corresponding to these residues. By a careful spectroscopic study of human normal adult hemoglobin, enzymatically prepared des(His146β)-hemoglobin, and the mutant hemoglobins Cowtown (β146His → Leu) and York (β146His → Pro), the authors have resolved some of these conflicting results. By a close incremental variation of pH over a wide range in chloride-free 0.1 M N-(2-hydroxyethyl)piperazine-N'-2-ethanesulfonic acid buffer, a single resonance has been found to be consistently missing in the proton nuclear magnetic resonance spectra of these hemoglobin variants. The results indicate that the contribution of the β146 histidyl residues is 0.52 H + /hemoglobin tetramer at pH 7.6, markedly less than 0.8 H + /hemoglobin tetramer estimated by study of the mutant hemoglobin Cowtown (β146His → Leu) by Shih and Perutz. They have found that at least two histidyl residues in the carbonmonoxy form of this mutant have pK values that are perturbed, and they suggest that these pK differences may in part account for this discrepancy. The results show that the pK values of β146 histidyl residues in the carbonmonoxy form of hemoglobin are substantially affected by the presence of chloride and other anions in the solvent, and thus, the contribution of this amino acid residue to the alkaline Bohr effect can be shown to vary widely in magnitude, depending on the solvent composition. These results demonstrate that the detailed molecular mechanisms of the alkaline Bohr effect are not unique but are affected both by the hemoglobin structure and by the interactions with the solvent components in which the hemoglobin molecule resides

Identification of amino acids in the human tetherin transmembrane domain responsible for HIV-1 Vpu interaction and susceptibility.

Science.gov (United States)

Kobayashi, Tomoko; Ode, Hirotaka; Yoshida, Takeshi; Sato, Kei; Gee, Peter; Yamamoto, Seiji P; Ebina, Hirotaka; Strebel, Klaus; Sato, Hironori; Koyanagi, Yoshio

2011-01-01

Tetherin, also known as BST-2/CD317/HM1.24, is an antiviral cellular protein that inhibits the release of HIV-1 particles from infected cells. HIV-1 viral protein U (Vpu) is a specific antagonist of human tetherin that might contribute to the high virulence of HIV-1. In this study, we show that three amino acid residues (I34, L37, and L41) in the transmembrane (TM) domain of human tetherin are critical for the interaction with Vpu by using a live cell-based assay. We also found that the conservation of an additional amino acid at position 45 and two residues downstream of position 22, which are absent from monkey tetherins, are required for the antagonism by Vpu. Moreover, computer-assisted structural modeling and mutagenesis studies suggest that an alignment of these four amino acid residues (I34, L37, L41, and T45) on the same helical face in the TM domain is crucial for the Vpu-mediated antagonism of human tetherin. These results contribute to the molecular understanding of human tetherin-specific antagonism by HIV-1 Vpu.

The role of a second-shell residue in modifying substrate and inhibitor interactions in the SHV beta-lactamase: a study of ambler position Asn276.

Science.gov (United States)

Drawz, Sarah M; Bethel, Christopher R; Hujer, Kristine M; Hurless, Kelly N; Distler, Anne M; Caselli, Emilia; Prati, Fabio; Bonomo, Robert A

2009-06-02

Inhibitor-resistant class A beta-lactamases of the TEM and SHV families that arise by single amino acid substitutions are a significant threat to the efficacy of beta-lactam/beta-lactamase inhibitor combinations. To better understand the basis of the inhibitor-resistant phenotype in SHV, we performed mutagenesis to examine the role of a second-shell residue, Asn276. Of the 19 variants expressed in Escherichia coli, only the Asn276Asp enzyme demonstrated reduced susceptibility to ampicillin/clavulanate (MIC increased from 50/2 --> 50/8 microg/mL) while maintaining high-level resistance to ampicillin (MIC = 8192 microg/mL). Steady-state kinetic analyses of Asn276Asp revealed slightly diminished k(cat)/K(m) for all substrates tested. In contrast, we observed a 5-fold increase in K(i) for clavulanate (7.4 +/- 0.9 microM for Asn276Asp vs 1.4 +/- 0.2 microM for SHV-1) and a 40% reduction in k(inact)/K(I) (0.013 +/- 0.002 microM(-1 )s(-1) for Asn276Asp vs 0.021 +/- 0.004 microM(-1) s(-1) for SHV-1). Timed electrospray ionization mass spectrometry of clavulanate-inhibited SHV-1 and SHV Asn276Asp showed nearly identical mass adducts, arguing for a similar pathway of inactivation. Molecular modeling shows that novel electrostatic interactions are formed between Arg244Neta2 and both 276AspOdelta1 and Odelta2; these new forces restrict the spatial position of Arg244, a residue important in the recognition of the C(3)/C(4) carboxylate of beta-lactam substrates and inhibitors. Testing the functional consequences of this interaction, we noted considerable free energy costs (+DeltaDeltaG) for substrates and inhibitors. A rigid carbapenem (meropenem) was most affected by the Asn276Asp substitution (46-fold increase in K(i) vs SHV-1). We conclude that residue 276 is an important second-shell residue in class A beta-lactamase-mediated resistance to substrates and inhibitors, and only Asn is able to precisely modulate the conformational flexibility of Arg244 required for successful

Contribution of microorganisms to non-extractable residue formation during biodegradation of ibuprofen in soil.

Science.gov (United States)

Nowak, Karolina M; Girardi, Cristobal; Miltner, Anja; Gehre, Matthias; Schäffer, Andreas; Kästner, Matthias

2013-02-15

Non-extractable residues (NER) formed during biodegradation of organic contaminants in soil are considered to be mainly composed of parent compounds or their primary metabolites with hazardous potential. However, in the case of biodegradable organic compounds, the soil NER may also contain microbial biomass components, for example fatty acids (FA) and amino acids (AA). After cell death, these biomolecules are subsequently incorporated into non-living soil organic matter (SOM) and are stabilised ultimately forming hardly extractable residues of biogenic origin. We investigated biodegradation of (13)C(6)-ibuprofen, in particular the metabolic incorporation of the (13)C-label into FA and AA and their fate in soil over 90 days. (13)C-FA and (13)C-AA amounts in the living microbial biomass fraction initially increased, then decreased over time and were continuously incorporated into the non-living SOM pool. The (13)C-FA in the non-living SOM remained stable from day 59 whereas the contents of (13)C-AA slightly increased until the end. After 90 days, nearly all NER were biogenic as they were made up almost completely by natural biomass compounds. The presented data demonstrated that the potential environmental risks related to the ibuprofen-derived NER are overestimated. Copyright © 2012 Elsevier B.V. All rights reserved.

Optimal definition of inter-residual contact in globular proteins based on pairwise interaction energy calculations, its robustness, and applications.

Science.gov (United States)

Fačkovec, Boris; Vondrášek, Jiří

2012-10-25

Although a contact is an essential measurement for the topology as well as strength of non-covalent interactions in biomolecules and their complexes, there is no general agreement in the definition of this feature. Most of the definitions work with simple geometric criteria which do not fully reflect the energy content or ability of the biomolecular building blocks to arrange their environment. We offer a reasonable solution to this problem by distinguishing between "productive" and "non-productive" contacts based on their interaction energy strength and properties. We have proposed a method which converts the protein topology into a contact map that represents interactions with statistically significant high interaction energies. We do not prove that these contacts are exclusively stabilizing, but they represent a gateway to thermodynamically important rather than geometry-based contacts. The process is based on protein fragmentation and calculation of interaction energies using the OPLS force field and relies on pairwise additivity of amino acid interactions. Our approach integrates the treatment of different types of interactions, avoiding the problems resulting from different contributions to the overall stability and the different effect of the environment. The first applications on a set of homologous proteins have shown the usefulness of this classification for a sound estimate of protein stability.

Identification of chemical signatures of gunshot residues in different fabrics

International Nuclear Information System (INIS)

Freitas, Joao Carlos Dias de

2010-01-01

The modern forensic science goes hand in hand with scientific research. The forensic scientists are faced every day with many cases requiring the analysis of residues from firing gun (gunshot residues). This works describes the development of a methodology to determine chemical signatures of shots from a firearm, by measuring the concentrations of Pb, Ba e Sb in the residues from these shots deposited near the entrance hole of bullets, based on the technique with high resolution inductively coupled plasma mass spectrometry (HRICP-MS). Shots were performed on five types of target-fabrics and collected testimonies from regions close to the entrance hole of projectiles. The results showed that the method enabled us to identify and distinguish the residues of the .38 caliber revolver and pistols .40 and 9mm caliber. The use of ternary graphs as a tool for data analysis helped to identify specific patterns of distribution of blank samples and gunshot residues deposited after firing revolvers and pistols. The methodology enabled the assignment of the origin of the shot through the confirmation of the residues collected also from the hands of shooters. As a result the methodology in police procedures and aims to add a valuable contribution to forensic investigations. (author)

Residual stress measurement by x-ray under the consideration of its penetration depth

International Nuclear Information System (INIS)

Doi, Osamu; Ukai, Takayoshi

1983-01-01

The authors derived the fundamental relations between the measured stress by X-ray and the residual stress distribution from the consideration of the contribution of internal stress in definite subsurface layer of metal to X-ray diffraction and proposed the exact formulas and their applications of residual stress measurements by successive thin layer removal in a plate, a hollow cylinder and a hollow sphere. (author)

Single molecule TPM analysis of the catalytic pentad mutants of Cre and Flp site-specific recombinases: contributions of the pentad residues to the pre-chemical steps of recombination

Science.gov (United States)

Fan, Hsiu-Fang; Cheng, Yong-Song; Ma, Chien-Hui; Jayaram, Makkuni

2015-01-01

Cre and Flp site-specific recombinase variants harboring point mutations at their conserved catalytic pentad positions were characterized using single molecule tethered particle motion (TPM) analysis. The findings reveal contributions of these amino acids to the pre-chemical steps of recombination. They suggest functional differences between positionally conserved residues in how they influence recombinase-target site association and formation of ‘non-productive’, ‘pre-synaptic’ and ‘synaptic’ complexes. The most striking difference between the two systems is noted for the single conserved lysine. The pentad residues in Cre enhance commitment to recombination by kinetically favoring the formation of pre-synaptic complexes. These residues in Flp serve a similar function by promoting Flp binding to target sites, reducing non-productive binding and/or enhancing the rate of assembly of synaptic complexes. Kinetic comparisons between Cre and Flp, and between their derivatives lacking the tyrosine nucleophile, are consistent with a stronger commitment to recombination in the Flp system. The effect of target site orientation (head-to-head or head-to-tail) on the TPM behavior of synapsed DNA molecules supports the selection of anti-parallel target site alignment prior to the chemical steps. The integrity of the synapse, whose establishment/stability is fostered by strand cleavage in the case of Flp but not Cre, appears to be compromised by the pentad mutations. PMID:25765648

Modeling Residual NAPL in Water-Wet Porous Media

Directory of Open Access Journals (Sweden)

R.J. Lenhard

2002-06-01

Full Text Available A model is outlined that predicts NAPL which is held in pore wedges and as films or lenses on solid and water surfaces and contributes negligibly to NAPL advection. This is conceptually referred to as residual NAPL. Since residual NAPL is immobile, it remains in the vadose zone after all free NAPL has drained. Residual NAPL is very important because it is a long-term source for groundwater contamination. Recent laboratory experiments have demonstrated that current models for predicting subsurface NAPL behavior are inadequate because they do not correctly predict residual NAPL. The main reason for the failure is a deficiency in the current constitutive theories for multiphase flow that are used in numerical simulators. Multiphase constitutive theory governs the relations among relative permeability, saturation, and pressure for fluid systems (i.e., air, NAPL, water. In this paper, we outline a model describing relations between fluid saturations and pressures that can be combined with existing multiphase constitutive theory to predict residual NAPL. We test the revised constitutive theory by applying it to a scenario involving NAPL imbibition and drainage, as well as water imbibition and drainage. The results suggest that the revised constitutive theory is able to predict the distribution of residual NAPL in the vadose zone as a function of saturation-path history. The revised model describing relations between fluid saturation and pressures will help toward developing or improving numerical multiphase flow simulators.

Evaluation of residue-residue contact predictions in CASP9

KAUST Repository

Monastyrskyy, Bohdan

2011-01-01

This work presents the results of the assessment of the intramolecular residue-residue contact predictions submitted to CASP9. The methodology for the assessment does not differ from that used in previous CASPs, with two basic evaluation measures being the precision in recognizing contacts and the difference between the distribution of distances in the subset of predicted contact pairs versus all pairs of residues in the structure. The emphasis is placed on the prediction of long-range contacts (i.e., contacts between residues separated by at least 24 residues along sequence) in target proteins that cannot be easily modeled by homology. Although there is considerable activity in the field, the current analysis reports no discernable progress since CASP8.

Leptospira Immunoglobulin-Like Protein B Interacts with the 20th Exon of Human Tropoelastin Contributing to Leptospiral Adhesion to Human Lung Cells.

Science.gov (United States)

Hsieh, Ching-Lin; Tseng, Andrew; He, Hongxuan; Kuo, Chih-Jung; Wang, Xuannian; Chang, Yung-Fu

2017-01-01

Leptospira immunoglobulin-like protein B (LigB), a surface adhesin, is capable of mediating the attachment of pathogenic leptospira to the host through interaction with various components of the extracellular matrix (ECM). Human tropoelastin (HTE), the building block of elastin, confers resilience and elasticity to lung, and other tissues. Previously identified Ig-like domains of LigB, including LigB4 and LigB12, bind to HTE, which is likely to promote Leptospira adhesion to lung tissue. However, the molecular mechanism that mediates the LigB-HTE interaction is unclear. In this study, the LigB-binding site on HTE was further pinpointed to a N-terminal region of the 20th exon of HTE (HTE20N). Alanine mutants of basic and aromatic residues on HTE20N significantly reduced binding to the LigB. Additionally, HTE-binding site was narrowed down to the first β-sheet of LigB12. On this binding surface, residues F1054, D1061, A1065, and D1066 were critical for the association with HTE. Most importantly, the recombinant HTE truncates could diminish the binding of LigB to human lung fibroblasts (WI-38) by 68%, and could block the association of LigA-expressing L. biflexa to lung cells by 61%. These findings should expand our understanding of leptospiral pathogenesis, particularly in pulmonary manifestations of leptospirosis.

Leptospira Immunoglobulin-Like Protein B Interacts with the 20th Exon of Human Tropoelastin Contributing to Leptospiral Adhesion to Human Lung Cells

Directory of Open Access Journals (Sweden)

Ching-Lin Hsieh

2017-05-01

Full Text Available Leptospira immunoglobulin-like protein B (LigB, a surface adhesin, is capable of mediating the attachment of pathogenic leptospira to the host through interaction with various components of the extracellular matrix (ECM. Human tropoelastin (HTE, the building block of elastin, confers resilience and elasticity to lung, and other tissues. Previously identified Ig-like domains of LigB, including LigB4 and LigB12, bind to HTE, which is likely to promote Leptospira adhesion to lung tissue. However, the molecular mechanism that mediates the LigB-HTE interaction is unclear. In this study, the LigB-binding site on HTE was further pinpointed to a N-terminal region of the 20th exon of HTE (HTE20N. Alanine mutants of basic and aromatic residues on HTE20N significantly reduced binding to the LigB. Additionally, HTE-binding site was narrowed down to the first β-sheet of LigB12. On this binding surface, residues F1054, D1061, A1065, and D1066 were critical for the association with HTE. Most importantly, the recombinant HTE truncates could diminish the binding of LigB to human lung fibroblasts (WI-38 by 68%, and could block the association of LigA-expressing L. biflexa to lung cells by 61%. These findings should expand our understanding of leptospiral pathogenesis, particularly in pulmonary manifestations of leptospirosis.

Residues of 14C-prochloraz in irradiated mangoes

International Nuclear Information System (INIS)

Costa, Maria A.; Tornisielo, Valdemar L.

2000-01-01

The Brazilian crops mangoes has expanding in the last years. However, tropical fruits crops are susceptible to infection that harms the crop yield. The control of these diseases is made through fungicides such as Prochloraz which possesses protecting eradicating action by controlling antracnose in mangoes. Agrochemicals are of great importance in the agriculture considering the of relationship cost/benefit. However they may cause a series of problems in the ecosystem, being the levels of agrochemicals residues in fruits one of these factors. The aim of this work was to evaluate the Prochloraz levels in mangoes treated in the post harvest. In the treatment of the mangoes, the interaction, fungicide with the gamma radiation with of 1,0 kGy dose, was used to induce Prochloraz degradation. Treated post-harvest mangoes were stored, at 12 deg C during 21 days. The results showed that the Prochloraz did not present reduction in the residual levels of the mangoes after 21 days storage, that is the safe period established by the Brazilian legislation on agrochemicals, in treated mangoes. The refrigerated storage (12 deg C) and the gamma radiation also did not contribute to the degradation of the fungicide in mangoes. In average the concentration of the fungicide Prochloraz in the peels (mean = 1,64 μg/g) was higher than in the mangoes pulp (mean = 0,06 μg/g), which allows the consumption of this fruit, since the peel is always discarded. The degradation product, formed in peels of mangoes in fruits treated in the post-harvest was the metabolite BTS 44596. The metabolite was found in very low levels, confirming that occurs degradation of the fungicide in mangoes. (author)

Measurement of residual stress in a cylinder by x-ray under the consideration of its penetration depth

International Nuclear Information System (INIS)

Doi, Osamu; Ukai, Takayoshi

1983-01-01

The authors propose an exact theory of residual stress measurement by successive thin layer removal in a hollow cylinder under the consideration of the contribution of residual stress within a definite subsurface, and show an example of its application. (author)

An evaluation on the environmental consequences of residual CFCs from obsolete household refrigerators in China

International Nuclear Information System (INIS)

Zhao Xiangyang; Duan Huabo; Li Jinhui

2011-01-01

Chlorofluorocarbons (CFCs) contained in household refrigerators consist mainly of CFC-11 and CFC-12, which will be eventually released into the environment. Consequentially, environmental releases of these refrigerants will lead to ozone depletion and contribute significantly to the greenhouse effect, if waste refrigerators are not disposed of properly. In the present paper, the potential release of residual CFCs and their substitutes from obsolete household refrigerators in China is examined, and their contributions to ozone depletion and greenhouse effect are compared with those of other recognized ozone-depleting substances (ODS) and greenhouse gases (GHGs). The results imply that annual potential amounts of released residual CFC-11 and CFC-12 will reach their maximums at 4600 and 2300 tons, respectively in 2011, and then decrease gradually to zero until 2020. Meanwhile, the amounts of their most widely used substitutes HCFC-141b and HFC-134a will keep increasing. Subsequently, the contribution ratio of these CFCs and their substitutes to ozone depletion will remain at 25% through 2011, and reach its peak value of 34% by 2018. The contribution to greenhouse effect will reach its peak value of 0.57% by 2010. Moreover, the contribution ratio of these CFCs to the total global release of CFCs will steadily increase, reaching its peak of 15% by 2018. Thus, this period from 2010 to 2018 is a crucial time during which residual CFCs and their substitutes from obsolete household refrigerators in China will contribute significantly to ozone depletion.

Void analysis of target residues at SPS energy -evidence of correlation with fractal behaviour

International Nuclear Information System (INIS)

Ghosh, Dipak; Deb, Argha; Das, Rupa . E-mail : dipakghosh_in@yahoo.com

2007-01-01

This paper presents an analysis of the target residues in 32 S -AgBr and 16 0 -AgBr interactions at 200 AGeV and 60AGeV respectively in terms of fractal moment by Takagi method and void probability scaling. The study reveals an interesting feature of the production process. In 16 O- AgBr interactions multifractal behaviour is present in both hemispheres and void probability does not show a scaling behaviour, but at high energy the situation changes. In 32 S -AgBr interactions for both hemisphere monofractal behaviour is indicated by that data and void probability also shows good scaling behaviour. This suggests that a possible correlation of void probability with fractal behaviour of target residues. (author)

Recycling of porcelain tile polishing residue in portland cement: hydration efficiency.

Science.gov (United States)

Pelisser, Fernando; Steiner, Luiz Renato; Bernardin, Adriano Michael

2012-02-21

Ceramic tiles are widely used by the construction industry, and the manufacturing process of ceramic tiles generates as a major residue mud derived from the polishing step. This residue is too impure to be reused in the ceramic process and is usually discarded as waste in landfills. But the analysis of the particle size and concentration of silica of this residue shows a potential use in the manufacture of building materials based on portland cement. Tests were conducted on cement pastes and mortars using the addition of 10% and 20% (mass) of the residue. The results of compressive strength in mortars made up to 56 days showed a significant increase in compressive strength greater than 50%. The result of thermogravimetry shows that portlandite is consumed by the cement formed by the silica present in the residue in order to form calcium silicate hydrate and featuring a pozzolanic reaction. This effect improves the performance of cement, contributes to research and application of supplementary cementitious materials, and optimizes the use of portland cement, reducing the environmental impacts of carbon dioxide emissions from its production.

Identification of Amino Acids in the Human Tetherin Transmembrane Domain Responsible for HIV-1 Vpu Interaction and Susceptibility▿ †

Science.gov (United States)

Kobayashi, Tomoko; Ode, Hirotaka; Yoshida, Takeshi; Sato, Kei; Gee, Peter; Yamamoto, Seiji P.; Ebina, Hirotaka; Strebel, Klaus; Sato, Hironori; Koyanagi, Yoshio

2011-01-01

Tetherin, also known as BST-2/CD317/HM1.24, is an antiviral cellular protein that inhibits the release of HIV-1 particles from infected cells. HIV-1 viral protein U (Vpu) is a specific antagonist of human tetherin that might contribute to the high virulence of HIV-1. In this study, we show that three amino acid residues (I34, L37, and L41) in the transmembrane (TM) domain of human tetherin are critical for the interaction with Vpu by using a live cell-based assay. We also found that the conservation of an additional amino acid at position 45 and two residues downstream of position 22, which are absent from monkey tetherins, are required for the antagonism by Vpu. Moreover, computer-assisted structural modeling and mutagenesis studies suggest that an alignment of these four amino acid residues (I34, L37, L41, and T45) on the same helical face in the TM domain is crucial for the Vpu-mediated antagonism of human tetherin. These results contribute to the molecular understanding of human tetherin-specific antagonism by HIV-1 Vpu. PMID:21068238

Intermolecular Modes between LH2 Bacteriochlorophylls and Protein Residues: The Effect on the Excitation Energies.

Science.gov (United States)

Anda, André; De Vico, Luca; Hansen, Thorsten

2017-06-08

Light-harvesting system 2 (LH2) executes the primary processes of photosynthesis in purple bacteria; photon absorption, and energy transportation to the reaction center. A detailed mechanistic insight into these operations is obscured by the complexity of the light-harvesting systems, particularly by the chromophore-environment interaction. In this work, we focus on the effects of the protein residues that are ligated to the bacteriochlorophylls (BChls) and construct potential energy surfaces of the ground and first optically excited state for the various BChl-residue systems where we in each case consider two degrees of freedom in the intermolecular region. We find that the excitation energies are only slightly affected by the considered modes. In addition, we see that axial ligands and hydrogen-bonded residues have opposite effects on both excitation energies and oscillator strengths by comparing to the isolated BChls. Our results indicate that only a small part of the chromophore-environment interaction can be associated with the intermolecular region between a BChl and an adjacent residue, but that it may be possible to selectively raise or lower the excitation energy at the axial and planar residue positions, respectively.

Nicotinic receptor transduction zone: invariant arginine couples to multiple electron-rich residues.

Science.gov (United States)

Mukhtasimova, Nuriya; Sine, Steven M

2013-01-22

Gating of the muscle-type acetylcholine receptor (AChR) channel depends on communication between the ACh-binding site and the remote ion channel. A key region for this communication is located within the structural transition zone between the ligand-binding and pore domains. Here, stemming from β-strand 10 of the binding domain, the invariant αArg209 lodges within the hydrophobic interior of the subunit and is essential for rapid and efficient channel gating. Previous charge-reversal experiments showed that the contribution of αArg209 to channel gating depends strongly on αGlu45, also within this region. Here we determine whether the contribution of αArg209 to channel gating depends on additional anionic or electron-rich residues in this region. Also, to reconcile diverging findings in the literature, we compare the dependence of αArg209 on αGlu45 in AChRs from different species, and compare the full agonist ACh with the weak agonist choline. Our findings reveal that the contribution of αArg209 to channel gating depends on additional nearby electron-rich residues, consistent with both electrostatic and steric contributions. Furthermore, αArg209 and αGlu45 show a strong interdependence in both human and mouse AChRs, whereas the functional consequences of the mutation αE45R depend on the agonist. The emerging picture shows a multifaceted network of interdependent residues that are required for communication between the ligand-binding and pore domains. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Effects of magnetic core geometry on false detection in residual current sensor

International Nuclear Information System (INIS)

Colin, Bruno; Chillet, Christian; Kedous-Lebouc, Afef; Mas, Patrick

2006-01-01

Under high-supply current, residual circuit breakers are subject to abnormal tripping, caused by false residual currents. Geometric or magnetic anomalies in the circuit breaker ring core seem to be responsible for these abnormal currents. This paper studies a few anomalies (spiral shape effect, conductor eccentricity, lamination effect) and calculates different contributions using the finite element simulations. The results show that the ring core, made of thin wound magnetic tape, is particularly sensitive to primary conductor eccentricity

Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.

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Aysima Hacisuleyman

2017-01-01

Full Text Available It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins.

Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.

Science.gov (United States)

Hacisuleyman, Aysima; Erman, Burak

2017-01-01

It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins.

Nicotinic Receptor Transduction Zone: Invariant Arginine Couples to Multiple Electron-Rich Residues

Science.gov (United States)

Mukhtasimova, Nuriya; Sine, Steven M.

2013-01-01

Summary Gating of the muscle-type acetylcholine receptor (AChR) channel depends on communication between the ACh-binding site and the remote ion channel. A key region for this communication is located within the structural transition zone between the ligand-binding and pore domains. Here, stemming from β-strand 10 of the binding domain, the invariant αArg209 lodges within the hydrophobic interior of the subunit and is essential for rapid and efficient channel gating. Previous charge-reversal experiments showed that the contribution of αArg209 to channel gating depends strongly on αGlu45, also within this region. Here we determine whether the contribution of αArg209 to channel gating depends on additional anionic or electron-rich residues in this region. Also, to reconcile diverging findings in the literature, we compare the dependence of αArg209 on αGlu45 in AChRs from different species, and compare the full agonist ACh with the weak agonist choline. Our findings reveal that the contribution of αArg209 to channel gating depends on additional nearby electron-rich residues, consistent with both electrostatic and steric contributions. Furthermore, αArg209 and αGlu45 show a strong interdependence in both human and mouse AChRs, whereas the functional consequences of the mutation αE45R depend on the agonist. The emerging picture shows a multifaceted network of interdependent residues that are required for communication between the ligand-binding and pore domains. PMID:23442857

Mineralization of nitrogen from nitrogen-15 labeled crop residues and utilization by rice

International Nuclear Information System (INIS)

Norman, R.J.; Gilmour, J.T.; Wells, B.R.

1990-01-01

The availability of N from the residues of the previous crop to the subsequent rice (Oryza sativa L.) crop is largely unknown. The objectives of this study were to (1) measure the mineralization of N from 15 N-labeled rice, soybean (Glycine max L.), and wheat (Triticum aestivum L.) residues and the uptake by a subsequent rice crop; and (2) compare the 15 N tracer method with the standard fertilizer-N response method used in field studies to quantify the N contribution from the crop residue to the next crop. Nitrogen mineralization from decomposing crop residues was measured by soil sampling prior to seeding the rice crop and after seeding by plant sampling the rice at maturity. The minimum estimate of the amount of residue N mineralized from the time of residue incorporation until rice harvest was 9, 52, and 38% of the rice, soybean, and wheat residue N, respectively. The amount of residue N recovered in the rice crop was 3, 11, and 37% of the rice, soybean, and wheat residue N, respectively. The lower the C/N ratio and the higher the amount of N in the residue, the lower was the amount of residue N recovered in the soil organic fraction at harvest and the higher was the amount of residue N mineralized. The 15 N tracer method compared favorably with the fertilizer N response method when the uptake efficiency of the fertilizer N was taken into account

Study of the interactions between a proline-rich protein and a flavan-3-ol by NMR: residual structures in the natively unfolded protein provides anchorage points for the ligands.

Science.gov (United States)

Pascal, Christine; Paté, Franck; Cheynier, Véronique; Delsuc, Marc-André

2009-09-01

Astringency is one of the major organoleptic properties of food and beverages that are made from plants, such as tea, chocolate, beer, or red wine. This sensation is thought to be due to interactions between tannins and salivary proline-rich proteins, which are natively unfolded proteins. A human salivary proline-rich protein, namely IB-5, was produced by the recombinant method. Its interactions with a model tannin, epigallocatechin gallate (EGCG), the major flavan-3-ol in green tea, were studied here. Circular dichroism experiments showed that IB-5 presents residual structures (PPII helices) when the ionic strength is close to that in saliva. In the presence of these residual structures, IB-5 undergoes an increase in structural content upon binding to EGCG. NMR data corroborated the presence of preformed structural elements within the protein prior to binding and a partial assignment was proposed, showing partial structuration. TOCSY experiments showed that amino acids that are involved in PPII helices are more likely to interact with EGCG than those in random coil regions, as if they were anchorage points for the ligand. The signal from IB-5 in the DOSY NMR spectrum revealed an increase in polydispersity upon addition of EGCG while the mean hydrodynamic radius remained unchanged. This strongly suggests the formation of IB-5/EGCG aggregates.

Leveraging the Pre-DFG Residue Thr-406 To Obtain High Kinase Selectivity in an Aminopyrazole-Type PAK1 Inhibitor Series.

Science.gov (United States)

Rudolph, Joachim; Aliagas, Ignacio; Crawford, James J; Mathieu, Simon; Lee, Wendy; Chao, Qi; Dong, Ping; Rouge, Lionel; Wang, Weiru; Heise, Christopher; Murray, Lesley J; La, Hank; Liu, Yanzhou; Manning, Gerard; Diederich, François; Hoeflich, Klaus P

2015-06-11

To increase kinase selectivity in an aminopyrazole-based PAK1 inhibitor series, analogues were designed to interact with the PAK1 deep-front pocket pre-DFG residue Thr-406, a residue that is hydrophobic in most kinases. This goal was achieved by installing lactam head groups to the aminopyrazole hinge binding moiety. The corresponding analogues represent the most kinase selective ATP-competitive Group I PAK inhibitors described to date. Hydrogen bonding with the Thr-406 side chain was demonstrated by X-ray crystallography, and inhibitory activities, particularly against kinases with hydrophobic pre-DFG residues, were mitigated. Leveraging hydrogen bonding side chain interactions with polar pre-DFG residues is unprecedented, and similar strategies should be applicable to other appropriate kinases.

Anion induced conformational preference of Cα NN motif residues in functional proteins.

Science.gov (United States)

Patra, Piya; Ghosh, Mahua; Banerjee, Raja; Chakrabarti, Jaydeb

2017-12-01

Among different ligand binding motifs, anion binding C α NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with C α NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping C α NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion. © 2017 Wiley Periodicals, Inc.

Whole-protein alanine-scanning mutagenesis of allostery: A large percentage of a protein can contribute to mechanism.

Science.gov (United States)

Tang, Qingling; Fenton, Aron W

2017-09-01

Many studies of allosteric mechanisms use limited numbers of mutations to test whether residues play "key" roles. However, if a large percentage of the protein contributes to allosteric function, mutating any residue would have a high probability of modifying allostery. Thus, a predicted mechanism that is dependent on only a few residues could erroneously appear to be supported. We used whole-protein alanine-scanning mutagenesis to determine which amino acid sidechains of human liver pyruvate kinase (hL-PYK; approved symbol PKLR) contribute to regulation by fructose-1,6-bisphosphate (Fru-1,6-BP; activator) and alanine (inhibitor). Each nonalanine/nonglycine residue of hL-PYK was mutated to alanine to generate 431 mutant proteins. Allosteric functions in active proteins were quantified by following substrate affinity over a concentration range of effectors. Results show that different residues contribute to the two allosteric functions. Only a small fraction of mutated residues perturbed inhibition by alanine. In contrast, a large percentage of mutated residues influenced activation by Fru-1,6-BP; inhibition by alanine is not simply the reverse of activation by Fru-1,6-BP. Moreover, the results show that Fru-1,6-BP activation would be extremely difficult to elucidate using a limited number of mutations. Additionally, this large mutational data set will be useful to train and test computational algorithms aiming to predict allosteric mechanisms. © 2017 Wiley Periodicals, Inc.

Impact of Corn Residue Removal on Crop and Soil Productivity

Science.gov (United States)

Johnson, J. M.; Wilhelm, W. W.; Hatfield, J. L.; Voorhees, W. B.; Linden, D.

2003-12-01

Over-reliance on imported fuels, increasing atmospheric levels of greenhouses and sustaining food production for a growing population are three of the most important problems facing society in the mid-term. The US Department of Energy and private enterprise are developing technology necessary to use high cellulose feedstock, such as crop residues, for ethanol production. Based on production levels, corn (Zea mays L.) residue has potential as a biofuel feedstock. Crop residues are a renewable and domestic fuel source, which can reduce the rate of fossil fuel use (both imported and domestic) and provide an additional farm commodity. Crop residues protect the soil from wind and water erosion, provide inputs to form soil organic matter (a critical component determining soil quality) and play a role in nutrient cycling. Crop residues impact radiation balance and energy fluxes and reduce evaporation. Therefore, the benefits of using crop residues as fuel, which removes crop residues from the field, must be balanced against negative environmental impacts (e.g. soil erosion), maintaining soil organic matter levels, and preserving or enhancing productivity. All ramifications of new management practices and crop uses must be explored and evaluated fully before an industry is established. There are limited numbers of long-term studies with soil and crop responses to residue removal that range from negative to negligible. The range of crop and soil responses to crop residue removal was attributed to interactions with climate, management and soil type. Within limits, corn residue can be harvested for ethanol production to provide a renewable, domestic source of energy feedstock that reduces greenhouse gases. Removal rates must vary based on regional yield, climatic conditions and cultural practices. Agronomists are challenged to develop a protocol (tool) for recommending maximum permissible removal rates that ensure sustained soil productivity.

Chemical modification of arginine residues in the lactose repressor

International Nuclear Information System (INIS)

Whitson, P.A.; Matthews, K.S.

1987-01-01

The lactose repressor protein was chemically modified with 2,3-butanedione and phenylglyoxal. Arginine reaction was quantitated by either amino aced analysis or incorporation of 14 C-labeled phenylglyoxal. Inducer binding activity was unaffected by the modification of arginine residues, while both operator and nonspecific DNA binding activities were diminished, although to differing degrees. The correlation of the decrease in DNA binding activities with the modification of ∼ 1-2 equiv of arginine per monomer suggests increased reactivity of a functionally essential residue(s). For both reagents, operator DNA binding activity was protected by the presence of calf thymus DNA, and the extent of reaction with phenylglyoxal was simultaneously diminished. This protection presumably results from steric restriction of reagent access to an arginine(s) that is (are) essential for DNA binding interactions. These experiments suggest that there is (are) an essential reactive arginine(s) critical for repressor binding to DNA

Contribution of the study of thermal interaction: modelling of a thermal blast in a multi-phase medium

International Nuclear Information System (INIS)

Scott, Edouard

1978-01-01

This research thesis aims at being a contribution to the safety of nuclear facilities by reporting the study of the interaction between nuclear fuel and coolant in simplified conditions. It focuses on the thermal aspect of this interaction between a very hot body and an easily vaporized cold body, which could produce a blast. Thus, this author addresses the field of existence of a thermal blast, and reports the development of a hydrodynamic model which takes the heterogeneous nature of the interacting medium into account, in order to precisely describe the conditions of fuel fragmentation. This model includes the propagation of a shock in a mixture, and the calculation of a multi-phase flow in the reaction zone, and proposes criteria for a self-sustained shock wave propagation in the reactive medium. Results are compared with those obtained with the Bankoff model [fr

Soil and crop residue CO2-C emission under tillage systems in sugarcane-producing areas of southern Brazil

Directory of Open Access Journals (Sweden)

Luís Gustavo Teixeira

2013-10-01

Full Text Available Appropriate management of agricultural crop residues could result in increases on soil organic carbon (SOC and help to mitigate gas effect. To distinguish the contributions of SOC and sugarcane (Saccharum spp. residues to the short-term CO2-C loss, we studied the influence of several tillage systems: heavy offset disk harrow (HO, chisel plow (CP, rotary tiller (RT, and sugarcane mill tiller (SM in 2008, and CP, RT, SM, moldboard (MP, and subsoiler (SUB in 2009, with and without sugarcane residues relative to no-till (NT in the sugarcane producing region of Brazil. Soil CO2-C emissions were measured daily for two weeks after tillage using portable soil respiration systems. Daily CO2-C emissions declined after tillage regardless of tillage system. In 2008, total CO2-C from SOC and/or residue decomposition was greater for RT and lowest for CP. In 2009, emission was greatest for MP and CP with residues, and smallest for NT. SOC and residue contributed 47 % and 41 %, respectively, to total CO2-C emissions. Regarding the estimated emissions from sugarcane residue and SOC decomposition within the measurement period, CO2-C factor was similar to sugarcane residue and soil organic carbon decomposition, depending on the tillage system applied. Our approach may define new emission factors that are associated to tillage operations on bare or sugarcane-residue-covered soils to estimate the total carbon loss.

Model of the complex of Parathyroid hormone-2 receptor and Tuberoinfundibular peptide of 39 residues

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Persson Bengt

2010-10-01

Full Text Available Abstract Background We aim to propose interactions between the parathyroid hormone-2 receptor (PTH2R and its ligand the tuberoinfundibular peptide of 39 residues (TIP39 by constructing a homology model of their complex. The two related peptides parathyroid hormone (PTH and parathyroid hormone related protein (PTHrP are compared with the complex to examine their interactions. Findings In the model, the hydrophobic N-terminus of TIP39 is buried in a hydrophobic part of the central cavity between helices 3 and 7. Comparison of the peptide sequences indicates that the main discriminator between the agonistic peptides TIP39 and PTH and the inactive PTHrP is a tryptophan-phenylalanine replacement. The model indicates that the smaller phenylalanine in PTHrP does not completely occupy the binding site of the larger tryptophan residue in the other peptides. As only TIP39 causes internalisation of the receptor and the primary difference being an aspartic acid in position 7 of TIP39 that interacts with histidine 396 in the receptor, versus isoleucine/histidine residues in the related hormones, this might be a trigger interaction for the events that cause internalisation. Conclusions A model is constructed for the complex and a trigger interaction for full agonistic activation between aspartic acid 7 of TIP39 and histidine 396 in the receptor is proposed.

Measurement properties and usability of non-contact scanners for measuring transtibial residual limb volume.

Science.gov (United States)

Kofman, Rianne; Beekman, Anna M; Emmelot, Cornelis H; Geertzen, Jan H B; Dijkstra, Pieter U

2018-06-01

Non-contact scanners may have potential for measurement of residual limb volume. Different non-contact scanners have been introduced during the last decades. Reliability and usability (practicality and user friendliness) should be assessed before introducing these systems in clinical practice. The aim of this study was to analyze the measurement properties and usability of four non-contact scanners (TT Design, Omega Scanner, BioSculptor Bioscanner, and Rodin4D Scanner). Quasi experimental. Nine (geometric and residual limb) models were measured on two occasions, each consisting of two sessions, thus in total 4 sessions. In each session, four observers used the four systems for volume measurement. Mean for each model, repeatability coefficients for each system, variance components, and their two-way interactions of measurement conditions were calculated. User satisfaction was evaluated with the Post-Study System Usability Questionnaire. Systematic differences between the systems were found in volume measurements. Most of the variances were explained by the model (97%), while error variance was 3%. Measurement system and the interaction between system and model explained 44% of the error variance. Repeatability coefficient of the systems ranged from 0.101 (Omega Scanner) to 0.131 L (Rodin4D). Differences in Post-Study System Usability Questionnaire scores between the systems were small and not significant. The systems were reliable in determining residual limb volume. Measurement systems and the interaction between system and residual limb model explained most of the error variances. The differences in repeatability coefficient and usability between the four CAD/CAM systems were small. Clinical relevance If accurate measurements of residual limb volume are required (in case of research), modern non-contact scanners should be taken in consideration nowadays.

Contribution from the interaction Hamiltonian to the expectation value of particle number with the non-equilibrium quantum field theory

International Nuclear Information System (INIS)

Hotta, Ryuuichi; Morozumi, Takuya; Takata, Hiroyuki

2012-01-01

We develop the method analyzing particle number non-conserving phenomena with non-equilibrium quantum field-theory. In this study, we consider a CP violating model with interaction Hamiltonian that breaks particle number conservation. To derive the quantum Boltzmann equation for the particle number, we solve Schwinger-Dyson equation, which are obtained from two particle irreducible closed-time-path (2PI CTP) effective action. In this calculation, we show the contribution from interaction Hamiltonian to the time evolution of expectation value of particle number.

Crystal Structure of the Extended-Spectrum β-Lactamase PER-2 and Insights into the Role of Specific Residues in the Interaction with β-Lactams and β-Lactamase Inhibitors

Science.gov (United States)

Ruggiero, Melina; Kerff, Frédéric; Herman, Raphaël; Sapunaric, Frédéric; Galleni, Moreno; Gutkind, Gabriel; Charlier, Paulette; Sauvage, Eric

2014-01-01

PER-2 belongs to a small (7 members to date) group of extended-spectrum β-lactamases. It has 88% amino acid identity with PER-1 and both display high catalytic efficiencies toward most β-lactams. In this study, we determined the X-ray structure of PER-2 at 2.20 Å and evaluated the possible role of several residues in the structure and activity toward β-lactams and mechanism-based inhibitors. PER-2 is defined by the presence of a singular trans bond between residues 166 to 167, which generates an inverted Ω loop, an expanded fold of this domain that results in a wide active site cavity that allows for efficient hydrolysis of antibiotics like the oxyimino-cephalosporins, and a series of exclusive interactions between residues not frequently involved in the stabilization of the active site in other class A β-lactamases. PER β-lactamases might be included within a cluster of evolutionarily related enzymes harboring the conserved residues Asp136 and Asn179. Other signature residues that define these enzymes seem to be Gln69, Arg220, Thr237, and probably Arg/Lys240A (“A” indicates an insertion according to Ambler's scheme for residue numbering in PER β-lactamases), with structurally important roles in the stabilization of the active site and proper orientation of catalytic water molecules, among others. We propose, supported by simulated models of PER-2 in combination with different β-lactams, the presence of a hydrogen-bond network connecting Ser70-Gln69-water-Thr237-Arg220 that might be important for the proper activity and inhibition of the enzyme. Therefore, we expect that mutations occurring in these positions will have impacts on the overall hydrolytic behavior. PMID:25070104

Effect of washing on pesticide residues in olives.

Science.gov (United States)

Guardia-Rubio, M; Ayora-Cañada, M J; Ruiz-Medina, A

2007-03-01

The present work aims at contributing to the knowledge of the fate of 5 pesticides in olives in order to evaluate how washing may affect the presence of these residues in this fruit (and consequently in olive oil). For this purpose, olives were sprayed with commercial formulations containing the active ingredients and a series of analyses were performed for 64 d by using gas chromatography with mass spectrometric detection. Selected pesticides, ranked by their importance, were diuron, terbuthylazine, simazine, alpha-endosulfan, and beta-endosulfan. The pesticide fraction, which was not removable from olives by washing, increased with time after treatment until their degradation started at week 6. Washing performed 1 d after treatment was the most effective in reducing residues, especially for simazine. Consequently, the washing step performed in olive mills could be effective in removing those herbicide residues present in olives as a consequence of contact with contaminated soil for a short time. This happens when olives are dropped and harvested off the ground by means of brushes or suction equipment.

Molecular dissection of the interaction between the SH3 domain and the SH2-Kinase Linker region in PTK6.

Science.gov (United States)

Kim, Han Ie; Jung, Jinwon; Lee, Eun-Saem; Kim, Yong-Chul; Lee, Weontae; Lee, Seung-Taek

2007-11-03

PTK6 (also known as Brk) is an intracellular tyrosine kinase that contains SH3, SH2, and tyrosine kinase catalytic (Kinase) domains. The SH3 domain of PTK6 interacts with the N-terminal half of the linker (Linker) region between the SH2 and Kinase domains. Site-directed mutagenesis and surface plasmon resonance studies showed that a tryptophan residue (Trp44) in the SH3 domain and proline residues in the Linker region, in the order of Pro177, Pro175, and Pro179, contribute to the interaction. The three-dimensional modeled structure of the SH3-Linker complex was in agreement with the biochemical data. Disruption of the intramolecular interaction between the SH3 domain and the Linker region by mutation of Trp44, Pro175, Pro177, and Pro179 markedly increased the catalytic activity of PTK6 in HEK 293 cells. These results demonstrate that Trp44 in the SH3 domain and Pro177, Pro175, and Pro179 in the N-terminal half of the Linker region play important roles in the SH3-Linker interaction to maintain the protein in an inactive conformation along with the phosphorylated Tyr447-SH2 interaction.

A study on the production of agricultural residues in Italy

Energy Technology Data Exchange (ETDEWEB)

Di Blasi, C.; Tanzi, V.; Lanzetta, M. [Universita degli Studi di Napoli Federico II, Dip di Ingegneria Chimica, Napoli (Italy)

1997-12-01

The Italian production of agricultural residues has been evaluated with a view to energy recovery through gasification. Two main categories of residues have been identified: the first, (A) is associated with the growing and collection of products with a nutritional value, whereas the second (B) includes the residues associated with the subsequent processing in order to obtain final products for commercialization. Category A, which comprises three further sub-categories: straw (A1); woody residues (A2); and stems and leaves (residues from vegetables, tobacco, sugar beet, (A3)), results in about 16.5 mt yr. The average amount of straw (A1) is 11 mt/yr, of which about 60% is waste to be eliminated. Woody residues (A2) (mainly pruning off-cuts from vineyards and olive groves) are about 3.5 mt/yr (85% unused). Category A3 amounts to about 2 mt/yr (90% unused). Straw is available mainly in the northern part of the country, whereas the other two sub-categories are widely distributed in central and southern regions. The yields of category B are estimated at 4 mt/yr, of which more than 3 mt/yr are waste products from grape and olive processing. Other residues, such as rice, sunflower and soya-bean husks (about 0.65 mt/yr), almond and nut shells and fruit stones (about 0.2 mt/yr), although not widely available on a national scale, can be significant on a local basis. The total amount of unused agricultural residues is about 14.5 mt/yr, which, if completely exploited through gasification, can contribute as much as 7-10% to the current national electricity needs. The regions of Veneto, Puglia, Friuli, Lombardia and Emilia Romagna appear to be good candidates for electricity production, given the significant surface concentration of unused residues (105-55 t km{sup 2}). (author)

Comparative modeling and docking studies of p16ink4/Cyclin D1/Rb pathway genes in lung cancer revealed functionally interactive residue of RB1 and its functional partner E2F1

Directory of Open Access Journals (Sweden)

e Zahra Syeda Naqsh

2013-01-01

Full Text Available Abstract Background Lung cancer is the major cause of mortality worldwide. Major signalling pathways that could play significant role in lung cancer therapy include (1 Growth promoting pathways (Epidermal Growth Factor Receptor/Ras/ PhosphatidylInositol 3-Kinase (2 Growth inhibitory pathways (p53/Rb/P14ARF, STK11 (3 Apoptotic pathways (Bcl-2/Bax/Fas/FasL. Insilico strategy was implemented to solve the mystery behind selected lung cancer pathway by applying comparative modeling and molecular docking studies. Results YASARA [v 12.4.1] was utilized to predict structural models of P16-INK4 and RB1 genes using template 4ELJ-A and 1MX6-B respectively. WHAT CHECK evaluation tool demonstrated overall quality of predicted P16-INK4 and RB1 with Z-score of −0.132 and −0.007 respectively which showed a strong indication of reliable structure prediction. Protein-protein interactions were explored by utilizing STRING server, illustrated that CDK4 and E2F1 showed strong interaction with P16-INK4 and RB1 based on confidence score of 0.999 and 0.999 respectively. In order to facilitate a comprehensive understanding of the complex interactions between candidate genes with their functional interactors, GRAMM-X server was used. Protein-protein docking investigation of P16-INK4 revealed four ionic bonds illustrating Arg47, Arg80,Cys72 and Met1 residues as actively participating in interactions with CDK4 while docking results of RB1 showed four hydrogen bonds involving Glu864, Ser567, Asp36 and Arg861 residues which interact strongly with its respective functional interactor E2F1. Conclusion This research may provide a basis for understanding biological insights of P16-INK4 and RB1 proteins which will be helpful in future to design a suitable drug to inhibit the disease pathogenesis as we have determined the interacting amino acids which can be targeted in order to design a ligand in-vitro to propose a drug for clinical trials. Protein -protein docking of

Interactions of a didomain fragment of the Drosophila Sex-lethal protein with single-stranded uridine-rich oligoribonucleotides derived from the transformer and Sex-lethal messenger RNA precursors: NMR with residue-selective [5-2H]uridine substitutions

International Nuclear Information System (INIS)

Kim, Insil; Muto, Yutaka; Watanabe, Satoru; Kitamura, Aya; Futamura, Yasuhiro; Yokoyama, Shigeyuki; Hosono, Kazumi; Kawai, Gota; Takaku, Hiroshi; Dohmae, Naoshi; Takio, Koji; Sakamoto, Hiroshi; Shimura, Yoshiro

2000-01-01

Proteins that contain two or more copies of the RNA-binding domain [ribonucleoprotein (RNP) domain or RNA recognition motif (RRM)] are considered to be involved in the recognition of single-stranded RNA, but the mechanisms of this recognition are poorly understood at the molecular level. For an NMR analysis of a single-stranded RNA complexed with a multi-RBD protein, residue-selective stable-isotope labeling techniques are necessary, rather than common assignment methods based on the secondary structure of RNA. In the present study, we analyzed the interaction of a Drosophila Sex-lethal (Sxl) protein fragment, consisting of two RBDs (RBD1-RBD2), with two distinct target RNAs derived from the tra and Sxl mRNA precursors with guanosine and adenosine, respectively, in a position near the 5'-terminus of a uridine stretch. First, we prepared a [5- 2 H]uridine phosphoramidite, and synthesized a series of 2 H-labeled RNAs, in which all of the uridine residues except one were replaced by [5- 2 H]uridine in the target sequence, GU 8 C. By observing the H5-H6 TOCSY cross peaks of the series of 2 H-labeled RNAs complexed with the Sxl RBD1-RBD2, all of the base H5-H6 proton resonances of the target RNA were unambiguously assigned. Then, the H5-H6 cross peaks of other target RNAs, GU 2 GU 8 , AU 8 , and UAU 8 , were assigned by comparison with those of GU 8 C. We found that the uridine residue prior to the G or A residue is essential for proper interaction with the protein, and that the interaction is tighter for A than for G. Moreover, the H1' resonance assignments were achieved from the H5-H6 assignments. The results revealed that all of the protein-bound nucleotide residues, except for only two, are in the unusual C2'-endo ribose conformation in the complex

Interactions of a didomain fragment of the Drosophila Sex-lethal protein with single-stranded uridine-rich oligoribonucleotides derived from the transformer and Sex-lethal messenger RNA precursors: NMR with residue-selective [5-2H]uridine substitutions

Energy Technology Data Exchange (ETDEWEB)

Kim, Insil; Muto, Yutaka; Watanabe, Satoru; Kitamura, Aya; Futamura, Yasuhiro; Yokoyama, Shigeyuki [University of Tokyo, Department of Biophysics and Biochemistry, Graduate School of Science (Japan); Hosono, Kazumi; Kawai, Gota; Takaku, Hiroshi [Chiba Institute of Technology, Department of Industrial Chemistry (Japan); Dohmae, Naoshi; Takio, Koji [Institute of Physical and Chemical Research (RIKEN) (Japan); Sakamoto, Hiroshi [Kobe University, Department of Biology, Faculty of Science (Japan); Shimura, Yoshiro [Biomolecular Engineering Research Institute (Japan)

2000-06-15

Proteins that contain two or more copies of the RNA-binding domain [ribonucleoprotein (RNP) domain or RNA recognition motif (RRM)] are considered to be involved in the recognition of single-stranded RNA, but the mechanisms of this recognition are poorly understood at the molecular level. For an NMR analysis of a single-stranded RNA complexed with a multi-RBD protein, residue-selective stable-isotope labeling techniques are necessary, rather than common assignment methods based on the secondary structure of RNA. In the present study, we analyzed the interaction of a Drosophila Sex-lethal (Sxl) protein fragment, consisting of two RBDs (RBD1-RBD2), with two distinct target RNAs derived from the tra and Sxl mRNA precursors with guanosine and adenosine, respectively, in a position near the 5'-terminus of a uridine stretch. First, we prepared a [5-{sup 2}H]uridine phosphoramidite, and synthesized a series of {sup 2}H-labeled RNAs, in which all of the uridine residues except one were replaced by [5-{sup 2}H]uridine in the target sequence, GU{sub 8}C. By observing the H5-H6 TOCSY cross peaks of the series of {sup 2}H-labeled RNAs complexed with the Sxl RBD1-RBD2, all of the base H5-H6 proton resonances of the target RNA were unambiguously assigned. Then, the H5-H6 cross peaks of other target RNAs, GU{sub 2}GU{sub 8}, AU{sub 8}, and UAU{sub 8}, were assigned by comparison with those of GU{sub 8}C. We found that the uridine residue prior to the G or A residue is essential for proper interaction with the protein, and that the interaction is tighter for A than for G. Moreover, the H1' resonance assignments were achieved from the H5-H6 assignments. The results revealed that all of the protein-bound nucleotide residues, except for only two, are in the unusual C2'-endo ribose conformation in the complex.

Characterization of conserved arginine residues on Cdt1 that affect licensing activity and interaction with Geminin or Mcm complex.

Science.gov (United States)

You, Zhiying; Ode, Koji L; Shindo, Mayumi; Takisawa, Haruhiko; Masai, Hisao

2016-05-02

All organisms ensure once and only once replication during S phase through a process called replication licensing. Cdt1 is a key component and crucial loading factor of Mcm complex, which is a central component for the eukaryotic replicative helicase. In higher eukaryotes, timely inhibition of Cdt1 by Geminin is essential to prevent rereplication. Here, we address the mechanism of DNA licensing using purified Cdt1, Mcm and Geminin proteins in combination with replication in Xenopus egg extracts. We mutagenized the 223th arginine of mouse Cdt1 (mCdt1) to cysteine or serine (R-S or R-C, respectively) and 342nd and 346th arginines constituting an arginine finger-like structure to alanine (RR-AA). The RR-AA mutant of Cdt1 could not only rescue the DNA replication activity in Cdt1-depleted extracts but also its specific activity for DNA replication and licensing was significantly increased compared to the wild-type protein. In contrast, the R223 mutants were partially defective in rescue of DNA replication and licensing. Biochemical analyses of these mutant Cdt1 proteins indicated that the RR-AA mutation disabled its functional interaction with Geminin, while R223 mutations resulted in ablation in interaction with the Mcm2∼7 complex. Intriguingly, the R223 mutants are more susceptible to the phosphorylation-induced inactivation or chromatin dissociation. Our results show that conserved arginine residues play critical roles in interaction with Geminin and Mcm that are crucial for proper conformation of the complexes and its licensing activity.

Consumption-based approach for assessing the contribution of hospitals towards the load of pharmaceutical residues in municipal wastewater.

Science.gov (United States)

Le Corre, Kristell S; Ort, Christoph; Kateley, Diana; Allen, Belinda; Escher, Beate I; Keller, Jurg

2012-09-15

Hospitals are considered as major sources of pharmaceutical residues discharged to municipal wastewater, but recent experimental studies showed that the contribution of hospitals to the loads of selected, quantifiable pharmaceuticals in sewage treatment plant (STP) influents was limited. However such conclusions are made based on the experimental analysis of pharmaceuticals in hospital wastewater which is hindered by a number of factors such as access to suitable sampling sites, difficulties in obtaining representative samples and availability of analytical methods. Therefore, this study explores a refined and extended consumption-based approach to predict the contribution of six selected Australian hospitals to the loads of 589 pharmaceuticals in municipal wastewater. In addition, the possibility that hospital-specific substances are present at levels that may pose a risk for human health was evaluated. For 63 to 84% of the pharmaceuticals investigated, the selected hospitals are not a major point source with individual contributions likely to be less than 15% which is in line with previous experimental studies. In contrast, between 10 and 20% of the pharmaceuticals consumed in the selected hospitals are exclusively used in these hospitals. For these hospital-specific substances, 57 distinct pharmaceuticals may cause concerns for human health as concentrations predicted in hospital effluents are less than 100-fold lower than effect thresholds. However, when concentrations were predicted in the influent of the corresponding STP, only 12 compounds (including the antineoplastic vincristine, the antibiotics tazobactam and piperacillin) remain in concentration close to effect thresholds, but further decrease is expected after removal in STP, dilution in the receiving stream and drinking water treatment. The results of this study suggest that risks of human exposure to the pharmaceuticals exclusively administered in the investigated hospitals are limited and

Residual fMRI sensitivity for identity changes in acquired prosopagnosia.

Science.gov (United States)

Fox, Christopher J; Iaria, Giuseppe; Duchaine, Bradley C; Barton, Jason J S

2013-01-01

While a network of cortical regions contribute to face processing, the lesions in acquired prosopagnosia are highly variable, and likely result in different combinations of spared and affected regions of this network. To assess the residual functional sensitivities of spared regions in prosopagnosia, we designed a rapid event-related functional magnetic resonance imaging (fMRI) experiment that included pairs of faces with same or different identities and same or different expressions. By measuring the release from adaptation to these facial changes we determined the residual sensitivity of face-selective regions-of-interest. We tested three patients with acquired prosopagnosia, and all three of these patients demonstrated residual sensitivity for facial identity changes in surviving fusiform and occipital face areas of either the right or left hemisphere, but not in the right posterior superior temporal sulcus. The patients also showed some residual capabilities for facial discrimination with normal performance on the Benton Facial Recognition Test, but impaired performance on more complex tasks of facial discrimination. We conclude that fMRI can demonstrate residual processing of facial identity in acquired prosopagnosia, that this adaptation can occur in the same structures that show similar processing in healthy subjects, and further, that this adaptation may be related to behavioral indices of face perception.

Residual fMRI sensitivity for identity changes in acquired prosopagnosia

Directory of Open Access Journals (Sweden)

Christopher J Fox

2013-10-01

Full Text Available While a network of cortical regions contribute to face processing, the lesions in acquired prosopagnosia are highly variable, and likely result in different combinations of spared and affected regions of this network. To assess the residual functional sensitivities of spared regions in prosopagnosia, we designed a rapid event-related functional magnetic resonance imaging (fMRI experiment that included pairs of faces with same or different identities and same or different expressions. By measuring the release from adaptation to these facial changes we determined the residual sensitivity of face-selective regions-of-interest. We tested three patients with acquired prosopagnosia, and all three of these patients demonstrated residual sensitivity for facial identity changes in surviving fusiform and occipital face areas of either the right or left hemisphere, but not in the right posterior superior temporal sulcus. The patients also showed some residual capabilities for facial discrimination with normal performance on the Benton Facial Recognition Test, but impaired performance on more complex tasks of facial discrimination. We conclude that fMRI can demonstrate residual processing of facial identity in acquired prosopagnosia, that this adaptation can occur in the same structures that show similar processing in healthy subjects, and further, that this adaptation may be related to behavioral indices of face perception.

Anaerobia Treatments of the domestic residual waters. Limitations potentialities

International Nuclear Information System (INIS)

Giraldo Gomez, Eugenio

1993-01-01

The quick growth of the Latin American cities has prevented that an appropriate covering of public services is achieved for the whole population, One of the undesirable consequences of this situation is the indiscriminate discharge from the domestic and industrial residual waters to the nearest bodies of water with its consequent deterioration and with disastrous consequences about the ecology and the public health. The developed countries have controlled this situation using systems of purification of the residual waters previously to their discharge in the receptor source. The same as the technology of the evacuation of the served waters, they have become numerous efforts for the application of the purification systems used in the countries developed to the socioeconomic, climatic and cultural conditions of our means. One of the results obtained in these efforts is the economic inability of the municipalities to pay the high investment costs and of operation of the traditional systems for the treatment of the residual waters. Contrary to another type of public services, the treatment of the residual waters needs of appropriate technological solutions for the Climatic and socioeconomic means of the developing countries, One of the technological alternatives for the purification of the residual waters that has had a great development in the last decades has been that of the biological treatments in t anaerobia ambient. The objective of this contribution is to present, to author's trial, the limitations and potentialities of this technology type with special emphasis in the case of the domestic residual waters

1H and 31P nuclear magnetic resonance investigation of the interaction between 2,3-diphosphoglycerate and human normal adult hemoglobin.

Science.gov (United States)

Russu, I M; Wu, S S; Bupp, K A; Ho, N T; Ho, C

1990-04-17

High-resolution 1H and 31P nuclear magnetic resonance spectroscopy has been used to investigate the binding of 2,3-diphosphoglycerate to human normal adult hemoglobin and the molecular interactions involved in the allosteric effect of the 2,3-diphosphoglycerate molecule on hemoglobin. Individual hydrogen ion NMR titration curves have been obtained for 22-26 histidyl residues of hemoglobin and for each phosphate group of 2,3-diphosphoglycerate with hemoglobin in both the deoxy and carbonmonoxy forms. The results indicate that 2,3-diphosphoglycerate binds to deoxyhemoglobin at the central cavity between the two beta chains and the binding involves the beta 2-histidyl residues. Moreover, the results suggest that the binding site of 2,3-diphosphoglycerate to carbonmonoxyhemoglobin contains the same (or at least some of the same) amino acid residues responsible for binding in the deoxy form. As a result of the specific interactions with 2,3-diphosphoglycerate, the beta 2-histidyl residues make a significant contribution to the alkaline Bohr effect under these experimental conditions (up to 0.5 proton/Hb tetramer). 2,3-Diphosphoglycerate also affects the individual hydrogen ion equilibria of several histidyl residues located away from the binding site on the surface of the hemoglobin molecule, and, possibly, in the heme pockets. These results give the first experimental demonstration that long-range electrostatic and/or conformational effects of the binding could play an important role in the allosteric effect of 2,3-diphosphoglycerate on hemoglobin.(ABSTRACT TRUNCATED AT 250 WORDS)

The Shigella flexneri OmpA amino acid residues 188EVQ190 are essential for the interaction with the virulence factor PhoN2.

Science.gov (United States)

Scribano, Daniela; Damico, Rosanna; Ambrosi, Cecilia; Superti, Fabiana; Marazzato, Massimiliano; Conte, Maria Pia; Longhi, Catia; Palamara, Anna Teresa; Zagaglia, Carlo; Nicoletti, Mauro

2016-12-01

Shigella flexneri is an intracellular pathogen that deploys an arsenal of virulence factors promoting host cell invasion, intracellular multiplication and intra- and inter-cellular dissemination. We have previously reported that the interaction between apyrase (PhoN2), a periplasmic ATP-diphosphohydrolase, and the C-terminal domain of the outer membrane (OM) protein OmpA is likely required for proper IcsA exposition at the old bacterial pole and thus for full virulence expression of Shigella flexneri (Scribano et al., 2014). OmpA, that is the major OM protein of Gram-negative bacteria, is a multifaceted protein that plays many different roles both in the OM structural integrity and in the virulence of several pathogens. Here, by using yeast two-hybrid technology and by constructing an in silico 3D model of OmpA from S. flexneri 5a strain M90T, we observed that the OmpA residues 188 EVQ 190 are likely essential for PhoN2-OmpA interaction. The 188 EVQ 190 amino acids are located within a flexible region of the OmpA protein that could represent a scaffold for protein-protein interaction.

Structural and interaction parameters of thermosensitive native α-elastin biohybrid microgel

Science.gov (United States)

Balaceanu, Andreea; Singh, Smriti; Demco, Dan E.; Möller, Martin

2014-09-01

The structural and water interaction parameters for native, α-elastin biohybrid microgel crosslinked with hydrophilic and hydrophobic crosslinkers are obtained from the volume phase transition temperature behaviour, 1H high-resolution magic-angle sample spinning transverse magnetization relaxation NMR, and modified Flory-Rehner swelling theory. Firstly, considering a homogeneous morphology the number of subchains in the biohybrid microgel, the residual water in deswollen state as a function of crosslink density and the temperature dependence of the Flory biopolymer-water interaction parameters are reported for the biohybrid microgels prepared with hydrophilic (PEG-DGE) and hydrophobic (BS3) crosslinkers. The Flory-Rehner classical approach is subsequently modified taking into account the heterogeneities observed by NMR transverse relaxation measurements. Two differently mobile regions are determined, a hydrophobic domain and a crosslinking domain with relative reduced mobility. For the first time, the influence of chain mobility on the Flory interaction parameter is investigated through a modified Flory state equation. The contributions of amino-acids located in the hydrophobic and crosslinking domains in the polypeptide sequence are separated while analyzing the biopolymer-water interaction.

Initial contents of residue quality parameters predict effects of larger soil fauna on decomposition of contrasting quality residues

Directory of Open Access Journals (Sweden)

Ratikorn Sanghaw

2017-10-01

Full Text Available A 52-week decomposition study employing the soil larger fauna exclusion technique through litter bags of two mesh sizes (20 and 0.135 mm was conducted in a long-term (18 yr field experiment. Organic residues of contrasting quality of N, lignin (L, polyphenols (PP and cellulose (CL all in grams per kilogram: rice straw (RS: 4.5N, 22.2L, 3.9PP, 449CL, groundnut stover (GN: 21.2N, 71.4L, 8.1PP, 361CL, dipterocarp leaf litter (DP: 5.1N, 303L, 68.9PP, 271CL and tamarind leaf litter (TM: 11.6N, 190L, 27.7PP, 212CL were applied to soil annually to assess and predict soil larger fauna effects (LFE on decomposition based on the initial contents of the residue chemical constituents. Mass losses in all residues were not different under soil fauna inclusion and exclusion treatments during the early stage (up to week 4 after residue incorporation but became significantly higher under the inclusion than the exclusion treatments during the later stage (week 8 onwards. LFE were highest (2–51% under the resistant DP at most decomposition stages. During the early stage (weeks 1–4, both the initial contents of labile (N and CL and recalcitrant C, and recalcitrant C interaction with labile constituents of residues showed significant correlations (r = 0.64–0.90 with LFE. In the middle stage (week 16, LFE under resistant DP and TM had significant positive correlations with L, L + PP and L/CL. They were also affected by these quality parameters as shown by the multiple regression analysis. In the later stages (weeks 26–52, the L/CL ratio was the most prominent quality parameter affecting LFE. Keywords: Mesofauna and macrofauna, Microorganisms, Recalcitrant and labile compounds, Residue chemical composition, Tropical sandy soil

Spring Chinook Salmon Interactions Indices and Residual/Precocial Monitoring in the Upper Yakima Basin; Yakima/Klickitat Fisheries Project Monitoring and Evaluation Report 5 of 7, 2003-2004 Annual Report.

Energy Technology Data Exchange (ETDEWEB)

Pearsons, Todd N.; Johnson, Christopher L.; James, Brenda B. (Washington Department of Fish and Wildlife, Olympia, WA)

2004-05-01

This report examines some of the factors that can influence the success of supplementation, which is currently being tested in the Yakima Basin using upper Yakima stock of spring chinook salmon. Supplementation success in the Yakima Basin is defined relative to four topic areas: natural production, genetics, ecological interactions, and harvest (Busack et al. 1997). The success of spring chinook salmon supplementation in the Yakima Basin is dependent, in part, upon fish culture practices and favorable physical and biological conditions in the natural environment (Busack et al. 1997; James et al. 1999; Pearsons et al., 2003). Shortfalls in either of these two topics (i.e., failure in culturing many fish that have high long-term fitness or environmental conditions that constrain spring chinook salmon production) will cause supplementation success to be limited. For example, inadvertent selection or propagation of spring chinook that residualize or precocially mature may hinder supplementation success. Spring chinook salmon that residualize (do not migrate during the normal migration period) may have lower survival rates than migrants and, additionally, may interact with wild fish and cause unacceptable impacts to non-target taxa. Large numbers of precocials (nonanadromous spawners) may increase competition for females and significantly skew ratios of offspring sired by nonanadromous males, which could result in more nonanadromous spring chinook in future generations. Conditions in the natural environment may also limit the success of spring chinook supplementation. For example, intra or interspecific competition may constrain spring chinook salmon production. Spring chinook salmon juveniles may compete with each other for food or space or compete with other species that have similar ecological requirements. Monitoring of spring chinook salmon residuals, precocials, prey abundance, carrying capacity, and competition will help researchers interpret why supplementation

Identification of residues on human receptor DPP4 critical for MERS-CoV binding and entry

Energy Technology Data Exchange (ETDEWEB)

Song, Wenfei [Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084 (China); Wang, Ying [Comprehensive AIDS Research Center, Research Center for Public Health, School of Medicine, Tsinghua University, Beijing 100084 (China); Wang, Nianshuang; Wang, Dongli [Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084 (China); Guo, Jianying; Fu, Lili [Comprehensive AIDS Research Center, Research Center for Public Health, School of Medicine, Tsinghua University, Beijing 100084 (China); Shi, Xuanling, E-mail: shixuanlingsk@tsinghua.edu.cn [Comprehensive AIDS Research Center, Research Center for Public Health, School of Medicine, Tsinghua University, Beijing 100084 (China)

2014-12-15

Middle East respiratory syndrome coronavirus (MERS-CoV) infects host cells through binding the receptor binding domain (RBD) on its spike glycoprotein to human receptor dipeptidyl peptidase 4 (hDPP4). Here, we report identification of critical residues on hDPP4 for RBD binding and virus entry through analysis of a panel of hDPP4 mutants. Based on the RBD–hDPP4 crystal structure we reported, the mutated residues were located at the interface between RBD and hDPP4, which potentially changed the polarity, hydrophobic or hydrophilic properties of hDPP4, thereby interfering or disrupting their interaction with RBD. Using surface plasmon resonance (SPR) binding analysis and pseudovirus infection assay, we showed that several residues in hDPP4–RBD binding interface were important on hDPP4–RBD binding and viral entry. These results provide atomic insights into the features of interactions between hDPP4 and MERS-CoV RBD, and also provide potential explanation for cellular and species tropism of MERS-CoV infection. - Highlights: • It has been demonstrated that MERS-CoV infects host cells through binding its envelope spike (S) glycoprotein to the host cellular receptor dipeptidyl peptidase 4 (DPP4). • To identify the critical residues on hDPP4 for RBD binding and virus entry, we constructed a panel of hDPP4 mutants based on structure-guided mutagenesis. • Using surface plasmon resonance (SPR) binding analysis and pseudovirus infection assay, we showed that several residues on hDPP4 had significant impacts on virus/receptor interactions and viral entry. • Our study has provided new insights into the features of interactions between hDPP4 and MERS-CoV RBD, and provides potential explanation for cellular and species tropism of MERS-CoV infection.

Interfacial Tryptophan Residues: A Role for the Cation-{pi} Effect?

DEFF Research Database (Denmark)

Petersen, Frederic Nicolas Rønne; Jensen, Morten Ø.; Helix Nielsen, Claus

2005-01-01

Integral membrane proteins are characterized by having a preference for aromatic residues, e.g., tryptophan (W), at the interface between the lipid bilayer core and the aqueous phase. The reason for this is not clear, but it seems that the preference is related to a complex interplay between steric...... between the nitrogen moiety of lipid molecule headgroups and the pi-electron distribution of gramicidin (gA) tryptophan residues (W(9), W(11), W(13), and W(15)) using molecular dynamics (MD) simulations of gA embedded in two hydrated lipid bilayers composed of 1-palmitoyl-2-oleoylphosphatidylethanolamine....... Our criteria for cation-pi interactions are based on distance and angular requirements, and the results from our model suggest that cation-pi interactions are relevant for W(PE)(11), W(PE)(13), W(PE)(15), and, to some extent, W(PC)(11) and W(PC)(13). In our model, W(9)does not seem to engage in cation...

Chaperone-like activity of β-casein and its effect on residual in vitro activity of horseradish peroxidase

DEFF Research Database (Denmark)

Sulewska, Anna Maria; Olsen, Karsten; Sørensen, Jens Christian

2014-01-01

, as similar experiment with bovine serum albumin resulted in residual activity of horseradish peroxidase that was significantly lower than without any addition. The effect of β-casein on HRP disappears when pH is below the isoelectric point of β-casein. It was also proven by light scattering studies that β...... proteins. Incubating HRP (0.1 mg mL-1) for 10 min at 72 °C resulted in residual activity of 59 ± 5%, while addition of 1 mg mL-1 β-casein resulted in increase in residual activity up to 85 ± 1%. Increased residual activity is not merely attributed to an effect of higher total protein concentration......-casein interacts with horseradish peroxidase when the temperature was increased from 25 to 70 °C whereas interactions seem to cease when temperature was lowered back to 25 °C. This study highlights how specific proteins can influence enzyme activity, which is of potential importance for various industries...

The interaction of fatigue cracks with a residual stress field using thermoelastic stress analysis and synchrotron X-ray diffraction experiments

Science.gov (United States)

Amjad, Khurram; Asquith, David; Sebastian, Christopher M.; Wang, Wei-Chung

2017-01-01

This article presents an experimental study on the fatigue behaviour of cracks emanating from cold-expanded holes utilizing thermoelastic stress analysis (TSA) and synchrotron X-ray diffraction (SXRD) techniques with the aim of resolving the long-standing ambiguity in the literature regarding potential relaxation, or modification, of beneficial compressive residual stresses as a result of fatigue crack propagation. The crack growth rates are found to be substantially lower as the crack tip moved through the residual stress zone induced by cold expansion. The TSA results demonstrated that the crack tip plastic zones were reduced in size by the presence of the residual compressive stresses induced by cold expansion. The crack tip plastic zones were found to be insignificant in size in comparison to the residual stress zone resulting from cold expansion, which implied that they were unlikely to have had a notable impact on the surrounding residual stresses induced by cold expansion. The residual stress distributions measured along the direction of crack growth, using SXRD, showed no signs of any significant stress relaxation or redistribution, which validates the conclusions drawn from the TSA data. Fractographic analysis qualitatively confirmed the influence on crack initiation of the residual stresses induced by the cold expansion. It was found that the application of single compressive overload caused a relaxation, or reduction in the residual stresses, which has wider implications for improving the fatigue life. PMID:29291095

Development of residual stress analysis procedure for fitness-for-service assessment of welded structure

International Nuclear Information System (INIS)

Kim, Jong Sung; Jin, Tae Eun; Dong, P.; Prager, M.

2003-01-01

In this study, a state of art review of existing residual stress analysis techniques and representative solutions is presented in order to develop the residual stress analysis procedure for Fitness-For-Service(FFS) assessment of welded structure. Critical issues associated with existing residual stress solutions and their treatments in performing FFS are discussed. It should be recognized that detailed residual stress evolution is an extremely complicated phenomenon that typically involves material-specific thermomechanical/metallurgical response, welding process physics, and structural interactions within a component being welded. As a result, computational procedures can vary significantly from highly complicated numerical techniques intended only to elucidate a small part of the process physics to cost-effective procedures that are deemed adequate for capturing some of the important features in a final residual stress distribution. Residual stress analysis procedure for FFS purposes belongs to the latter category. With this in mind, both residual stress analysis techniques and their adequacy for FFS are assessed based on both literature data and analyses performed in this investigation

Nitrogen mineralization from selected 15N-labelled crop residues and humus as affected by inorganic nitrogen

International Nuclear Information System (INIS)

Santos, J.A.

1987-01-01

The use of cover crops or crop residues as a source of N to succeeding crops has become a matter of increasing importance for economic and environmental reason. Greenhouse and field studies were conducted to determine the N contribution of four 15 N labelled crop residues, rye (Secale cereale L.), wheat (Triticum aestivum L.), crimson clover (Trifolium encarnatum L.), and hairy vetch (Vicia sativa L.), to successive crops and to evaluate the effect of different organic (ON) and inorganic N (IN) combinations on mineralization of the above residues. Total 15 N recovery from the residues ranged from 51% to 85% and 4% to 74% for the greenhouse and field studies, respectively

An Evaluation Method for Activation Analysis using Pre-evaluated Contribution of Nuclides with Impurity

Energy Technology Data Exchange (ETDEWEB)

Woo, Myeong Hyeon; Kim, Song Hyun; Kim, Do Hyun; Shin, Chang Ho [Hanyang University, Seoul (Korea, Republic of); Kim, Gee Suck [KAERI, Daejeon (Korea, Republic of)

2016-05-15

Nuclides in radiation facilities become unstable from nuclear reaction. It emits residual radiation to be stable. Some unstable nuclides remain after operation in the material. It continuously emits the radiation, which has a harmful effect to worker when they try maintenance and plant decommissioning. It is known that residual radiation from impurity occupies a large portion of the radiation dose. If impurity concentration is higher than expectation, the effects of residual radiation could be underestimated. Therefore, estimation of residual radiation is repeatedly calculated according to impurity concentration. In this study, an approach estimating the activation was proposed using pre-evaluated nuclide's contribution to reduce the calculation time and effort of worker. In this study, in order to reduce the calculation time and effort of worker, activation analysis method based on pre-evaluated nuclide contribution was proposed. This method was verified using concreate activation problem, which is located in nuclear power plant. The results show that our proposed method has good agreement with Bateman equation.

InterProSurf: a web server for predicting interacting sites on protein surfaces

Science.gov (United States)

Negi, Surendra S.; Schein, Catherine H.; Oezguen, Numan; Power, Trevor D.; Braun, Werner

2009-01-01

Summary A new web server, InterProSurf, predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex. The prediction method is based on solvent accessible surface area of residues in the isolated subunits, a propensity scale for interface residues and a clustering algorithm to identify surface regions with residues of high interface propensities. Here we illustrate the application of InterProSurf to determine which areas of Bacillus anthracis toxins and measles virus hemagglutinin protein interact with their respective cell surface receptors. The computationally predicted regions overlap with those regions previously identified as interface regions by sequence analysis and mutagenesis experiments. PMID:17933856

A survey of residual analysis and a new test of residual trend.

Science.gov (United States)

McDowell, J J; Calvin, Olivia L; Klapes, Bryan

2016-05-01

A survey of residual analysis in behavior-analytic research reveals that existing methods are problematic in one way or another. A new test for residual trends is proposed that avoids the problematic features of the existing methods. It entails fitting cubic polynomials to sets of residuals and comparing their effect sizes to those that would be expected if the sets of residuals were random. To this end, sampling distributions of effect sizes for fits of a cubic polynomial to random data were obtained by generating sets of random standardized residuals of various sizes, n. A cubic polynomial was then fitted to each set of residuals and its effect size was calculated. This yielded a sampling distribution of effect sizes for each n. To test for a residual trend in experimental data, the median effect size of cubic-polynomial fits to sets of experimental residuals can be compared to the median of the corresponding sampling distribution of effect sizes for random residuals using a sign test. An example from the literature, which entailed comparing mathematical and computational models of continuous choice, is used to illustrate the utility of the test. © 2016 Society for the Experimental Analysis of Behavior.

Experimental determination and theoretical analysis of local residual stress at grain scale

NARCIS (Netherlands)

Basu, Indranil; Ocelík, Václav; De Hosson, Jeff Th M.

2017-01-01

Grain/phase boundaries contribute significantly to build up of residual stresses, owing to varied plastic/thermal response of different grain orientations or phases during thermomechanical treatment. Hence, accurate quantification of such local scale stress gradients in commercial components is

Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis

Science.gov (United States)

Singer, M. S.; Oliveira, L.; Vriend, G.; Shepherd, G. M.

1995-01-01

A family of G-protein-coupled receptors is believed to mediate the recognition of odor molecules. In order to identify potential ligand-binding residues, we have applied correlated mutation analysis to receptor sequences from the rat. This method identifies pairs of sequence positions where residues remain conserved or mutate in tandem, thereby suggesting structural or functional importance. The analysis supported molecular modeling studies in suggesting several residues in positions that were consistent with ligand-binding function. Two of these positions, dominated by histidine residues, may play important roles in ligand binding and could confer broad specificity to mammalian odor receptors. The presence of positive (overdominant) selection at some of the identified positions provides additional evidence for roles in ligand binding. Higher-order groups of correlated residues were also observed. Each group may interact with an individual ligand determinant, and combinations of these groups may provide a multi-dimensional mechanism for receptor diversity.

CONTRIBUTION OF QUADRATIC RESIDUE DIFFUSERS TO EFFICIENCY OF TILTED PROFILE PARALLEL HIGHWAY NOISE BARRIERS

Directory of Open Access Journals (Sweden)

M. R. Monazzam ، P. Nassiri

2009-10-01

Full Text Available This paper presents the results of an investigation on the acoustic performance of tilted profile parallel barriers with quadratic residue diffuser (QRD tops and faces. A 2D boundary element method (BEM is used to predict the barrier insertion loss. The results of rigid and with absorptive coverage are also calculated for comparisons. Using QRD on the top surface and faces of all tilted profile parallel barrier models introduced here is found to improve the efficiency of barriers compared with rigid equivalent parallel barrier at the examined receiver positions. Applying a QRD with frequency design of 400 Hz on 5 degrees tilted parallel barrier improves the overall performance of its equivalent rigid barrier by 1.8 dB(A. Increase in the treated surfaces with reactive elements shifts the effective performance toward lower frequencies. It is found that by tilting the barriers from 0 to 10 degrees in parallel set up, the degradation effects in parallel barriers is reduced but the absorption effect of fibrous materials and also diffusivity of the quadratic residue diffuser is reduced significantly. In this case all the designed barriers have better performance with 10 degrees tilting in parallel set up. The most economic traffic noise parallel barrier which produces significantly high performance, is achieved by covering the top surface of the barrier closed to the receiver by just a QRD with frequency design of 400 Hz and tilting angle of 10 degrees. The average A-weighted insertion loss in this barrier is predicted to be 16.3 dB (A.

Functional validation of Ca2+-binding residues from the crystal structure of the BK ion channel.

Science.gov (United States)

Kshatri, Aravind S; Gonzalez-Hernandez, Alberto J; Giraldez, Teresa

2018-04-01

BK channels are dually regulated by voltage and Ca 2+ , providing a cellular mechanism to couple electrical and chemical signalling. Intracellular Ca 2+ concentration is sensed by a large cytoplasmic region in the channel known as "gating ring", which is formed by four tandems of regulator of conductance for K + (RCK1 and RCK2) domains. The recent crystal structure of the full-length BK channel from Aplysia californica has provided new information about the residues involved in Ca 2+ coordination at the high-affinity binding sites located in the RCK1 and RCK2 domains, as well as their cooperativity. Some of these residues have not been previously studied in the human BK channel. In this work we have investigated, through site directed mutagenesis and electrophysiology, the effects of these residues on channel activation by voltage and Ca 2+ . Our results demonstrate that the side chains of two non-conserved residues proposed to coordinate Ca 2+ in the A. californica structure (G523 and E591) have no apparent functional role in the human BK Ca 2+ sensing mechanism. Consistent with the crystal structure, our data indicate that in the human channel the conserved residue R514 participates in Ca 2+ coordination in the RCK1 binding site. Additionally, this study provides functional evidence indicating that R514 also interacts with residues E902 and Y904 connected to the Ca 2+ binding site in RCK2. Interestingly, it has been proposed that this interaction may constitute a structural correlate underlying the cooperative interactions between the two high-affinity Ca 2+ binding sites regulating the Ca 2+ dependent gating of the BK channel. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

Interactions between charged residues in the transmembrane segments of the voltage-sensing domain in the hERG channel.

Science.gov (United States)

Zhang, M; Liu, J; Jiang, M; Wu, D-M; Sonawane, K; Guy, H R; Tseng, G-N

2005-10-01

Studies on voltage-gated K channels such as Shaker have shown that positive charges in the voltage-sensor (S4) can form salt bridges with negative charges in the surrounding transmembrane segments in a state-dependent manner, and different charge pairings can stabilize the channels in closed or open states. The goal of this study is to identify such charge interactions in the hERG channel. This knowledge can provide constraints on the spatial relationship among transmembrane segments in the channel's voltage-sensing domain, which are necessary for modeling its structure. We first study the effects of reversing S4's positive charges on channel activation. Reversing positive charges at the outer (K525D) and inner (K538D) ends of S4 markedly accelerates hERG activation, whereas reversing the 4 positive charges in between either has no effect or slows activation. We then use the 'mutant cycle analysis' to test whether D456 (outer end of S2) and D411 (inner end of S1) can pair with K525 and K538, respectively. Other positive charges predicted to be able, or unable, to interact with D456 or D411 are also included in the analysis. The results are consistent with predictions based on the distribution of these charged residues, and confirm that there is functional coupling between D456 and K525 and between D411 and K538.

Complex T Cell Interactions Contribute to Helicobacter pylori Gastritis in Mice

Science.gov (United States)

Gray, Brian M.; Fontaine, Clinton A.; Poe, Sara A.

2013-01-01

Disease due to the gastric pathogen Helicobacter pylori varies in severity from asymptomatic to peptic ulcer disease and cancer. Accumulating evidence suggests that one source of this variation is an abnormal host response. The goal of this study was to use a mouse model of H. pylori gastritis to investigate the roles of regulatory T cells (Treg) as well as proinflammatory T cells (Th1 and Th17) in gastritis, gastric T cell engraftment, and gastric cytokine production. Our results support published data indicating that severe gastritis in T cell recipient mice is due to failure of Treg engraftment, that Treg ameliorate gastritis, and that the proinflammatory response is attributable to interactions between several cell subsets and cytokines. We confirmed that gamma interferon (IFN-γ) is essential for induction of gastritis but showed that IFN-γ-producing CD4 T cells are not necessary. Interleukin 17A (IL-17A) also contributed to gastritis, but to a lesser extent than IFN-γ. Tumor necrosis factor alpha (TNF-α) and IL-17F were also elevated in association with disease. These results indicate that while H. pylori-specific CD4+ T cells and IFN-γ are both essential for induction of gastritis due to H. pylori, IFN-γ production by T cells is not essential. It is likely that other proinflammatory cytokines, such as IL-17F and TNF-α, shown to be elevated in this model, also contribute to the induction of disease. We suggest that gastritis due to H. pylori is associated with loss of immunoregulation and alteration of several cytokines and cell subsets and cannot be attributed to a single immune pathway. PMID:23264048

Novel approaches to determining residual stresses by ultramicroindentation techniques: Application to sandblasted austenitic stainless steel

International Nuclear Information System (INIS)

Frutos, E.; Multigner, M.; Gonzalez-Carrasco, J.L.

2010-01-01

This research addresses the determination of residual stresses in sandblasted austenitic steel by ultramicroindentation techniques using a sharp indenter, of which the sensitivity to residual stress effects is said to be inferior to that of spherical ones. The introduction of an angular correction in the model of Wang et al. which relates variations in the maximum load to the presence of residual stresses is proposed. Similarly, the contribution to the hardness of grain size refinement and work hardening, developed as a consequence of the severe plastic deformation during blasting, is determined in order to avoid overestimation of the residual stresses. Measurements were performed on polished cross sections along a length of several microns, thus obtaining a profile of the residual stresses. Results show good agreement with those obtained by synchrotron radiation on the same specimens, which validates the method and demonstrates that microindentation using sharp indenters may be sensitive to the residual stress effect.

Novel approaches to determining residual stresses by ultramicroindentation techniques: Application to sandblasted austenitic stainless steel

Energy Technology Data Exchange (ETDEWEB)

Frutos, E. [Centro de Bioingenieria, Biomateriales y Nanomedicina, CIBER-BBN, Instituto de Salud Carlos III (Spain)] [Centro Nacional de Investigaciones Metalurgicas, CENIM-CSIC, 28040 Madrid (Spain); Multigner, M. [Centro Nacional de Investigaciones Metalurgicas, CENIM-CSIC, 28040 Madrid (Spain)] [Centro de Bioingenieria, Biomateriales y Nanomedicina, CIBER-BBN, Instituto de Salud Carlos III (Spain); Gonzalez-Carrasco, J.L., E-mail: jlg@cenim.csic.es [Centro Nacional de Investigaciones Metalurgicas, CENIM-CSIC, 28040 Madrid (Spain)] [Centro de Bioingenieria, Biomateriales y Nanomedicina, CIBER-BBN, Instituto de Salud Carlos III (Spain)

2010-07-15

This research addresses the determination of residual stresses in sandblasted austenitic steel by ultramicroindentation techniques using a sharp indenter, of which the sensitivity to residual stress effects is said to be inferior to that of spherical ones. The introduction of an angular correction in the model of Wang et al. which relates variations in the maximum load to the presence of residual stresses is proposed. Similarly, the contribution to the hardness of grain size refinement and work hardening, developed as a consequence of the severe plastic deformation during blasting, is determined in order to avoid overestimation of the residual stresses. Measurements were performed on polished cross sections along a length of several microns, thus obtaining a profile of the residual stresses. Results show good agreement with those obtained by synchrotron radiation on the same specimens, which validates the method and demonstrates that microindentation using sharp indenters may be sensitive to the residual stress effect.

Safety aspects of targets for ADTT: Activity, volatile products, residual heat release

International Nuclear Information System (INIS)

Gai, E.V.; Ignatyuk, A.V.; Lunev, V.P.; Shubin, Yu.N.

1999-01-01

Safety aspects of heavy metal liquid targets for the accelerator driven systems connected with the activity accumulation and residual energy release due to the irradiation with high energy proton beam are discussed. The results obtained for the lead-bismuth target that are under construction in IPPE now in the frame of ISTC Project No. 559 are briefly presented. The calculations and the analysis of the accumulation of the spallation reaction products, activity and energy release at various moments after the accelerator shutdown are presented. The concentrations of the reaction products, the total and partial activities, the activities of volatile products are determined. The contributions of the short-lived nuclides important for the prediction of the facility behaviour in regimes with the accelerator beam trips. The calculations and analysis of the residual energy release due to different decay type have been performed. The conclusions are as follows. The obtained results showed that long lived radioactivity accumulates mainly due to primary nuclear reactions. Secondary reactions are responsible for the production of small number of long-lived isotopes Bi-207, Po-210 and some others, being generated by radiative capture of low energy neutrons. It is possible to make a conclusion that neutrons in the energy range 20 - 800 MeV and protons with energy above 100 MeV give main contribution to the total activity generation although these parts of spectra inside the target give comparatively small contribution to the total flux. The correct consideration of short-lived nuclides contribution is the main problem in the analysis of the target behaviour in the case of short accelerator shutdowns. They make the determining contribution to the both activity and the heat release at the first moments after the accelerator shutdown, creating the intermediate links and additional channels for the long-lived nuclides accumulation chains. The strong dependence of calculated

Treatment and processing of residues of fermentation; Behandlung und Verwertung von Gaerrueckstaenden

Energy Technology Data Exchange (ETDEWEB)

Doehler, H.; Schliebner, P. [Kuratorium fuer Technik und Bauwesen in der Landwirtschaft (KTBL), Darmstadt (Germany)

2007-07-01

With the transformation of the EEG (Renewable Energy Resources Act), the number of biogas plants increased rapidly. Additionally, an enlargement of the performance of the plants and a regional concentration process take place. Recently, processing routes for liquid manure will be considered in order to reduce problems of the surplus of nutrients as well as the costs of the transport of the water-rich residues of fermentation. Under this aspect, the authors of the contribution under consideration report on procedures for the processing of residues of fermentation as well as costs and utilization of these procedures. By the example of an agrarian society, four procedures for the output and processing of residues of fermentation are compared with one another regarding to expenditure of work time, investments and economy: Output of residues of fermentation, treatment of residues of fermentation by separation, processing of residues of fermentation by means of diaphragm technology, processing of residues of fermentation by means of evaporation technology. The processing routes reduce the residues of fermentation by 60 %. Thus, the costs of output and the necessary storage capacities for residues of fermentation are reduced. Presently, no savings regarding to work completion by the processing of the residues of fermentation can be obtained. The specific total costs of the investigated procedures are between 2.64 Euro/m{sup 3} according to the procedure with separation and to 8.64 Euro/m{sup 3} according to the diaphragm processing route. An enhanced demand of investment does not cause compellingly the highest specific total costs of the procedures. In comparison to the output of residues of fermentation, the examined procedures for the processing of residues of fermentation do not result in economical and ergonomic advantages. The high costs of investment and operating cost of the processing of residues of fermentation cannot be compensated by the reduced costs of output

The role and effect of residual stress on pore generation during anodization of aluminium thin films

International Nuclear Information System (INIS)

Liao, M.W.; Chung, C.K.

2013-01-01

Highlights: •Al films of varying residual stress were prepared by sputtering. •Variation of the residual stress in the Al films influences pore growth during anodization. •The change in average pore size with residual stress is fairly small. •Interaction of residual stress with oxide growth stress leads to change in structure. •Residual tensile stress increases the pore density of porous alumina. -- Abstract: The role and effect of residual stress on pore generation of anodized aluminium oxide (AAO) have been investigated into anodizing the various-residual-stresses aluminium films. The plane stresses were characterised by X-ray diffraction with sin 2 ψ method. The pore density roughly linearly increased with residual stress from 64.6 (−132.5 MPa) to 90.5 pores/μm 2 (135.9 MPa). However, the average pore size around 40 nm was not changed significantly except for the rougher film. The tensile residual stress lessened the compressive oxide growth stress to reduce AAO plastic deformation for higher pore density. The findings provide new foundations for realizing AAO films on silicon

KFC Server: interactive forecasting of protein interaction hot spots.

Science.gov (United States)

Darnell, Steven J; LeGault, Laura; Mitchell, Julie C

2008-07-01

The KFC Server is a web-based implementation of the KFC (Knowledge-based FADE and Contacts) model-a machine learning approach for the prediction of binding hot spots, or the subset of residues that account for most of a protein interface's; binding free energy. The server facilitates the automated analysis of a user submitted protein-protein or protein-DNA interface and the visualization of its hot spot predictions. For each residue in the interface, the KFC Server characterizes its local structural environment, compares that environment to the environments of experimentally determined hot spots and predicts if the interface residue is a hot spot. After the computational analysis, the user can visualize the results using an interactive job viewer able to quickly highlight predicted hot spots and surrounding structural features within the protein structure. The KFC Server is accessible at http://kfc.mitchell-lab.org.

Prevalence, Predictors and Clinical Outcome of Residual Pulmonary Hypertension Following Tricuspid Annuloplasty.

Science.gov (United States)

Chen, Yan; Liu, Ju-Hua; Chan, Daniel; Sit, Ko-Yung; Wong, Chun-Ka; Ho, Kar-Lai; Ho, Lai-Ming; Zhen, Zhe; Lam, Yui-Ming; Lau, Chu-Pak; Au, Wing-Kok; Tse, Hung-Fat; Yiu, Kai-Hang

2016-07-22

Tricuspid annuloplasty is increasingly performed during left heart valve surgery, but the long-term clinical outcome postoperatively is not satisfactory. The aim of this study was to determine whether residual pulmonary hypertension (PHT) contributes to the adverse outcome. One-hundred thirty-seven patients (age 61±11 years; men, 30%) who underwent tricuspid annuloplasty during left-side valve surgery were enrolled. The mean pulmonary artery systolic pressure before surgery was 49±13 mm Hg and 32±15 mm Hg following surgery. Patients were divided into 3 groups according to postoperative pulmonary artery systolic pressure: no residual PHT (n=78, 57%), mild residual PHT (n=43, 31%), or significant residual PHT (n=16, 12%). A preoperative larger right ventricular (RV) geometry and tricuspid valve tethering area were associated with mild or significant residual PHT. A total of 24 adverse events (20 heart failures and 4 cardiovascular deaths) occurred during a median follow-up of 25 months. Kaplan-Meier survival curve demonstrated that patients with significant residual PHT had the highest percentage of adverse events followed by those with mild residual PHT. Patients with no residual PHT had a very low risk of adverse events. Multivariable Cox regression analysis revealed that both mild (hazard ratio=4.94; 95% CI =1.34-18.16; P=0.02) and significant residual PHT (hazard ratio=8.67; 95% CI =2.43-30.98; P<0.01) were independent factors associated with adverse events. The present study demonstrated that 43% of patients who underwent tricuspid annuloplasty had residual PHT. The presence of mild or significant residual PHT was associated with adverse events in these patients. © 2016 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

Interaction study of rice stripe virus proteins reveals a region of the nucleocapsid protein (NP) required for NP self-interaction and nuclear localization.

Science.gov (United States)

Lian, Sen; Cho, Won Kyong; Jo, Yeonhwa; Kim, Sang-Min; Kim, Kook-Hyung

2014-04-01

Rice stripe virus (RSV), which belongs to the genus Tenuivirus, is an emergent virus problem. The RSV genome is composed of four single-strand RNAs (RNA1-RNA4) and encodes seven proteins. We investigated interactions between six of the RSV proteins by yeast-two hybrid (Y2H) assay in vitro and by bimolecular fluorescence complementation (BiFC) in planta. Y2H identified self-interaction of the nucleocapsid protein (NP) and NS3, while BiFC revealed self-interaction of NP, NS3, and NCP. To identify regions(s) and/or crucial amino acid (aa) residues required for NP self-interaction, we generated various truncated and aa substitution mutants. Y2H assay showed that the N-terminal region of NP (aa 1-56) is necessary for NP self-interaction. Further analysis with substitution mutants demonstrated that additional aa residues located at 42-47 affected their interaction with full-length NP. These results indicate that the N-terminal region (aa 1-36 and 42-47) is required for NP self-interaction. BiFC and co-localization studies showed that the region required for NP self-interaction is also required for NP localization at the nucleus. Overall, our results indicate that the N-terminal region (aa 1-47) of the NP is important for NP self-interaction and that six aa residues (42-47) are essential for both NP self-interaction and nuclear localization. Copyright © 2014 Elsevier B.V. All rights reserved.

A unified momentum equation approach for computing thermal residual stresses during melting and solidification

Science.gov (United States)

Yeo, Haram; Ki, Hyungson

2018-03-01

In this article, we present a novel numerical method for computing thermal residual stresses from a viewpoint of fluid-structure interaction (FSI). In a thermal processing of a material, residual stresses are developed as the material undergoes melting and solidification, and liquid, solid, and a mixture of liquid and solid (or mushy state) coexist and interact with each other during the process. In order to accurately account for the stress development during phase changes, we derived a unified momentum equation from the momentum equations of incompressible fluids and elastoplastic solids. In this approach, the whole fluid-structure system is treated as a single continuum, and the interaction between fluid and solid phases across the mushy zone is naturally taken into account in a monolithic way. For thermal analysis, an enthalpy-based method was employed. As a numerical example, a two-dimensional laser heating problem was considered, where a carbon steel sheet was heated by a Gaussian laser beam. Momentum and energy equations were discretized on a uniform Cartesian grid in a finite volume framework, and temperature-dependent material properties were used. The austenite-martensite phase transformation of carbon steel was also considered. In this study, the effects of solid strains, fluid flow, mushy zone size, and laser heating time on residual stress formation were investigated.

Three cysteine residues of SLC52A1, a receptor for the porcine endogenous retrovirus-A (PERV-A), play a critical role in cell surface expression and infectivity.

Science.gov (United States)

Colon-Moran, Winston; Argaw, Takele; Wilson, Carolyn A

2017-07-01

Porcine endogenous retrovirus-A (PERV-A), a gammaretrovirus, infects human cells in vitro, thus raising the potential risk of cross-species transmission in xenotransplantation. Two members of the solute carrier family 52 (SLC52A1 and SLC52A2) are PERV-A receptors. Site-directed mutagenesis of the cDNA encoding SLC52A1 identified that only one of two putative glycosylation signals is occupied by glycans. In addition, we showed that glycosylation of SLC52A1 is not necessary for PERV-A receptor function. We also identified that at a minimum, three cysteine residues are sufficient for SLC52A1 cell surface expression. Mutation of cysteine at position 365 and either of the two cysteine residues in the C-terminal tail at positions 442 or 446 reduced SLC52A1 surface expression and PERV-A infection suggesting that these residues may contribute to overall structural stability and receptor function. Understanding interactions between PERV-A and its cellular receptor may provide novel strategies to prevent zoonotic infection in the setting of xenotransplantation. Published by Elsevier Inc.

Effect of inorganic chelate of zinc and restaurant residual oil added ...

African Journals Online (AJOL)

Effect of inorganic chelate of zinc and restaurant residual oil added to feed mixture ... The interaction effects of RRO and ZnO did not result to a significant change in ... Therefore, the effects of RRO deteriorated the quality of meat by raising the ...

Effect of subseabed salt domes on Tidal Residual currents in the Persian Gulf

Science.gov (United States)

Mashayekh Poul, Hossein; Backhaus, Jan; Dehghani, Ali; Huebner, Udo

2016-05-01

Geological studies in the Persian Gulf (PG) have revealed the existence of subseabed salt-domes. With suitable filtering of a high-resolution PG seabed topography, it is seen that the domes leave their signature in the seabed, i.e., numerous hills and valleys with amplitudes of several tens of meters and radii from a few up to tens of kilometers. It was suspected that the "shark skin" of the PG seabed may affect the tidal residual flow. The interaction of tidal dynamics and these obstacles was investigated in a nonlinear hydrodynamic numerical tidal model of the PG. The model was first used to characterize flow patterns of residual currents generated by a tidal wave passing over symmetric, elongated and tilted obstacles. Thereafter it was applied to the entire PG. The model was forced at its open boundary by the four dominant tidal constituents residing in the PG. Each tidal constituent was simulated separately. Results, i.e., tidal residual currents in the PG, as depicted by Lagrangian trajectories reveal a stationary flow that is very rich in eddies. Each eddy can be identified with a topographic obstacle. This confirms that the tidal residual flow field is strongly influenced by the nonlinear interaction of the tidal wave with the bottom relief which, in turn, is deformed by salt-domes beneath the seabed. Different areas of maximum residual current velocities are identified for major tidal constituents. The pattern of trajectories indicates the presence of two main cyclonic gyres and several adjacent gyres rotating in opposite directions and a strong coastal current in the northern PG.

Vision restoration after brain and retina damage: the "residual vision activation theory".

Science.gov (United States)

Sabel, Bernhard A; Henrich-Noack, Petra; Fedorov, Anton; Gall, Carolin

2011-01-01

Vision loss after retinal or cerebral visual injury (CVI) was long considered to be irreversible. However, there is considerable potential for vision restoration and recovery even in adulthood. Here, we propose the "residual vision activation theory" of how visual functions can be reactivated and restored. CVI is usually not complete, but some structures are typically spared by the damage. They include (i) areas of partial damage at the visual field border, (ii) "islands" of surviving tissue inside the blind field, (iii) extrastriate pathways unaffected by the damage, and (iv) downstream, higher-level neuronal networks. However, residual structures have a triple handicap to be fully functional: (i) fewer neurons, (ii) lack of sufficient attentional resources because of the dominant intact hemisphere caused by excitation/inhibition dysbalance, and (iii) disturbance in their temporal processing. Because of this resulting activation loss, residual structures are unable to contribute much to everyday vision, and their "non-use" further impairs synaptic strength. However, residual structures can be reactivated by engaging them in repetitive stimulation by different means: (i) visual experience, (ii) visual training, or (iii) noninvasive electrical brain current stimulation. These methods lead to strengthening of synaptic transmission and synchronization of partially damaged structures (within-systems plasticity) and downstream neuronal networks (network plasticity). Just as in normal perceptual learning, synaptic plasticity can improve vision and lead to vision restoration. This can be induced at any time after the lesion, at all ages and in all types of visual field impairments after retinal or brain damage (stroke, neurotrauma, glaucoma, amblyopia, age-related macular degeneration). If and to what extent vision restoration can be achieved is a function of the amount of residual tissue and its activation state. However, sustained improvements require repetitive

Nonsensing residues in S3-S4 linker's C terminus affect the voltage sensor set point in K+ channels.

Science.gov (United States)

Carvalho-de-Souza, Joao L; Bezanilla, Francisco

2018-02-05

Voltage sensitivity in ion channels is a function of highly conserved arginine residues in their voltage-sensing domains (VSDs), but this conservation does not explain the diversity in voltage dependence among different K + channels. Here we study the non-voltage-sensing residues 353 to 361 in Shaker K + channels and find that residues 358 and 361 strongly modulate the voltage dependence of the channel. We mutate these two residues into all possible remaining amino acids (AAs) and obtain Q-V and G-V curves. We introduced the nonconducting W434F mutation to record sensing currents in all mutants except L361R, which requires K + depletion because it is affected by W434F. By fitting Q-Vs with a sequential three-state model for two voltage dependence-related parameters ( V 0 , the voltage-dependent transition from the resting to intermediate state and V 1 , from the latter to the active state) and G-Vs with a two-state model for the voltage dependence of the pore domain parameter ( V 1/2 ), Spearman's coefficients denoting variable relationships with hydrophobicity, available area, length, width, and volume of the AAs in 358 and 361 positions could be calculated. We find that mutations in residue 358 shift Q-Vs and G-Vs along the voltage axis by affecting V 0 , V 1 , and V 1/2 according to the hydrophobicity of the AA. Mutations in residue 361 also shift both curves, but V 0 is affected by the hydrophobicity of the AA in position 361, whereas V 1 and V 1/2 are affected by size-related AA indices. Small-to-tiny AAs have opposite effects on V 1 and V 1/2 in position 358 compared with 361. We hypothesize possible coordination points in the protein that residues 358 and 361 would temporarily and differently interact with in an intermediate state of VSD activation. Our data contribute to the accumulating knowledge of voltage-dependent ion channel activation by adding functional information about the effects of so-called non-voltage-sensing residues on VSD dynamics. © 2018

Structural characteristics of an antigen required for its interaction with Ia and recognition by T cells

DEFF Research Database (Denmark)

Sette, A; Buus, S; Colon, S

1987-01-01

A detailed analysis of the residues within an immunogenic peptide that endow it with the capacity to interact with Ia and to be recognized by T cells is presented. Ia interacts with only a few of the peptide residues and overall exhibits a very broad specificity. Some residues appear to interact...... both with Ia and with T cells, leading to a model in which a peptide antigen is 'sandwiched' between Ia and the T-cell receptor....

Evaluation of residue-residue contact predictions in CASP9

KAUST Repository

Monastyrskyy, Bohdan; Fidelis, Krzysztof; Tramontano, Anna; Kryshtafovych, Andriy

2011-01-01

This work presents the results of the assessment of the intramolecular residue-residue contact predictions submitted to CASP9. The methodology for the assessment does not differ from that used in previous CASPs, with two basic evaluation measures

Thermogravimetric study of the pyrolysis of biomass residues from tomato processing industry

Energy Technology Data Exchange (ETDEWEB)

Mangut, V.; Sabio, E.; Ganan, J.; Gonzalez, J.F.; Ramiro, A.; Gonzalez, C.M.; Roman, S.; Al-Kassir, A. [Department of Chemical and Energy Engineering, University of Extremadura, Avda. de Elvas s/n, 06071 Badajoz (Spain)

2006-01-15

There is an increasing concern with the environmental problems associated with the increasing CO{sub 2}, NO{sub x} and SO{sub x} emissions resulting from the rising use of fossil fuels. Renewable energy, mainly biomass, can contribute to reduce the fossil fuels consumption. Biomass is a renewable resource with a widespread world distribution. Tomato processing industry produces a high amount of biomass residue (peel and seeds) that could be used for thermal energy and electricity. A characterization and thermogravimetric study has been carried out. The residue has a high HHV and volatile content, and a low ash, and S contents. A kinetic model has been developed based on the degradation of hemicellulose, cellulose, lignin and oil that describe the pyrolysis of peel, seeds and peel and seeds residues. (author)

Meditope-Fab interaction: threading the hole.

Science.gov (United States)

Bzymek, Krzysztof P; Ma, Yuelong; Avery, Kendra N; Horne, David A; Williams, John C

2017-12-01

Meditope, a cyclic 12-residue peptide, binds to a unique binding side between the light and heavy chains of the cetuximab Fab. In an effort to improve the affinity of the interaction, it was sought to extend the side chain of Arg8 in the meditope, a residue that is accessible from the other side of the meditope binding site, in order to increase the number of interactions. These modifications included an n-butyl and n-octyl extension as well as hydroxyl, amine and carboxyl substitutions. The atomic structures of the complexes and the binding kinetics for each modified meditope indicated that each extension threaded through the Fab `hole' and that the carboxyethylarginine substitution makes a favorable interaction with the Fab, increasing the half-life of the complex by threefold compared with the unmodified meditope. Taken together, these studies provide a basis for the design of additional modifications to enhance the overall affinity of this unique interaction.

Interaction of 18-residue peptides derived from amphipathic helical ...

Indian Academy of Sciences (India)

Madhsudhan

interaction of proteins and peptides with membranes (Segrest ... favour surface activity have been described by Eisenberg et ... amphipathicity and propensity for α-helical conformation ..... Membrane destabilisation occurs due to electrostatic.

Pyrolysis of olive residue/low density polyethylene mixture:Part I Thermogravimetric kinetics

Institute of Scientific and Technical Information of China (English)

无

2008-01-01

This paper demonstrates the thermal pyrolysis of olive residue, low density polyethylene (LDPE) and olive residue/LDPE mixture in an inert atmosphere of N2 using thermogravimetric analysis (TGA). Measurements were carried out in the temperature range 300K~973K at heating rates of 2K/min, 10K/min, 20K/min and 50K/min. Based on the results obtained, three temperature regimes were selected for studying the non-isothermal kinetics of olive residue/LDPE mixture. The first two were dominated by the olive residue pyrolysis, while the third was linked to the LDPE pyrolysis, which occurred at much higher temperatures. Discrepancies between the experimental and calculated TG/DTG profiles were considered as a measurement of the extent of interactions occurring on co-pyrolysis. The maximum degradation temperatures of each component in the mixture were higher than those the individual components;thus an increase in thermal stability was expected. The kinetic parameters associated with thermal degradation were determined using Friedman isoconversional method.

The heparin/heparan sulfate sequence that interacts with cyclophilin B contains a 3-O-sulfated N-unsubstituted glucosamine residue.

Science.gov (United States)

Vanpouille, Christophe; Deligny, Audrey; Delehedde, Maryse; Denys, Agnès; Melchior, Aurélie; Liénard, Xavier; Lyon, Malcolm; Mazurier, Joël; Fernig, David G; Allain, Fabrice

2007-08-17

Many of the biological functions of heparan sulfate (HS) proteoglycans can be attributed to specialized structures within HS moieties, which are thought to modulate binding and function of various effector proteins. Cyclophilin B (CyPB), which was initially identified as a cyclosporin A-binding protein, triggers migration and integrin-mediated adhesion of peripheral blood T lymphocytes by a mechanism dependent on interaction with cell surface HS. Here we determined the structural features of HS that are responsible for the specific binding of CyPB. In addition to the involvement of 2-O,6-O, and N-sulfate groups, we also demonstrated that binding of CyPB was dependent on the presence of N-unsubstituted glucosamine residues (GlcNH2), which have been reported to be precursors for sulfation by 3-O-sulfotransferases-3 (3-OST-3). Interestingly, 3-OST-3B isoform was found to be the main 3-OST isoenzyme expressed in peripheral blood T lymphocytes and Jurkat T cells. Moreover, down-regulation of the expression of 3-OST-3 by RNA interference potently reduced CyPB binding and consequent activation of p44/42 mitogen-activated protein kinases. Altogether, our results strongly support the hypothesis that 3-O-sulfation of GlcNH2 residues could be a key modification that provides specialized HS structures for CyPB binding to responsive cells. Given that 3-O-sulfation of GlcNH2-containing HS by 3-OST-3 also provides binding sites for glycoprotein gD of herpes simplex virus type I, these findings suggest an intriguing structural linkage between the HS sequences involved in CyPB binding and viral infection.

Residual transpiration as a component of salinity stress tolerance mechanism: a case study for barley.

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Hasanuzzaman, Md; Davies, Noel W; Shabala, Lana; Zhou, Meixue; Brodribb, Tim J; Shabala, Sergey

2017-06-19

While most water loss from leaf surfaces occurs via stomata, part of this loss also occurs through the leaf cuticle, even when the stomata are fully closed. This component, termed residual transpiration, dominates during the night and also becomes critical under stress conditions such as drought or salinity. Reducing residual transpiration might therefore be a potentially useful mechanism for improving plant performance when water availability is reduced (e.g. under saline or drought stress conditions). One way of reducing residual transpiration may be via increased accumulation of waxes on the surface of leaf. Residual transpiration and wax constituents may vary with leaf age and position as well as between genotypes. This study used barley genotypes contrasting in salinity stress tolerance to evaluate the contribution of residual transpiration to the overall salt tolerance, and also investigated what role cuticular waxes play in this process. Leaves of three different positions (old, intermediate and young) were used. Our results show that residual transpiration was higher in old leaves than the young flag leaves, correlated negatively with the osmolality, and was positively associated with the osmotic and leaf water potentials. Salt tolerant varieties transpired more water than the sensitive variety under normal growth conditions. Cuticular waxes on barley leaves were dominated by primary alcohols (84.7-86.9%) and also included aldehydes (8.90-10.1%), n-alkanes (1.31-1.77%), benzoate esters (0.44-0.52%), phytol related compounds (0.22-0.53%), fatty acid methyl esters (0.14-0.33%), β-diketones (0.07-0.23%) and alkylresorcinols (1.65-3.58%). A significant negative correlation was found between residual transpiration and total wax content, and residual transpiration correlated significantly with the amount of primary alcohols. Both leaf osmolality and the amount of total cuticular wax are involved in controlling cuticular water loss from barley leaves under well

The maximum possible stress intensity factor for a crack in an unknown residual stress field

International Nuclear Information System (INIS)

Coules, H.E.; Smith, D.J.

2015-01-01

Residual and thermal stress fields in engineering components can act on cracks and structural flaws, promoting or inhibiting fracture. However, these stresses are limited in magnitude by the ability of materials to sustain them elastically. As a consequence, the stress intensity factor which can be applied to a given defect by a self-equilibrating stress field is also limited. We propose a simple weight function method for determining the maximum stress intensity factor which can occur for a given crack or defect in a one-dimensional self-equilibrating stress field, i.e. an upper bound for the residual stress contribution to K I . This can be used for analysing structures containing defects and subject to residual stress without any information about the actual stress field which exists in the structure being analysed. A number of examples are given, including long radial cracks and fully-circumferential cracks in thick-walled hollow cylinders containing self-equilibrating stresses. - Highlights: • An upper limit to the contribution of residual stress to stress intensity factor. • The maximum K I for self-equilibrating stresses in several geometries is calculated. • A weight function method can determine this maximum for 1-dimensional stress fields. • Simple MATLAB scripts for calculating maximum K I provided as supplementary material.

Residual distribution for general time-dependent conservation laws

International Nuclear Information System (INIS)

Ricchiuto, Mario; Csik, Arpad; Deconinck, Herman

2005-01-01

We consider the second-order accurate numerical solution of general time-dependent hyperbolic conservation laws over unstructured grids in the framework of the Residual Distribution method. In order to achieve full conservation of the linear, monotone and first-order space-time schemes of (Csik et al., 2003) and (Abgrall et al., 2000), we extend the conservative residual distribution (CRD) formulation of (Csik et al., 2002) to prismatic space-time elements. We then study the design of second-order accurate and monotone schemes via the nonlinear mapping of the local residuals of linear monotone schemes. We derive sufficient and necessary conditions for the well-posedness of the mapping. We prove that the schemes obtained with the CRD formulation satisfy these conditions by construction. Thus the nonlinear schemes proposed in this paper are always well defined. The performance of the linear and nonlinear schemes are evaluated on a series of test problems involving the solution of the Euler equations and of a two-phase flow model. We consider the resolution of strong shocks and complex interacting flow structures. The results demonstrate the robustness, accuracy and non-oscillatory character of the proposed schemes. d schemes

Residues of the UL25 Protein of Herpes Simplex Virus That Are Required for Its Stable Interaction with Capsids ▿

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Cockrell, Shelley K.; Huffman, Jamie B.; Toropova, Katerina; Conway, James F.; Homa, Fred L.

2011-01-01

The herpes simplex virus 1 (HSV-1) UL25 gene product is a minor capsid component that is required for encapsidation, but not cleavage, of replicated viral DNA. UL25 is located on the capsid surface in a proposed heterodimer with UL17, where five copies of the heterodimer are found at each of the capsid vertices. Previously, we demonstrated that amino acids 1 to 50 of UL25 are essential for its stable interaction with capsids. To further define the UL25 capsid binding domain, we generated recombinant viruses with either small truncations or amino acid substitutions in the UL25 N terminus. Studies of these mutants demonstrated that there are two important regions within the capsid binding domain. The first 27 amino acids are essential for capsid binding of UL25, while residues 26 to 39, which are highly conserved in the UL25 homologues of other alphaherpesviruses, were found to be critical for stable capsid binding. Cryo-electron microscopy reconstructions of capsids containing either a small tag on the N terminus of UL25 or the green fluorescent protein (GFP) fused between amino acids 50 and 51 of UL25 demonstrate that residues 1 to 27 of UL25 contact the hexon adjacent to the penton. A second region, most likely centered on amino acids 26 to 39, contacts the triplex that is one removed from the penton. Importantly, both of these UL25 capsid binding regions are essential for the stable packaging of full-length viral genomes. PMID:21411517

The role of CH/π interactions in the high affinity binding of streptavidin and biotin.

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Ozawa, Motoyasu; Ozawa, Tomonaga; Nishio, Motohiro; Ueda, Kazuyoshi

2017-08-01

The streptavidin-biotin complex has an extraordinarily high affinity (Ka: 10 15 mol -1 ) and contains one of the strongest non-covalent interactions known. This strong interaction is widely used in biological tools, including for affinity tags, detection, and immobilization of proteins. Although hydrogen bond networks and hydrophobic interactions have been proposed to explain this high affinity, the reasons for it remain poorly understood. Inspired by the deceased affinity of biotin observed for point mutations of streptavidin at tryptophan residues, we hypothesized that a CH/π interaction may also contribute to the strong interaction between streptavidin and biotin. CH/π interactions were explored and analyzed at the biotin-binding site and at the interface of the subunits by the fragment molecular orbital method (FMO) and extended applications: PIEDA and FMO4. The results show that CH/π interactions are involved in the high affinity for biotin at the binding site of streptavidin. We further suggest that the involvement of CH/π interactions at the subunit interfaces and an extended CH/π network play more critical roles in determining the high affinity, rather than involvement at the binding site. Copyright © 2017 Elsevier Inc. All rights reserved.

Foot-printing of Protein Interactions by Tritium Labeling

International Nuclear Information System (INIS)

Mousseau, Guillaume; Thomas, Olivier P.; Agez, Morgane; Thai, Robert; Cintrat, Jean-Christophe; Rousseau, Bernard; Raffy, Quentin; Renault, Jean Philippe; Pin, Serge; Ochsenbein, Francoise

2010-01-01

A new foot-printing method for mapping protein interactions has been developed, using tritium as a radioactive label. As residues involved in an interaction are less labeled when the complex is formed, they can be identified via comparison of the tritium incorporation of each residue of the bound protein with that of the unbound one. Application of this foot-printing method to the complex formed by the histone H3 fragment H3 122-135 and the protein hAsflA 1-156 afforded data in good agreement with NMR results. (authors)

On machine surface to the unit event causing residual stress

International Nuclear Information System (INIS)

Arunachalama, R.M.; Mannanb, M.A.; Spowageca, A.

2005-01-01

Integrity and reduce overall costs. Within the framework of surface integrity investigations, special emphasis is given to the measurement of residual stresses because they contribute directly to premature failure of components. Since the highest residual stresses are to be found in surface layers, these deserve special attention when dealing with dynamically, heavily loaded machine parts such as gas turbine components used in aero engines. Of the many techniques available for the measurement of residual stresses, the most highly developed and widely used non-destructive method is based on X-ray diffraction (XRD). However, it is not possible to use this technique for inspection of all the components, since it is time consuming, complicated as well as expensive. In this paper, a method is being proposed that augments the XRD method but at the same time capable of inspecting all the components. A non-destructive, visual inspection technique has been developed that can correlate the characteristic features on the surface to the unit event causing the residual stress and the type of residual stress generated on the machined surface. Pictures of the machined surfaces have been taken using a digital video microscope at a magnification of 500 and the surface feature correlated to the unit event causing the residual stress. Sharp and well defined long grooves indicate that the plastic deformation is dominated by a mechanical unit event while appearance of streaks and small areas of smeared material indicate that the plastic deformation is dominated by a thermal unit event. These trends have been confirmed by measuring the residual stresses using XRD. The proposed technique is an attempt at establishing a simple methodology that would be useful to industries manufacturing aerospace and other components that require good surface integrity. (Author)

Sugarcane field residue and bagasse allelopathic impact on vegetable seed germination

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The chemical interaction between plants, which is referred to as allelopathy, may result in the inhibition of plant growth and development. The objective of this research was to determine the allelopathic impact of sugarcane (Saccharum officinarum) var. ‘HoCP 96-540’ field residue and sugarcane baga...

Contribution of the study of a nuclear reactor accident: residual power aspects and thermodynamic of U-UO_2 and UO_2-ZrO_2 systems

International Nuclear Information System (INIS)

Baichi, Mehdi

2001-01-01

This work is a contribution to the study of early delocalization and fission product releases during the formation of corium coming from a nuclear reactor accident. The first part deals with an analysis of corium cooling. The contribution to the power of each corium element has been calculated with time. The main elements are represented but the addition of Pu, Mo and Nb has been proposed. The last release experimental data taken into account result in a loss of residual power of 25% exclusive of corium between the emergency stop and ten days. The second part deals with the early delocalization observed during Vercors experiments. A critical selection on the U-UO_2 and UO_2-ZrO_2 systems has been carried out. In order to complete the small and inconsistent data, thermodynamic activity measurements have been performed by mass spectrometry. The UO_2 activity on UO_2-ZrO_2 presents a positive deviation from ideality at 2200 K and approximates ideality at 2400 K. All the data have been used for optimizing the systems with Thermo-Calc. This work has allowed to calculate the ternary systems and to define the required approach to analyze the metallic phase and corium oxides densities. (author) [fr

Cover crops and crop residue management under no-till systems improve soils and environmental quality

Science.gov (United States)

Kumar, Sandeep; Wegner, Brianna; Vahyala, Ibrahim; Osborne, Shannon; Schumacher, Thomas; Lehman, Michael

2015-04-01

Crop residue harvest is a common practice in the Midwestern USA for the ethanol production. However, excessive removal of crop residues from the soil surface contributes to the degradation of important soil quality indicators such as soil organic carbon (SOC). Addition of a cover crop may help to mitigate these negative effects. The present study was set up to assess the impacts of corn (Zea mays L.) residue removal and cover crops on various soil quality indicators and surface greenhouse gas (GHG) fluxes. The study was being conducted on plots located at the North Central Agricultural Research Laboratory (NCARL) in Brookings, South Dakota, USA. Three plots of a corn and soybean (Glycine max (L.) Merr.) rotation under a no-till (NT) system are being monitored for soils and surface gas fluxes. Each plot has three residue removal (high residue removal, HRR; medium residue removal, MRR; and low residue removal, LRR) treatments and two cover crops (cover crops and no cover crops) treatments. Both corn and soybean are represented every year. Gas flux measurements were taken weekly using a closed static chamber method. Data show that residue removal significantly impacted soil quality indicators while more time was needed for an affect from cover crop treatments to be noticed. The LRR treatment resulted in higher SOC concentrations, increased aggregate stability, and increased microbial activity. The LRR treatment also increased soil organic matter (SOM) and particulate organic matter (POM) concentrations. Cover crops used in HRR (high corn residue removal) improved SOC (27 g kg-1) by 6% compared to that without cover crops (25.4 g kg-1). Cover crops significantly impacted POM concentration directly after the residue removal treatments were applied in 2012. CO2 fluxes were observed to increase as temperature increased, while N2O fluxes increased as soil moisture increased. CH4 fluxes were responsive to both increases in temperature and moisture. On average, soils under

Modes of Interaction of Pleckstrin Homology Domains with Membranes: Toward a Computational Biochemistry of Membrane Recognition.

Science.gov (United States)

Naughton, Fiona B; Kalli, Antreas C; Sansom, Mark S P

2018-02-02

Pleckstrin homology (PH) domains mediate protein-membrane interactions by binding to phosphatidylinositol phosphate (PIP) molecules. The structural and energetic basis of selective PH-PIP interactions is central to understanding many cellular processes, yet the molecular complexities of the PH-PIP interactions are largely unknown. Molecular dynamics simulations using a coarse-grained model enables estimation of free-energy landscapes for the interactions of 12 different PH domains with membranes containing PIP 2 or PIP 3 , allowing us to obtain a detailed molecular energetic understanding of the complexities of the interactions of the PH domains with PIP molecules in membranes. Distinct binding modes, corresponding to different distributions of cationic residues on the PH domain, were observed, involving PIP interactions at either the "canonical" (C) and/or "alternate" (A) sites. PH domains can be grouped by the relative strength of their C- and A-site interactions, revealing that a higher affinity correlates with increased C-site interactions. These simulations demonstrate that simultaneous binding of multiple PIP molecules by PH domains contributes to high-affinity membrane interactions, informing our understanding of membrane recognition by PH domains in vivo. Copyright © 2017. Published by Elsevier Ltd.

Species distribution models contribute to determine the effect of climate and interspecific interactions in moving hybrid zones.

Science.gov (United States)

Engler, J O; Rödder, D; Elle, O; Hochkirch, A; Secondi, J

2013-11-01

Climate is a major factor delimiting species' distributions. However, biotic interactions may also be prominent in shaping geographical ranges, especially for parapatric species forming hybrid zones. Determining the relative effect of each factor and their interaction of the contact zone location has been difficult due to the lack of broad scale environmental data. Recent developments in species distribution modelling (SDM) now allow disentangling the relative contributions of climate and species' interactions in hybrid zones and their responses to future climate change. We investigated the moving hybrid zone between the breeding ranges of two parapatric passerines in Europe. We conducted SDMs representing the climatic conditions during the breeding season. Our results show a large mismatch between the realized and potential distributions of the two species, suggesting that interspecific interactions, not climate, account for the present location of the contact zone. The SDM scenarios show that the southerly distributed species, Hippolais polyglotta, might lose large parts of its southern distribution under climate change, but a similar gain of novel habitat along the hybrid zone seems unlikely, because interactions with the other species (H. icterina) constrain its range expansion. Thus, whenever biotic interactions limit range expansion, species may become 'trapped' if range loss due to climate change is faster than the movement of the contact zone. An increasing number of moving hybrid zones are being reported, but the proximate causes of movement often remain unclear. In a global context of climate change, we call for more interest in their interactions with climate change. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Remote Sensing of Residue Management in Farms using Landsat 8 Sensor Imagery

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M. A Rostami

2017-10-01

study were NDVI, BAI, NBR and NBRT. Classification accuracy was evaluated and expressed by confusion matrix and Kappa coefficient. Natural surfaces are rarely composed of a single uniform material. Spectral mixing occurs when materials with different spectral properties are represented by a single image pixel. The condition where scale of the mixing is large (macroscopic, mixing would occur in a linear fashion. However for microscopic situations, the mixing is generally nonlinear. The linear model ahich wasadopted in this study, assumes that there is no interaction between materials. Assumption of LSUA is that each pixel on the surface is a physical mixture of several constituents weighted by surface abundance, and the spectrum of the mixture is a linear combination of the endmember reflectance spectra. Within the context of this study, LSUA is a classification method that can determine contribution of each material (or endmember such as soil or residue for each image pixel. Results and Discussion The spectral response curve extracted from Landsat 8 image used as input into the LSUA model in ENVI software. As expected, crop burned residue (Ash spectra had lower reflectance when compared to the soil, residue and green plant spectra. The contrast between residue, green plant, soil and residue ash spectra was particularly evident in the NIR and SWIR bands. It is suggested that these bands are essential for residue discrimination. Differences of reflectance in the visible bands were minimal, providing little discrimination between residue, green plant, soil and residue ash. Burned area estimated by LSUA method from Landsat 8 image was correlated against the ground data (measured coincident to the ground data. The overall accuracy of classification with BAI index and LSUA method was 91.7 and 88.3 and Kappa coefficient was 0.89 and 0.84 respectively. Results indicated that burned field area can be located and its area can be estimated using Landsat 8 images. The Index BAI was

Personalized Social Network Activity Feeds for Increased Interaction and Content Contribution

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Shlomo eBerkovsky

2015-10-01

Full Text Available Online social networks were originally conceived as means of sharing information and activities with friends, and their success has been one of the primary contributors of the tremendous growth of the Web. Social network activity feeds were devised as a means to aggregate recent actions of friends into a convenient list. But the volume of actions and content generated by social network users is overwhelming, such that keeping users up-to-date with friend activities is an ongoing challenge for social network providers. Personalization has been proposed as a solution to combat social network information overload and help users to identify the nuggets of relevant information in the incoming flood of network activities. In this paper, we propose and thoroughly evaluate a personalized model for predicting the relevance of the activity feed items, which informs the ranking of the feeds and facilitates personalization. Results of a live study show that the proposed feed personalization approach successfully identifies and promotes relevant feed items and boosts the uptake of the feeds. In addition, it increases the contribution of user-generated content to the social network and spurs interaction between users.

Identification of interaction domains within the UL37 tegument protein of herpes simplex virus type 1.

Science.gov (United States)

Bucks, Michelle A; Murphy, Michael A; O'Regan, Kevin J; Courtney, Richard J

2011-07-20

Herpes simplex virus type 1 (HSV-1) UL37 is a 1123 amino acid tegument protein that self-associates and binds to the tegument protein UL36 (VP1/2). Studies were undertaken to identify regions of UL37 involved in these protein-protein interactions. Coimmunoprecipitation assays showed that residues within the carboxy-terminal half of UL37, amino acids 568-1123, are important for interaction with UL36. Coimmunoprecipitation assays also revealed that amino acids 1-300 and 568-1123 of UL37 are capable of self-association. UL37 appears to self-associate only under conditions when UL36 is not present or is present in low amounts, suggesting UL36 and UL37 may compete for binding. Transfection-infection experiments were performed to identify domains of UL37 that complement the UL37 deletion virus, K∆UL37. The carboxy-terminal region of UL37 (residues 568-1123) partially rescues the K∆UL37 infection. These results suggest the C-terminus of UL37 may contribute to its essential functional role within the virus-infected cell. Copyright © 2011 Elsevier Inc. All rights reserved.

Adaptive vibrational configuration interaction (A-VCI): A posteriori error estimation to efficiently compute anharmonic IR spectra

Science.gov (United States)

Garnier, Romain; Odunlami, Marc; Le Bris, Vincent; Bégué, Didier; Baraille, Isabelle; Coulaud, Olivier

2016-05-01

A new variational algorithm called adaptive vibrational configuration interaction (A-VCI) intended for the resolution of the vibrational Schrödinger equation was developed. The main advantage of this approach is to efficiently reduce the dimension of the active space generated into the configuration interaction (CI) process. Here, we assume that the Hamiltonian writes as a sum of products of operators. This adaptive algorithm was developed with the use of three correlated conditions, i.e., a suitable starting space, a criterion for convergence, and a procedure to expand the approximate space. The velocity of the algorithm was increased with the use of a posteriori error estimator (residue) to select the most relevant direction to increase the space. Two examples have been selected for benchmark. In the case of H2CO, we mainly study the performance of A-VCI algorithm: comparison with the variation-perturbation method, choice of the initial space, and residual contributions. For CH3CN, we compare the A-VCI results with a computed reference spectrum using the same potential energy surface and for an active space reduced by about 90%.

Residue-specific annotation of disorder-to-order transition and cathepsin inhibition of a propeptide-like crammer from D. melanogaster.

Directory of Open Access Journals (Sweden)

Tien-Sheng Tseng

Full Text Available Drosophila melanogaster crammer is a novel cathepsin inhibitor involved in long-term memory formation. A molten globule-to-ordered structure transition is required for cathepsin inhibition. This study reports the use of alanine scanning to probe the critical residues in the two hydrophobic cores and the salt bridges of crammer in the context of disorder-to-order transition and cathepsin inhibition. Alanine substitution of the aromatic residues W9, Y12, F16, Y20, Y32, and W53 within the hydrophobic cores, and charged residues E8, R28, R29, and E67 in the salt bridges considerably decrease the ability of crammer to inhibit Drosophila cathepsin B (CTSB. Far-UV circular dichroism (CD, intrinsic fluorescence, and nuclear magnetic resonance (NMR spectroscopies show that removing most of the aromatic and charged side-chains substantially reduces thermostability, alters pH-dependent helix formation, and disrupts the molten globule-to-ordered structure transition. Molecular modeling indicates that W53 in the hydrophobic Core 2 is essential for the interaction between crammer and the prosegment binding loop (PBL of CTSB; the salt bridge between R28 and E67 is critical for the appropriate alignment of the α-helix 4 toward the CTSB active cleft. The results of this study show detailed residue-specific dissection of folding transition and functional contributions of the hydrophobic cores and salt bridges in crammer, which have hitherto not been characterized for cathepsin inhibition by propeptide-like cysteine protease inhibitors. Because of the involvements of cathepsin inhibitors in neurodegenerative diseases, these structural insights can serve as a template for further development of therapeutic inhibitors against human cathepsins.

Residual Stresses in a NiCrY-Coated Powder Metallurgy Disk Superalloy

Science.gov (United States)

Gabb, Timothy P.; Rogers, Richard B.; Nesbitt, James A.; Puleo, Bernadette J.; Miller, Robert A.; Telesman, Ignacy; Draper, Susan L.; Locci, Ivan E.

2017-01-01

Protective ductile coatings will be necessary to mitigate oxidation and corrosion attack on superalloy disks exposed to increasing operating temperatures in some turbine engine environments. However, such coatings must be resistant to harmful surface cracking during service. The objective of this study was to investigate how residual stresses evolve in such coatings. Cylindrical gage fatigue specimens of powder metallurgy-processed disk superalloy LSHR were coated with a NiCrY coating, shot peened, and then subjected to fatigue in air at room and high temperatures. The effects of shot peening and fatigue cycling on average residual stresses and other aspects of the coating were assessed. Shot peening did induce beneficial compressive residual stresses in the coating and substrate. However, these stresses became more tensile in the coating with subsequent heating and contributed to cracking of the coating in long intervals of cycling at 760 C. Substantial compressive residual stresses remained in the substrate adjacent to the coating, sufficient to suppress fatigue cracking. The coating continued to protect the substrate from hot corrosion pitting, even after fatigue cracks initiated in the coating.

PHILOSOPHY OF MIND; THEORETICAL AND EXPERIMENTAL CONTRIBUTION TO THE EMERGING VISION OF MIND-BRAIN INTERACTION.

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Paul Ruiz Santos

2011-12-01

Full Text Available This work aims to contribute to the discussion of mind-brain interactions from an emergentism point of view of the Philosophy of Mind, using some of the naturalized theories. Some proposed bridges between mind and brain based on experimental naturalization are neuro-psychoanalysis, mirror neurons, and psychosomatics, among others. Naturalization can be achieved by earching for the link between psychological and biological processes. This biological-based approach can be developed avoiding mplification and reductionism of psychological processes. We discuss the access to new insights about the mind-brain relationship and its implications through neurophenomenology, from an emerging and interactionist point of view.

Analysis of shot-peening and residual stress relaxation in the nickel-based superalloy RR1000

International Nuclear Information System (INIS)

Foss, B.J.; Gray, S.; Hardy, M.C.; Stekovic, S.; McPhail, D.S.; Shollock, B.A.

2013-01-01

This work assesses the residual stress relaxation of the nickel-based alloy RR1000 due to thermal exposure and dwell-fatigue loading. A number of different characterization methods, including X-ray residual stress analysis, electron back-scattered diffraction, microhardness testing and focused ion beam secondary electron imaging, contributed to a detailed study of the shot-peened region. Thermal exposure at 700 °C resulted in a large reduction in the residual stresses and work-hardening effects in the alloy, but the subsurface remained in a beneficial compressive state. Oxidizing environments caused recrystallization in the near surface, but did not affect the residual stress-relaxation behaviour. Dwell-fatigue loading caused the residual stresses to return to approximately zero at nearly all depths. This work forms part of an ongoing investigation to determine the effects of shot-peening in this alloy with the motivation to improve the fatigue and oxidation resistance at 700 °C

Integrated modeling of groundwater-surface water interactions in a tile-drained agricultural field: The importance of directly measured flow route contributions

NARCIS (Netherlands)

Rozemeijer, J.C.; Velde, Y. van der; McLaren, R.G.; Geer, F.C. van; Broers, H.P.; Bierkens, M.F.P.

2010-01-01

Understanding the dynamics of groundwater-surface water interaction is needed to evaluate and simulate water and solute transport in catchments. However, direct measurements of the contributions of different flow routes from specific surfaces within a catchment toward the surface water are rarely

Determining the effect of cartridge case coatings on GSR using post-fire priming cup residue.

Science.gov (United States)

Terry, Molly; Fookes, Barry; Bridge, Candice M

2017-07-01

Ammunition is typically composed of a lead-based priming mixture which contributes to the characteristics most commonly used for the identification of gunshot residue (GSR). Due to the health risks often associated with lead, the use of lead-free primers in ammunitions is becoming more popular. Thus, the presence of GSR is becoming more difficult to discern based on the traditional means, i.e. the presence of lead (Pb), barium (Ba), and antimony (Sb). While research has been conducted on the differences between lead-based and lead-free muzzle discharge residue, few have researched other components of ammunition which may lead to other means of characterizing GSR. This research, therefore, covers that gap by focusing on the priming cup present in ammunition and the residue which may originate from it, that can contribute to muzzle discharge residue. In this study, a lead-based and a lead-free ammunition from four different manufacturers were chosen. The cartridges were fired using a Glock 17, 9mm Parabellum, collected post-fire, and subsequently de-primed resulting in the removal of the anvil. The GSR present on the anvils and cups was analyzed using scanning electron microscopy coupled with energy dispersive x-ray spectrometry (SEM-EDX). The data was then processed using unit vector analysis for normalization and analyzed using principal component analysis (PCA) and linear discriminant analysis (LDA). This data was then used to determine the components of the cartridge case which contribute to GSR and develop a method of characterization between lead-free and lead-based ammunition. Such a method will improve the detection of GSR by strengthening the criteria of identification. Copyright © 2017 Elsevier B.V. All rights reserved.

Numerical simulation of residual stress in piping components at Framatome-ANP

International Nuclear Information System (INIS)

Gilies, P.; Franco, C.; Cipiere, M.-F.; Ould, P.

2005-01-01

Numerous manufacturing processes induce residual stresses and distortions in piping components and associated welds: quenching of cast pipings, machining and welding. In Pressurized Water Reactors, most of the components have a large thickness for sustaining pressure and distortions are a minor source of concern. This is not the case for residual stresses which may have a strong influence on several type of damage such as fatigue, corrosion, brittle fracture. In low toughness components, residual stress fields may contribute to ductile tearing initiation. These potential damages are mitigated after welding by stress relief heat treatment, which is applied in a systematic manner to ferritic components of the primary system in nuclear reactors. This treatment is not applied on austenitic piping for which the heat treatment temperature is limited due to the risk of sensitization and residual stresses are difficult to eliminate completely. Since on site measurements are costly and difficult to perform, numerical simulation appears to be an attractive tool for estimating residual stress distributions. Framatome-ANP is working on modelling manufacturing processes with that purpose in mind. This paper presents three kinds of applications illustrating efforts on welding, quenching and machining simulation. First a comparison is shown between computations and measurements of residual stress induced by welding of a dissimilar weld metal junction. Then numerical simulations of quenching of a cast stainless steel nozzle are presented. Finally quenching followed by machining and grinding of this cast component are considered in a full simulation of the manufacturing process. Computed distortions and residual stresses are compared with experimental measurements at different stages of the manufacturing process. (authors)

Residual gas analysis

International Nuclear Information System (INIS)

Berecz, I.

1982-01-01

Determination of the residual gas composition in vacuum systems by a special mass spectrometric method was presented. The quadrupole mass spectrometer (QMS) and its application in thin film technology was discussed. Results, partial pressure versus time curves as well as the line spectra of the residual gases in case of the vaporization of a Ti-Pd-Au alloy were demonstrated together with the possible construction schemes of QMS residual gas analysers. (Sz.J.)

Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions

Directory of Open Access Journals (Sweden)

Inbar Yuval

2010-07-01

Full Text Available Abstract Background Accurate evaluation and modelling of residue-residue interactions within and between proteins is a key aspect of computational structure prediction including homology modelling, protein-protein docking, refinement of low-resolution structures, and computational protein design. Results Here we introduce a method for accurate protein structure modelling and evaluation based on a novel 4-distance description of residue-residue interaction geometry. Statistical 4-distance preferences were extracted from high-resolution protein structures and were used as a basis for a knowledge-based potential, called Hunter. We demonstrate that 4-distance description of side chain interactions can be used reliably to discriminate the native structure from a set of decoys. Hunter ranked the native structure as the top one in 217 out of 220 high-resolution decoy sets, in 25 out of 28 "Decoys 'R' Us" decoy sets and in 24 out of 27 high-resolution CASP7/8 decoy sets. The same concept was applied to side chain modelling in protein structures. On a set of very high-resolution protein structures the average RMSD was 1.47 Å for all residues and 0.73 Å for buried residues, which is in the range of attainable accuracy for a model. Finally, we show that Hunter performs as good or better than other top methods in homology modelling based on results from the CASP7 experiment. The supporting web site http://bioinfo.weizmann.ac.il/hunter/ was developed to enable the use of Hunter and for visualization and interactive exploration of 4-distance distributions. Conclusions Our results suggest that Hunter can be used as a tool for evaluation and for accurate modelling of residue-residue interactions in protein structures. The same methodology is applicable to other areas involving high-resolution modelling of biomolecules.

Assessing the Availability of Wood Residues and Residue Markets in Virginia

OpenAIRE

Alderman, Delton R. Jr.

1998-01-01

A statewide mail survey of primary and secondary wood product manufacturers was undertaken to quantify the production and consumption of wood residues in Virginia. Two hundred and sixty-six wood product manufacturers responded to the study and they provided information on the production, consumption, markets, income or disposal costs, and disposal methods of wood residues. Hardwood and pine sawmills produce approximately 66 percent of Virginia's wood residues. Virginia's wood product man...

Feasibility of ultrasonic and eddy current methods for measurement of residual stress in shot peened metals

International Nuclear Information System (INIS)

Lavrentyev, Anton I.; Stucky, Paul A.; Veronesi, William A.

2000-01-01

Shot peening is a well-known method for extending the fatigue life of metal components by introducing compressive residual stresses near their surfaces. The capability to nondestructively evaluate the near surface residual stress would greatly aid the assurance of proper fatigue life in shot-peened components. This paper presents preliminary results from a feasibility study examining the use of ultrasonic and eddy current NDE methods for residual stress measurement in components where the stress has been introduced by shot peening. With an ultrasonic method, a variation of ultrasonic surface wave speed with shot peening intensity was measured. Near surface conductivity was measured by eddy current methods. Since the effective penetration depth of both methods employed is inversely related to the excitation frequency, by making measurements at different frequencies, each method has the potential to provide the stress-depth profile. Experiments were conducted on aluminum specimens (alloy 7075-T7351) peened within the Almen peening intensity range of 4C to 16C. The experimental results obtained demonstrate a correlation between peening intensity and Rayleigh wave velocity and between peening intensity and conductivity. The data suggests either of the methods may be suitable, with limitations, for detecting unsatisfactory levels of shot peening. Several factors were found to contribute to the measured responses: surface roughness, near surface plastic deformation (cold work) and residual stress. The contribution of each factor was studied experimentally. The feasibility of residual stress determination from the measured data is discussed

Health condition and residual life of deteriorating technical systems

Energy Technology Data Exchange (ETDEWEB)

Reinertsen, Rune

1998-12-31

Many offshore installations in the Norwegian Sector of the North Sea approach the end of their useful life. The same is true of many power plants and technical systems in general. This thesis describes the theory and improves the methods for the determination of the health condition and residual life of technical systems. Rather than developing new methods it discusses new ways of using existing statistical methods. The main contributions are: (1) A survey of the literature of diagnosis, prediction and life extension for deteriorating technical systems, (2) A discussion of some consequences of selecting the wrong life model, (3) A description of problems related to the determination of mean residual life of non-repairable technical systems, (4) Presentation of the concept of `technical health` to describe the soundness of a system exposed to failure mechanisms, (5) A model for predicting the technical health and residual life of a corroding system, (6) Recommends requirements and methods for using expert knowledge in safety and reliability analysis, (7) A general inspection strategy for system fault diagnosis by using Shannon entropy, (8) Points out weaknesses and strengths of risk measures used in the offshore industry today. 237 refs., 23 figs., 6 tabs.

Health condition and residual life of deteriorating technical systems

Energy Technology Data Exchange (ETDEWEB)

Reinertsen, Rune

1997-12-31

Many offshore installations in the Norwegian Sector of the North Sea approach the end of their useful life. The same is true of many power plants and technical systems in general. This thesis describes the theory and improves the methods for the determination of the health condition and residual life of technical systems. Rather than developing new methods it discusses new ways of using existing statistical methods. The main contributions are: (1) A survey of the literature of diagnosis, prediction and life extension for deteriorating technical systems, (2) A discussion of some consequences of selecting the wrong life model, (3) A description of problems related to the determination of mean residual life of non-repairable technical systems, (4) Presentation of the concept of `technical health` to describe the soundness of a system exposed to failure mechanisms, (5) A model for predicting the technical health and residual life of a corroding system, (6) Recommends requirements and methods for using expert knowledge in safety and reliability analysis, (7) A general inspection strategy for system fault diagnosis by using Shannon entropy, (8) Points out weaknesses and strengths of risk measures used in the offshore industry today. 237 refs., 23 figs., 6 tabs.

Residues of cypermethrin and endosulfan in soils of Swat valley

Directory of Open Access Journals (Sweden)

M. Nafees

2009-05-01

Full Text Available Swat Valley was studied for two widely used pesticides; cypermethrin and endosulfan. A total of 63 soil samples were collected from 27 villages selected for this purpose. The collected soil samples were extracted with n-hexane, pesticides were separated, identified and quantified by a GC-ECD system. Endosulfan was 0.24 - 1.51 mg kg-1 and 0.13 - 12.67 mg kg-1 in rainfed and irrigated areas, respectively. The residual level of cypermethrin was comparatively high with a level of0.14 to 27.62 mg kg-1 and 0.05 to 73.75 mg kg-1 in rainfed and irrigated areas, respectively. For assessing the possible causes of pesticide residues in soil, 360 farmers were interviewed. It was found that both, cypermethrin and endosulfan, apart from agriculture were also widely misused for fishing in the entire stretch of River Swat and its tributaries. River Swat is used for irrigation in Swat Valley and this wide misuse of pesticides can also contribute to pesticide residue in soil.

Temperature-dependent dynamical transitions of different classes of amino acid residue in a globular protein.

Science.gov (United States)

Miao, Yinglong; Yi, Zheng; Glass, Dennis C; Hong, Liang; Tyagi, Madhusudan; Baudry, Jerome; Jain, Nitin; Smith, Jeremy C

2012-12-05

The temperature dependences of the nanosecond dynamics of different chemical classes of amino acid residue have been analyzed by combining elastic incoherent neutron scattering experiments with molecular dynamics simulations on cytochrome P450cam. At T = 100-160 K, anharmonic motion in hydrophobic and aromatic residues is activated, whereas hydrophilic residue motions are suppressed because of hydrogen-bonding interactions. In contrast, at T = 180-220 K, water-activated jumps of hydrophilic side chains, which are strongly coupled to the relaxation rates of the hydrogen bonds they form with hydration water, become apparent. Thus, with increasing temperature, first the hydrophobic core awakens, followed by the hydrophilic surface.

Mutational properties of amino acid residues: implications for evolvability of phosphorylatable residues

DEFF Research Database (Denmark)

Creixell, Pau; Schoof, Erwin M.; Tan, Chris Soon Heng

2012-01-01

in terms of their mutational activity. Moreover, we highlight the importance of the genetic code and physico-chemical properties of the amino acid residues as likely causes of these inequalities and uncover serine as a mutational hot spot. Finally, we explore the consequences that these different......; it is typically assumed that all amino acid residues are equally likely to mutate or to result from a mutation. Here, by reconstructing ancestral sequences and computing mutational probabilities for all the amino acid residues, we refute this assumption and show extensive inequalities between different residues...... mutational properties have on phosphorylation site evolution, showing that a higher degree of evolvability exists for phosphorylated threonine and, to a lesser extent, serine in comparison with tyrosine residues. As exemplified by the suppression of serine's mutational activity in phosphorylation sites, our...

Characterization and electrolytic cleaning of poly(methyl methacrylate) residues on transferred chemical vapor deposited graphene

Science.gov (United States)

Sun, Jianbo; Finklea, Harry O.; Liu, Yuxin

2017-03-01

Poly(methyl methacrylate) (PMMA) residue has long been a critical challenge for practical applications of the transferred chemical vapor deposited (CVD) graphene. Thermal annealing is empirically used for the removal of the PMMA residue; however experiments imply that there are still small amounts of residues left after thermal annealing which are hard to remove with conventional methods. In this paper, the thermal degradation of the PMMA residue upon annealing was studied by Raman spectroscopy. The study reveals that post-annealing residues are generated by the elimination of methoxycarbonyl side chains in PMMA and are believed to be absorbed on graphene via the π-π interaction between the conjugated unsaturated carbon segments and graphene. The post-annealing residues are difficult to remove by further annealing in a non-oxidative atmosphere due to their thermal and chemical stability. An electrolytic cleaning method was shown to be effective in removing these post-annealing residues while preserving the underlying graphene lattice based on Raman spectroscopy and atomic force microscopy studies. Additionally, a solution-gated field effect transistor was used to study the transport properties of the transferred CVD graphene before thermal annealing, after thermal annealing, and after electrolytic cleaning, respectively. The results show that the carrier mobility was significantly improved, and that the p-doping was reduced by removing PMMA residues and post-annealing residues. These studies provide a more in-depth understanding on the thermal annealing process for the removal of the PMMA residues from transferred CVD graphene and a new approach to remove the post-annealing residues, resulting in a residue-free graphene.

Multi-scale trade-off analysis of cereal residue use for livestock feeding vs. soil mulching in the Mid-Zambezi Valley, Zimbabwe

NARCIS (Netherlands)

Baudron, F.; Delmotte, S.; Corbeels, M.; Herrera, J.M.; Tittonell, P.A.

2015-01-01

Cereal residues represent a major resource for livestock feeding during the dry season in southern Africa. When kept on the soil surface instead of feeding them to livestock, crop residues can contribute to increasing soil fertility and maintaining crop productivity in the short- and the long-term.

Manufacturing inspection of electrical steels using Magnetic Barkhausen Noise: residual stress detection

Energy Technology Data Exchange (ETDEWEB)

Samimi, A.A., E-mail: 9aa8@queensu.ca [Queen' s Univ., Applied Magnetics Group, Kingston, Ontario (Canada); Krause, T.W. [Royal Military College of Canada, NDE Lab., Kingston, Ontario (Canada); Clapham, L. [Queen' s Univ., Applied Magnetics Group, Kingston, Ontario (Canada); Gallaugher, M.; Ding, Y.; Chromik, R. [McGill Univ., Dept. of Mining and Materials Engineering, Montreal, Quebec (Canada)

2016-09-15

Non-oriented Electrical Steel (NOES) is the magnetic core lamination material used for flux transfer in rotary machines. The presence of residual stress associated with material processing may be detrimental to magnetic domain structure refinement and as a result, magnetic performance of NOES. Therefore, manufacturing inspection of NOES that identifies the presence of residual stress could contribute to the production of more energy efficient cores. However, standard materials evaluation is limited to destructive and off-line techniques. The present work employed Magnetic Barkhausen Noise (MBN) for nondestructive identification of local residual stress associated with stages in material processing. Analysis of MBN from single strips of NOES demonstrated clear response to applied tensile stress, mechanical shearing, the presence of an insulating coating and punching. The results establish the potential of MBN as a nondestructive testing technology for quality control of electrical steels at various stages of manufacture. (author)

Evaluation of residue-residue contact prediction in CASP10

KAUST Repository

Monastyrskyy, Bohdan

2013-08-31

We present the results of the assessment of the intramolecular residue-residue contact predictions from 26 prediction groups participating in the 10th round of the CASP experiment. The most recently developed direct coupling analysis methods did not take part in the experiment likely because they require a very deep sequence alignment not available for any of the 114 CASP10 targets. The performance of contact prediction methods was evaluated with the measures used in previous CASPs (i.e., prediction accuracy and the difference between the distribution of the predicted contacts and that of all pairs of residues in the target protein), as well as new measures, such as the Matthews correlation coefficient, the area under the precision-recall curve and the ranks of the first correctly and incorrectly predicted contact. We also evaluated the ability to detect interdomain contacts and tested whether the difficulty of predicting contacts depends upon the protein length and the depth of the family sequence alignment. The analyses were carried out on the target domains for which structural homologs did not exist or were difficult to identify. The evaluation was performed for all types of contacts (short, medium, and long-range), with emphasis placed on long-range contacts, i.e. those involving residues separated by at least 24 residues along the sequence. The assessment suggests that the best CASP10 contact prediction methods perform at approximately the same level, and comparably to those participating in CASP9.

Evaluating the residual stress in PbTiO3 thin films prepared by a polymeric chemical method

International Nuclear Information System (INIS)

Valim, D; Filho, A G Souza; Freire, P T C; Filho, J Mendes; Guarany, C A; Reis, R N; Araujo, E B

2004-01-01

We report a study of residual stress in PbTiO 3 (PT) thin films prepared on Si substrates by a polymeric chemical method. The E(1TO) frequency was used to evaluate the residual stress through an empirical equation available for bulk PT. We find that the residual stress in PT films increases as the film thickness decreases and conclude that it originates essentially from the contributions of extrinsic and intrinsic factors. Polarized Raman experiments showed that the PT films prepared by a polymeric chemical method are somewhat a-domain (polar axis c parallel to the substrate) oriented

Proceedings of the 7. biennial residue-to-revenue residual wood conference 2007

International Nuclear Information System (INIS)

Raulin, J.

2007-01-01

This conference provided information on the highest and best use of residual wood, which is quickly becoming a valuable commodity. Issues concerning forest residues, sawmill wastes, agricultural residues and urban organic materials were discussed along with trends in Canadian surplus mill waste production. The evolving nature and technologies of the biomass business were highlighted with particular focus on how to generate energy and save money through the use of residual wood. Residual wood energy projects and developments in Canada, North America and Europe were outlined along with biomass development in relation to forest fires and insect disturbances. Cogeneration technologies using wood wastes for thermal heat, steam and electricity were also presented, along with transportation fuel technologies for the production of ethanol. It was noted that with the rising cost of energy, the forest industry is seeking energy solutions based on the use of residual wood. The range of economically practical residual wood solutions continues to grow as energy prices increase. The conference was attended by more than 200 delegates from the forest industry, suppliers and government representatives, to discuss policies and procedures currently in place. Industry investment is being stimulated by the potential for biofuels and biochemicals, as well as the co-operation between the forest and energy sectors. The conference featured 23 presentations, of which 12 have been catalogued separately for inclusion in this database. refs., tabs., figs

Influence of MSD crack pattern on the residual strength of flat stiffened sheets

Science.gov (United States)

Nilsson, K.-F.

A parameter study of the residual strength for a multiple site damaged (MSD) stiffened sheet is presented. The analysis is based on an elastic-plastic fracture analysis using the yield-strip model for interaction between a lead crack and the smaller MSD cracks. Two crack growth criteria, one with a pronounced crack growth resistance and one with no crack growth resistance and five different MSD crack patterns, are analysed for different sizes of the lead crack and the smaller MSD cracks. The analysis indicates that the residual strength reduction depends on all these parameters and that MSD may totally erode the crack arrest capability of a tear strap. Another important outcome is that for certain combinations also very small MSD cracks may induce a significant residual strength reduction.

Measurement of the yields of residual nuclei in interactions 17.9 GeV/c α-particles with sup(159)Tb, sup(181)Ta and sup(207,2)Pb nuclei

International Nuclear Information System (INIS)

Butsev, V.S.; Butseva, G.L.; Kostin, V.Ya.; Migalenya, V.Ya.

1984-01-01

The results of investigations of 17.9 GeV/c α-particle interactions with Tb, Ta and Ph nuclei are presented. Measurements have been carried out of the relative yields of residual nuclei for the (α+Tb), (α+Ta) and (α+Pb) reactions in the 24 93 Tc, 133 Ce and 198 Tl the isomeric ratios are determined, that are compared with the isomeric ratios measured in reactions induced by 500 MeV protons and by 25.2 GeV 12 C ions

The peripheral binding of 14-3-3γ to membranes involves isoform-specific histidine residues.

Directory of Open Access Journals (Sweden)

Helene J Bustad

Full Text Available Mammalian 14-3-3 protein scaffolds include seven conserved isoforms that bind numerous phosphorylated protein partners and regulate many cellular processes. Some 14-3-3-isoforms, notably γ, have elevated affinity for membranes, which might contribute to modulate the subcellular localization of the partners and substantiate the importance of investigating molecular mechanisms of membrane interaction. By applying surface plasmon resonance we here show that the binding to phospholipid bilayers is stimulated when 14-3-3γ is complexed with its partner, a peptide corresponding to the Ser19-phosphorylated N-terminal region of tyrosine hydroxylase. Moreover, membrane interaction is dependent on salts of kosmotropic ions, which also stabilize 14-3-3γ. Electrostatic analysis of available crystal structures of γ and of the non-membrane-binding ζ-isoform, complemented with molecular dynamics simulations, indicate that the electrostatic potential distribution of phosphopeptide-bound 14-3-3γ is optimal for interaction with the membrane through amphipathic helices at the N-terminal dimerization region. In addition, His158, and especially His195, both specific to 14-3-3γ and located at the convex lateral side, appeared to be pivotal for the ligand induced membrane interaction, as corroborated by site-directed mutagenesis. The participation of these histidine residues might be associated to their increased protonation upon membrane binding. Overall, these results reveal membrane-targeting motifs and give insights on mechanisms that furnish the 14-3-3γ scaffold with the capacity for tuned shuffling from soluble to membrane-bound states.

An estimation of cogeneration potential by using refinery residuals in Mexico

International Nuclear Information System (INIS)

Marin-Sanchez, J.E.; Rodriguez-Toral, M.A.

2007-01-01

Electric power generation in Mexico is mainly based on fossil fuels, specifically heavy fuel oil, although the use of natural gas combined cycles (NGCC) is becoming increasingly important. This is the main destination that has promoted growing imports of natural gas, currently accounting for about 20% of the total national annual consumption. Available crude oil is becoming heavier; thus refineries should be able to process it, and to handle greater quantities of refinery residuals. If all refinery residuals are used in cogeneration plants serving petroleum refineries, the high heat/power ratio of refinery needs, leads to the availability of appreciable quantities of electricity that can be exported to the public utility. Thus, in a global perspective, Mexican imports of natural gas may be reduced by cogeneration using refinery residuals. This is not the authors' idea; in fact, PEMEX, the national oil company, has been entitled by the Mexican congress to sell its power leftovers to The Federal Electricity Commission (CFE) in order to use cogeneration in the way described for the years to come. A systematic way of determining the cogeneration potential by using refinery residuals from Mexican refineries is presented here, taking into account residual quantities and composition, from a national perspective, considering expected scenarios for Maya crude content going to local refineries in the years to come. Among different available technologies for cogeneration using refinery residuals, it is believed that the integrated gasification combined cycle (IGCC) would be the best option. Thus, considering IGCC plants supplying heat and power to refineries where it is projected to have refinery residuals for cogeneration, the expected electric power that can be sent to the public utility is quantified, along with the natural gas imports mitigation that may be attained. This in turn would contribute to a necessary fuel diversification policy balancing energy, economy and

Fate and persistence of 14C pesticide residues in different soils: effects of 14C pesticide contaminated run-off soil water on biological systems. Part of a coordinated programme on isotopic-tracer-aided studies of agrochemical residue - soil biota interactions

International Nuclear Information System (INIS)

Lichtenstein, E.

1982-09-01

The interaction of selected fungicides, herbicides and N-fertilizers with microorganisms in cranberry soils and their effects on the degradation of 14 C-phenyl-parathion were investigated. Incubation of soils with parathion of p-nitrophenol for 4 days, followed by the addition of 14 C-parathion resulted after 24 h in an enhanced degradation of the insecticide to 14 CO 2 (34-39% of the applied radiocarbon as opposed to 2% in controls) and also in an increased binding of 14 C to the soil. The fungicide captafol inhibited the degradation of soil-applied 14 C-parathion as evidenced by a reduction of both 14 CO 2 evolution and 14 C-bound residues. Maneb and benomyl suppressed the degradation of 14 C-parathion to 14 CO 2 but not the formation of bound residues. Addition of 2,4-D to 14 C-parathion treated soil also resulted in an increased persistence of the insecticide. Studies conducted with the insecticide and (NH 4 ) 2 SO 4 , NH 4 NO 3 , KNO 3 or urea showed that under all experimental conditions the total amounts of 14 C recovered were similar, yet the distribution of 14 C-compounds into benzene-soluble, water-soluble and bound residues was not. This possibly indicated a change in the pathway of 14 C-parathion degradation. The insecticide was most persistent in soils containing (NH 4 ) 2 SO 4 , as demonstrated by a recovery of 29% of the applied radiocarbon in benzene-soluble form. Analyses by TIC of this benzene extraction phase revealed the presence of 14 C-parathion, 14 C-p-aminophenol and 14 C-aminoparathion

The involvement of beta-1,4-galactosyltransferase and N-acetylglucosamine residues in fertilization has been lost in the horse

Directory of Open Access Journals (Sweden)

Magistrini Michèle

2008-11-01

Full Text Available Abstract Background In human and rodents, sperm-zona pellucida binding is mediated by a sperm surface Galactosyltransferase that recognizes N-Acetylglucosamine residues on a glycoprotein ZPC. In large domestic mammals, the role of these molecules remains unclear: in bovine, they are involved in sperm-zona pellucida binding, whereas in porcine, they are not necessary. Our aim was to clarify the role of Galactosyltransferase and N-Acetylglucosamine residues in sperm-zona pellucida binding in ungulates. For this purpose, we analyzed the mechanism of sperm-zona pellucida interaction in a third ungulate: the horse, since the Galactosyltransferase and N-Acetylglucosamine residues have been localized on equine gametes. Methods We masked the Galactosyltransferase and N-Acetylglucosamine residues before the co-incubation of gametes. Galactosyltransferase was masked either with an anti-Galactosyltransferase antibody or with the enzyme substrate, UDP Galactose. N-Acetylglucosamine residues were masked either with a purified Galactosyltransferase or with an anti-ZPC antibody. Results and discussion The number of spermatozoa bound to the zona pellucida did not decrease after the masking of Galactosyltransferase or N-Acetylglucosamine. So, these two molecules may not be necessary in the mechanism of in vitro sperm-zona pellucida interaction in the horse. Conclusion The involvement of Galactosyltransferase and N-Acetylglucosamine residues in sperm-zona pellucida binding may have been lost during evolution in some ungulates, such as porcine and equine species.

Logistics cost analysis of rice residues for second generation bioenergy production in Ghana

DEFF Research Database (Denmark)

Vijay Ramamurthi, Pooja; Cristina Fernandes, Maria; Nielsen, Per Sieverts

2014-01-01

This study explores the techno-economic potential of rice residues as a bioenergy resource to meet Ghana’s energy demands. Major rice growing regions of Ghana have 70–90% of residues available for bioenergy production. To ensure cost-effective biomass logistics, a thorough cost analysis was made...... for two bioenergy routes. Logistics costs for a 5MWe straw combustion plant were 39.01, 47.52 and 47.89USD/t for Northern, Ashanti and Volta regions respectively. Logistics cost for a 0.25MWe husk gasification plant (with roundtrip distance 10km) was 2.64USD/t in all regions. Capital cost (66......–72%) contributes significantly to total logistics costs of straw, however for husk logistics, staff (40%) and operation and maintenance costs (46%) dominate. Baling is the major processing logistic cost for straw, contributing to 46–48% of total costs. Scale of straw unit does not have a large impact on logistic...

Contributions to the R-curve behaviour of ceramic materials

International Nuclear Information System (INIS)

Fett, T.

1994-12-01

Several ceramic materials show an increase in crack growth resistance with increasing crack extension. Especially, in case of coarse-grained alumina this ''R-curve effect'' is caused by crack-face interactions in the wake of the advancing crack. Similar effects occur for whisker reinforced ceramics. Due to the crack-face interactions so-called ''bridging stresses'' are generated which transfer forces between the two crack surfaces. A second reason for an increase of crack-growth resistance are stress-induced phase transformations in zirconia ceramics with the tetragonal phase changing to the monoclinic phase. These transformations will affect the stress field in the surroundings of crack tips. The transformation generates a crack-tip transformation zone and, due to the stress balance, also residual stresses in the whole crack region which result in a residual stress intensity factor. This additional stress intensity factor is also a reason for the R-curve behaviour. In this report both effects are outlined in detail. (orig.) [de

Interaction of the alpha-toxin of Staphylococcus aureus with the liposome membrane.

Science.gov (United States)

Ikigai, H; Nakae, T

1987-02-15

When the liposome membrane is exposed to the alpha-toxin of Staphylococcus aureus, fluorescence of the tryptophan residue(s) of the toxin molecule increases concomitantly with the degree of toxin-hexamer formation (Ikigai, H., and Nakae, T. (1985) Biochem. Biophys. Res. Commun. 130, 175-181). In the present study, the toxin-membrane interaction was distinguished from the hexamer formation by the fluorescence energy transfer from the tryptophan residue(s) of the toxin molecule to the dansylated phosphatidylethanolamine in phosphatidylcholine liposome. Measurement of these two parameters yielded the following results. The effect of the toxin concentration and phospholipid concentration on these two parameters showed first order kinetics. The effect of liposome size on the energy transfer and the fluorescence increment of the tryptophan residue(s) was only detectable in small liposomes. Under moderately acidic or basic conditions, the fluorescence energy transfer always preceded the fluorescence increment of the tryptophan residue(s). The fluorescence increment at 336 nm at temperatures below 20 degrees C showed a latent period, whereas the fluorescence energy transfer did not. These results were thought to indicate that when alpha-toxin damages the target membrane, the molecule interacts with the membrane first, and then undergoes oligomerization within the membrane.

Molecular insight on the non-covalent interactions between carbapenems and uc(l,d)-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study

Science.gov (United States)

Ntombela, Thandokuhle; Fakhar, Zeynab; Ibeji, Collins U.; Govender, Thavendran; Maguire, Glenn E. M.; Lamichhane, Gyanu; Kruger, Hendrik G.; Honarparvar, Bahareh

2018-05-01

Tuberculosis remains a dreadful disease that has claimed many human lives worldwide and elimination of the causative agent Mycobacterium tuberculosis also remains elusive. Multidrug-resistant TB is rapidly increasing worldwide; therefore, there is an urgent need for improving the current antibiotics and novel drug targets to successfully curb the TB burden. uc(l,d)-Transpeptidase 2 is an essential protein in Mtb that is responsible for virulence and growth during the chronic stage of the disease. Both uc(d,d)- and uc(l,d)-transpeptidases are inhibited concurrently to eradicate the bacterium. It was recently discovered that classic penicillins only inhibit uc(d,d)-transpeptidases, while uc(l,d)-transpeptidases are blocked by carbapenems. This has contributed to drug resistance and persistence of tuberculosis. Herein, a hybrid two-layered ONIOM (B3LYP/6-31G+(d): AMBER) model was used to extensively investigate the binding interactions of LdtMt2 complexed with four carbapenems (biapenem, imipenem, meropenem, and tebipenem) to ascertain molecular insight of the drug-enzyme complexation event. In the studied complexes, the carbapenems together with catalytic triad active site residues of LdtMt2 (His187, Ser188 and Cys205) were treated at with QM [B3LYP/6-31+G(d)], while the remaining part of the complexes were treated at MM level (AMBER force field). The resulting Gibbs free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) for all complexes showed that the carbapenems exhibit reasonable binding interactions towards LdtMt2. Increasing the number of amino acid residues that form hydrogen bond interactions in the QM layer showed significant impact in binding interaction energy differences and the stabilities of the carbapenems inside the active pocket of LdtMt2. The theoretical binding free energies obtained in this study reflect the same trend of the experimental observations. The electrostatic, hydrogen bonding and Van der Waals interactions between the carbapenems and Ldt

A Soluble, Folded Protein without Charged Amino Acid Residues

DEFF Research Database (Denmark)

Højgaard, Casper; Kofoed, Christian; Espersen, Roall

2016-01-01

side chains can maintain solubility, stability, and function. As a model, we used a cellulose-binding domain from Cellulomonas fimi, which, among proteins of more than 100 amino acids, presently is the least charged in the Protein Data Bank, with a total of only four titratable residues. We find......Charges are considered an integral part of protein structure and function, enhancing solubility and providing specificity in molecular interactions. We wished to investigate whether charged amino acids are indeed required for protein biogenesis and whether a protein completely free of titratable...... that the protein shows a surprising resilience toward extremes of pH, demonstrating stability and function (cellulose binding) in the pH range from 2 to 11. To ask whether the four charged residues present were required for these properties of this protein, we altered them to nontitratable ones. Remarkably...

Solid residues

International Nuclear Information System (INIS)

Mulder, E.; Duin, P.J. van; Grootenboer, G.J.

1995-01-01

A summary is presented of the many investigations that have been done on solid residues of atmospheric fluid bed combustion (AFBC). These residues are bed ash, cyclone ash and bag filter ash. Physical and chemical properties are discussed and then the various uses of residues (in fillers, bricks, gravel, and for recovery of aluminium) are summarised. Toxicological properties of fly ash and stack ash are discussed as are risks of pneumoconiosis for workers handling fly ash, and contamination of water by ashes. On the basis of present information it is concluded that risks to public health from exposure to emissions of coal fly ash from AFBC appear small or negligible as are health risk to workers in the coal fly ash processing industry. 35 refs., 5 figs., 12 tabs

Collective multipole excitations based on correlated realistic nucleon-nucleon interactions

International Nuclear Information System (INIS)

Paar, N.; Papakonstantinou, P.; Hergert, H.; Roth, R.

2006-01-01

We investigate collective multipole excitations for closed shell nuclei from 16 O to 208 Pb using correlated realistic nucleon-nucleon interactions in the framework of the random phase approximation (RPA). The dominant short-range central and tensor correlations a re treated explicitly within the Unitary Correlation Operator Method (UCOM), which provides a phase-shift equivalent correlated interaction VUCOM adapted to simple uncorrelated Hilbert spaces. The same unitary transformation that defines the correlated interaction is used to derive correlated transition operators. Using VUCOM we solve the Hartree-Fock problem and employ the single-particle states as starting point for the RPA. By construction, the UCOM-RPA is fully self-consistent, i.e. the same correlated nucleon-nucleon interact ion is used in calculations of the HF ground state and in the residual RPA interaction. Consequently, the spurious state associated with the center-of-mass motion is properly removed and the sum-rules are exhausted within ±3%. The UCOM-RPA scheme results in a collective character of giant monopole, dipole, and quadrupole resonances in closed-shell nuclei across the nuclear chart. For the isoscalar giant monopole resonance, the resonance energies are in agreement with experiment hinting at a reasonable compressibility. However, in the 1 - and 2 + channels the resonance energies are overestimated due to missing long-range correlations and three-body contributions. (orig.)

Spectrofluorometric and Molecular Modeling Studies on Binding of Nitrite Ion with Bovine Hemoglobin: Effect of Nitrite Ion on Amino Acid Residues

Science.gov (United States)

Madrakian, T.; Bagheri, H.; Afkhami, A.

2015-05-01

The interaction between nitrite ion and bovine hemoglobin was investigated by a spectrofluorometric technique. The experimental results indicated that the interaction causes a static quenching of the fluorescence of bovine hemoglobin, that the binding reaction is spontaneous, and that H-bonding interactions play a major role in binding of this ion to bovine hemoglobin. The formation constant for this interaction was calculated. Based on Förster's theory of nonradiative energy transfer, the binding distance between this ion and bovine hemoglobin was determined. Furthermore, the interaction of nitrite ion with tyrosine and tryptophan was investigated with synchronous fluorescence. There was no significant shift of the maximum emission wavelength with interactions of the mentioned ion with bovine hemoglobin, which implies that interaction of nitrite ion with bovine hemoglobin does not affect the microenvironment around the tryptophan and tyrosine residues. Furthermore, the effect of nitrite ion on amino acid residues of bovine hemoglobin was studied by a molecular docking technique.

Polymorphisms at Amino Acid Residues 141 and 154 Influence Conformational Variation in Ovine PrP

Science.gov (United States)

Yang, Sujeong; Thackray, Alana M.; Hopkins, Lee; Monie, Tom P.; Burke, David F.; Bujdoso, Raymond

2014-01-01

Polymorphisms in ovine PrP at amino acid residues 141 and 154 are associated with susceptibility to ovine prion disease: Leu141Arg154 with classical scrapie and Phe141Arg154 and Leu141His154 with atypical scrapie. Classical scrapie is naturally transmissible between sheep, whereas this may not be the case with atypical scrapie. Critical amino acid residues will determine the range or stability of structural changes within the ovine prion protein or its functional interaction with potential cofactors, during conversion of PrPC to PrPSc in these different forms of scrapie disease. Here we computationally identified that regions of ovine PrP, including those near amino acid residues 141 and 154, displayed more conservation than expected based on local structural environment. Molecular dynamics simulations showed these conserved regions of ovine PrP displayed genotypic differences in conformational repertoire and amino acid side-chain interactions. Significantly, Leu141Arg154 PrP adopted an extended beta sheet arrangement in the N-terminal palindromic region more frequently than the Phe141Arg154 and Leu141His154 variants. We supported these computational observations experimentally using circular dichroism spectroscopy and immunobiochemical studies on ovine recombinant PrP. Collectively, our observations show amino acid residues 141 and 154 influence secondary structure and conformational change in ovine PrP that may correlate with different forms of scrapie. PMID:25126555

Uncovering the local inelastic interactions during manufacture of ductile cast iron: How the substructure of the graphite particles can induce residual stress concentrations in the matrix

Science.gov (United States)

Andriollo, Tito; Hellström, Kristina; Sonne, Mads Rostgaard; Thorborg, Jesper; Tiedje, Niels; Hattel, Jesper

2018-02-01

Recent X-ray diffraction (XRD) measurements have revealed that plastic deformation and a residual elastic strain field can be present around the graphite particles in ductile cast iron after manufacturing, probably due to some local mismatch in thermal contraction. However, as only one component of the elastic strain tensor could be obtained from the XRD data, the shape and magnitude of the associated residual stress field have remained unknown. To compensate for this and to provide theoretical insight into this unexplored topic, a combined experimental-numerical approach is presented in this paper. First, a material equivalent to the ductile cast iron matrix is manufactured and subjected to dilatometric and high-temperature tensile tests. Subsequently, a two-scale hierarchical top-down model is devised, calibrated on the basis of the collected data and used to simulate the interaction between the graphite particles and the matrix during manufacturing of the industrial part considered in the XRD study. The model indicates that, besides the viscoplastic deformation of the matrix, the effect of the inelastic deformation of the graphite has to be considered to explain the magnitude of the XRD strain. Moreover, the model shows that the large elastic strain perturbations recorded with XRD close to the graphite-matrix interface are not artifacts due to e.g. sharp gradients in chemical composition, but correspond to residual stress concentrations induced by the conical sectors forming the internal structure of the graphite particles. In contrast to common belief, these results thus suggest that ductile cast iron parts cannot be considered, in general, as stress-free at the microstructural scale.

Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis

Directory of Open Access Journals (Sweden)

Yushen Du

2016-11-01

Full Text Available Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp, we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available.

BECN2 interacts with ATG14 through a metastable coiled-coil to mediate autophagy: BECN2 CCD Structure and Interaction with ATG14

Energy Technology Data Exchange (ETDEWEB)

Su, Minfei; Li, Yue; Wyborny, Shane; Neau, David; Chakravarthy, Srinivas; Levine, Beth; Colbert, Christopher L.; Sinha, Sangita C. (NDSU); (IIT); (Cornell); (UTSMC)

2017-03-12

ATG14 binding to BECN/Beclin homologs is essential for autophagy, a critical catabolic homeostasis pathway. Here, we show that the α-helical, coiled-coil domain (CCD) of BECN2, a recently identified mammalian BECN1 paralog, forms an antiparallel, curved homodimer with seven pairs of nonideal packing interactions, while the BECN2 CCD and ATG14 CCD form a parallel, curved heterodimer stabilized by multiple, conserved polar interactions. Compared to BECN1, the BECN2 CCD forms a weaker homodimer, but binds more tightly to the ATG14 CCD. Mutation of nonideal BECN2 interface residues to more ideal pairs improves homodimer self-association and thermal stability. Unlike BECN1, all BECN2 CCD mutants bind ATG14, although more weakly than wild type. Thus, polar BECN2 CCD interface residues result in a metastable homodimer, facilitating dissociation, but enable better interactions with polar ATG14 residues stabilizing the BECN2:ATG14 heterodimer. These structure-based mechanistic differences in BECN1 and BECN2 homodimerization and heterodimerization likely dictate competitive ATG14 recruitment.

Multiple Taf subunits of TFIID interact with Ino2 activation domains and contribute to expression of genes required for yeast phospholipid biosynthesis.

Science.gov (United States)

Hintze, Stefan; Engelhardt, Maike; van Diepen, Laura; Witt, Eric; Schüller, Hans-Joachim

2017-12-01

Expression of phospholipid biosynthetic genes in yeast requires activator protein Ino2 which can bind to the UAS element inositol/choline-responsive element (ICRE) and trigger activation of target genes, using two separate transcriptional activation domains, TAD1 and TAD2. However, it is still unknown which cofactors mediate activation by TADs of Ino2. Here, we show that multiple subunits of basal transcription factor TFIID (TBP-associated factors Taf1, Taf4, Taf6, Taf10 and Taf12) are able to interact in vitro with activation domains of Ino2. Interaction was no longer observed with activation-defective variants of TAD1. We were able to identify two nonoverlapping regions in the N-terminus of Taf1 (aa 1-100 and aa 182-250) each of which could interact with TAD1 of Ino2 as well as with TAD4 of activator Adr1. Specific missense mutations within Taf1 domain aa 182-250 affecting basic and hydrophobic residues prevented interaction with wild-type TAD1 and caused reduced expression of INO1. Using chromatin immunoprecipitation we demonstrated Ino2-dependent recruitment of Taf1 and Taf6 to ICRE-containing promoters INO1 and CHO2. Transcriptional derepression of INO1 was no longer possible with temperature-sensitive taf1 and taf6 mutants cultivated under nonpermissive conditions. This result supports the hypothesis of Taf-dependent expression of structural genes activated by Ino2. © 2017 John Wiley & Sons Ltd.

Ouabain affinity determining residues lie close to the Na/K pump ion pathway.

Science.gov (United States)

Artigas, Pablo; Gadsby, David C

2006-08-15

The Na/K pump establishes essential ion concentration gradients across animal cell membranes. Cardiotonic steroids, such as ouabain, are specific inhibitors of the Na/K pump. We exploited the marine toxin, palytoxin, to probe both the ion translocation pathway through the Na/K pump and the site of its interaction with ouabain. Palytoxin uncouples the pump's gates, which normally open strictly alternately, thus allowing both gates to sometimes be open, so transforming the pump into an ion channel. Palytoxin therefore permits electrophysiological analysis of even a single Na/K pump. We used outside-out patch recording of Xenopus alpha1beta3 Na/K pumps, which were made ouabain-resistant by point mutation, after expressing them in Xenopus oocytes. Endogenous, ouabain-sensitive, Xenopus alpha1beta3 Na/K pumps were silenced by continuous exposure to ouabain. We found that side-chain charge of two residues at either end of the alpha subunit's first extracellular loop, known to make a major contribution to ouabain affinity, strongly influenced conductance of single palytoxin-bound pump-channels by an electrostatic mechanism. The effects were mimicked by modification of cysteines introduced at those two positions with variously charged methanethiosulfonate reagents. The consequences of these modifications demonstrate that both residues lie in a wide vestibule near the mouth of the pump's ion pathway. Bound ouabain protects the site with the strongest influence on conductance from methanethiosulfonate modification, while leaving the site with the weaker influence unprotected. The results suggest a method for mapping the footprint of bound cardiotonic steroid on the extracellular surface of the Na/K pump.

Properties of Residue from Olive Oil Extraction as a Raw Material for Sustainable Construction Materials. Part I: Physical Properties

Directory of Open Access Journals (Sweden)

Almudena Díaz-García

2017-01-01

Full Text Available Action on climate, the environment, and the efficient use of raw materials and resources are important challenges facing our society. Against this backdrop, the construction industry must adapt to new trends and environmentally sustainable construction systems, thus requiring lines of research aimed at keeping energy consumption in new buildings as low as possible. One of the main goals of this research is to efficiently contribute to reducing the amount of residue from olive oil extraction using a two-phase method. This can be achieved by producing alternative structural materials to be used in the construction industry by means of a circular economy. The technical feasibility of adding said residue to ceramic paste was proven by analyzing the changes produced in the physical properties of the paste, which were then compared to the properties of the reference materials manufactured with clay without residue. Results obtained show that the heating value of wet pomace can contribute to the thermal needs of the sintering process, contributing 30% of energy in pieces containing 3% of said material. Likewise, adding larger amounts of wet pomace to the clay body causes a significant decrease in bulk density values.

Properties of Residue from Olive Oil Extraction as a Raw Material for Sustainable Construction Materials. Part I: Physical Properties.

Science.gov (United States)

Díaz-García, Almudena; Martínez-García, Carmen; Cotes-Palomino, Teresa

2017-01-25

Action on climate, the environment, and the efficient use of raw materials and resources are important challenges facing our society. Against this backdrop, the construction industry must adapt to new trends and environmentally sustainable construction systems, thus requiring lines of research aimed at keeping energy consumption in new buildings as low as possible. One of the main goals of this research is to efficiently contribute to reducing the amount of residue from olive oil extraction using a two-phase method. This can be achieved by producing alternative structural materials to be used in the construction industry by means of a circular economy. The technical feasibility of adding said residue to ceramic paste was proven by analyzing the changes produced in the physical properties of the paste, which were then compared to the properties of the reference materials manufactured with clay without residue. Results obtained show that the heating value of wet pomace can contribute to the thermal needs of the sintering process, contributing 30% of energy in pieces containing 3% of said material. Likewise, adding larger amounts of wet pomace to the clay body causes a significant decrease in bulk density values.

Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.

Science.gov (United States)

Krystek, S; Stouch, T; Novotny, J

1993-12-05

An empirical function was used to calculate free energy change (delta G) of complex formation between the following inhibitors and enzymes: Kunitz inhibitor (BPTI) with trypsin, trypsinogen and kallikrein; turkey ovomucoid 3rd domain (OMTKY3) with alpha-chymotrypsin and the Streptomyces griseus protease B; the potato chymotrypsin inhibitor with the protease B; and the barely chymotrypsin inhibitor and eglin-c with subtilisin and thermitase. Using X-ray coordinates of the nine complexes, we estimated the contributions that hydrophobic effect, electrostatic interactions and side-chain conformational entropy make towards the stability of the complexes. The calculated delta G values showed good agreement with the experimentally measured ones, the only exception being the kallikrein/BPTI complex whose X-ray structure was solved at an exceptionally low pH. In complexes with different enzymes, the same inhibitor residues contributed identically towards complex formation (delta G(residue) Spearman rank correlation coefficient 0.7 to 1.0). The most productive enzyme-contacting residues in OMTKY3, eglin-c, and the chymotrypsin inhibitors were found in analogous positions on their respective binding loops; thus, our calculations identified a functional (energetic) motif that parallels the well-known structural similarity of the binding loops. The delta G values calculated for BPTI complexed with trypsin (-21.7 kcal) and trypsinogen (-23.4 kcal) were similar and close to the experimental delta G value of the trypsin/BPTI complex (-18.1 kcal), lending support to the suggestion that the 10(7) difference in the observed stabilities (KA) of these two complexes reflects the energetic cost of conformational changes induced in trypsinogen during the pre-equilibrium stages of complex formation. In almost all of the complexes studied, the stabilization free energy contributed by the inhibitors was larger than that donated by the enzymes. In the trypsin-BPTI complex, the calculated

Defining the contributions of permanent electrostatics, Pauli repulsion, and dispersion in density functional theory calculations of intermolecular interaction energies

Energy Technology Data Exchange (ETDEWEB)

Horn, Paul R., E-mail: prhorn@berkeley.edu; Mao, Yuezhi; Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu [Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA and Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley, California 94720 (United States)

2016-03-21

In energy decomposition analysis of Kohn-Sham density functional theory calculations, the so-called frozen (or pre-polarization) interaction energy contains contributions from permanent electrostatics, dispersion, and Pauli repulsion. The standard classical approach to separate them suffers from several well-known limitations. We introduce an alternative scheme that employs valid antisymmetric electronic wavefunctions throughout and is based on the identification of individual fragment contributions to the initial supersystem wavefunction as determined by an energetic optimality criterion. The density deformations identified with individual fragments upon formation of the initial supersystem wavefunction are analyzed along with the distance dependence of the new and classical terms for test cases that include the neon dimer, ammonia borane, water-Na{sup +}, water-Cl{sup −}, and the naphthalene dimer.

Ferrochelatase from Rhodopseudomonas sphaeroides: substrate specificity and role of sulfhydryl and arginyl residues

International Nuclear Information System (INIS)

Dailey, H.A.; Fleming, J.E.; Harbin, B.M.

1986-01-01

Purified ferrochelatase from the bacterium Rhodopseudomonas sphaeroides was examined to determine the roles of cationic and sulfhydryl residues in substrate binding. Reaction of the enzyme sulfhydryl residues with N-ethylmaleimide or monobromobimane resulted in a rapid loss of enzyme activity. Ferrous iron, but not porphyrin substrate, had a protective effect against inactivation by these two reagents. Quantitation with 3 H-labeled N-ethylmaleimide revealed that inactivation required one to two sulfhydryl groups to be modified. Modification of arginyl residues with either 2,3-butanedione or camphorquinone 10-sulfonate resulted in a loss of ferrochelatase activity. A kinetic analysis of the modified enzyme showed that the K/sub m/ for ferrous iron was not altered but that the K/sub m/ for the prophyrin substrate was increased. These data suggested that arginyl residues may be involved in porphyrin binding, possibly via charge pair interactions between the arginyl residue and the anionic porphyrin propionate side chain. Modification of lysyl residues had no effect on enzyme activity. The authors also examined the ability of bacterial ferrochelatase to use various 2,4-disubstituted porphyrins as substrates. The authors found that 2,4-bis-acetal- and 2,4-disulfonate deuteroporphyrins were effective substrates for the purified bacterial enzyme and that N-methylprotoporphyrin was an effective inhibitor of the enzyme. Data for the ferrochelatase of R. sphaeroides are compared with previously published data for the eucaryotic enzyme

Differential expression and localization of glycosidic residues in in vitro- and in vivo-matured cumulus-oocyte complexes in equine and porcine species.

Science.gov (United States)

Accogli, Gianluca; Douet, Cécile; Ambruosi, Barbara; Martino, Nicola Antonio; Uranio, Manuel Filioli; Deleuze, Stefan; Dell'Aquila, Maria Elena; Desantis, Salvatore; Goudet, Ghylène

2014-12-01

Glycoprotein oligosaccharides play major roles during reproduction, yet their function in gamete interactions is not fully elucidated. Identification and comparison of the glycan pattern in cumulus-oocyte complexes (COCs) from species with different efficiencies of in vitro spermatozoa penetration through the zona pellucida (ZP) could help clarify how oligosaccharides affect gamete interactions. We compared the expression and localization of 12 glycosidic residues in equine and porcine in vitro-matured (IVM) and preovulatory COCs by means of lectin histochemistry. The COCs glycan pattern differed between animals and COC source (IVM versus preovulatory). Among the 12 carbohydrate residues investigated, the IVM COCs from these two species shared: (a) sialo- and βN-acetylgalactosamine (GalNAc)-terminating glycans in the ZP; (b) sialylated and fucosylated glycans in cumulus cells; and (c) GalNAc and N-acetylglucosamine (GlcNAc) glycans in the ooplasm. Differences in the preovulatory COCs of the two species included: (a) sialoglycans and GlcNAc terminating glycans in the equine ZP versus terminal GalNAc and internal GlcNAc in the porcine ZP; (b) terminal galactosides in equine cumulus cells versus terminal GlcNAc and fucose in porcine cohorts; and (c) fucose in the mare ooplasm versus lactosamine and internal GlcNAc in porcine oocyte cytoplasm. Furthermore, equine and porcine cumulus cells and oocytes contributed differently to the synthesis of ZP glycoproteins. These results could be attributed to the different in vitro fertilization efficiencies between these two divergent, large-animal models. © 2014 Wiley Periodicals, Inc.

Interactions of the gasotransmitters contribute to microvascular tone (dysregulation in the preterm neonate.

Directory of Open Access Journals (Sweden)

Rebecca M Dyson

Full Text Available Hydrogen sulphide (H2S, nitric oxide (NO, and carbon monoxide (CO are involved in transitional microvascular tone dysregulation in the preterm infant; however there is conflicting evidence on the interaction of these gasotransmitters, and their overall contribution to the microcirculation in newborns is not known. The aim of this study was to measure the levels of all 3 gasotransmitters, characterise their interrelationships and elucidate their combined effects on microvascular blood flow.90 preterm neonates were studied at 24h postnatal age. Microvascular studies were performed by laser Doppler. Arterial COHb levels (a measure of CO were determined through co-oximetry. NO was measured as nitrate and nitrite in urine. H2S was measured as thiosulphate by liquid chromatography. Relationships between levels of the gasotransmitters and microvascular blood flow were assessed through partial correlation controlling for the influence of gestational age. Structural equation modelling was used to examine the combination of these effects on microvascular blood flow and derive a theoretical model of their interactions.No relationship was observed between NO and CO (p = 0.18, r = 0.18. A positive relationship between NO and H2S (p = 0.008, r = 0.28 and an inverse relationship between CO and H2S (p = 0.01, r = -0.33 exists. Structural equation modelling was used to examine the combination of these effects on microvascular blood flow. The model with the best fit is presented.The relationships between NO and H2S, and CO and H2S may be of importance in the preterm newborn, particularly as NO levels in males are associated with higher H2S levels and higher microvascular blood flow and CO in females appears to convey protection against vascular dysregulation. Here we present a theoretical model of these interactions and their overall effects on microvascular flow in the preterm newborn, upon which future mechanistic studies may be based.

Handling of Solid Residues

International Nuclear Information System (INIS)

Medina Bermudez, Clara Ines

1999-01-01

The topic of solid residues is specifically of great interest and concern for the authorities, institutions and community that identify in them a true threat against the human health and the atmosphere in the related with the aesthetic deterioration of the urban centers and of the natural landscape; in the proliferation of vectorial transmitters of illnesses and the effect on the biodiversity. Inside the wide spectrum of topics that they keep relationship with the environmental protection, the inadequate handling of solid residues and residues dangerous squatter an important line in the definition of political and practical environmentally sustainable. The industrial development and the population's growth have originated a continuous increase in the production of solid residues; of equal it forms, their composition day after day is more heterogeneous. The base for the good handling includes the appropriate intervention of the different stages of an integral administration of residues, which include the separation in the source, the gathering, the handling, the use, treatment, final disposition and the institutional organization of the administration. The topic of the dangerous residues generates more expectation. These residues understand from those of pathogen type that are generated in the establishments of health that of hospital attention, until those of combustible, inflammable type, explosive, radio-active, volatile, corrosive, reagent or toxic, associated to numerous industrial processes, common in our countries in development

Literature mining of protein-residue associations with graph rules learned through distant supervision

Directory of Open Access Journals (Sweden)

Ravikumar KE

2012-10-01

Full Text Available Abstract Background We propose a method for automatic extraction of protein-specific residue mentions from the biomedical literature. The method searches text for mentions of amino acids at specific sequence positions and attempts to correctly associate each mention with a protein also named in the text. The methods presented in this work will enable improved protein functional site extraction from articles, ultimately supporting protein function prediction. Our method made use of linguistic patterns for identifying the amino acid residue mentions in text. Further, we applied an automated graph-based method to learn syntactic patterns corresponding to protein-residue pairs mentioned in the text. We finally present an approach to automated construction of relevant training and test data using the distant supervision model. Results The performance of the method was assessed by extracting protein-residue relations from a new automatically generated test set of sentences containing high confidence examples found using distant supervision. It achieved a F-measure of 0.84 on automatically created silver corpus and 0.79 on a manually annotated gold data set for this task, outperforming previous methods. Conclusions The primary contributions of this work are to (1 demonstrate the effectiveness of distant supervision for automatic creation of training data for protein-residue relation extraction, substantially reducing the effort and time involved in manual annotation of a data set and (2 show that the graph-based relation extraction approach we used generalizes well to the problem of protein-residue association extraction. This work paves the way towards effective extraction of protein functional residues from the literature.

Literature mining of protein-residue associations with graph rules learned through distant supervision.

Science.gov (United States)

Ravikumar, Ke; Liu, Haibin; Cohn, Judith D; Wall, Michael E; Verspoor, Karin

2012-10-05

We propose a method for automatic extraction of protein-specific residue mentions from the biomedical literature. The method searches text for mentions of amino acids at specific sequence positions and attempts to correctly associate each mention with a protein also named in the text. The methods presented in this work will enable improved protein functional site extraction from articles, ultimately supporting protein function prediction. Our method made use of linguistic patterns for identifying the amino acid residue mentions in text. Further, we applied an automated graph-based method to learn syntactic patterns corresponding to protein-residue pairs mentioned in the text. We finally present an approach to automated construction of relevant training and test data using the distant supervision model. The performance of the method was assessed by extracting protein-residue relations from a new automatically generated test set of sentences containing high confidence examples found using distant supervision. It achieved a F-measure of 0.84 on automatically created silver corpus and 0.79 on a manually annotated gold data set for this task, outperforming previous methods. The primary contributions of this work are to (1) demonstrate the effectiveness of distant supervision for automatic creation of training data for protein-residue relation extraction, substantially reducing the effort and time involved in manual annotation of a data set and (2) show that the graph-based relation extraction approach we used generalizes well to the problem of protein-residue association extraction. This work paves the way towards effective extraction of protein functional residues from the literature.

Contributions of conserved residues at the gating interface of glycine receptors

DEFF Research Database (Denmark)

Pless, Stephan Alexander; Leung, Ada W Y; Galpin, Jason D

2011-01-01

and the in vivo nonsense suppression method to incorporate unnatural amino acids to probe the electrostatic and hydrophobic contributions of five highly conserved side chains near the interface, Glu-53, Phe-145, Asp-148, Phe-187, and Arg-218. Our results suggest a salt bridge between Asp-148 in loop 7 and Arg-218......Glycine receptors (GlyRs) are chloride channels that mediate fast inhibitory neurotransmission and are members of the pentameric ligand-gated ion channel (pLGIC) family. The interface between the ligand binding domain and the transmembrane domain of pLGICs has been proposed to be crucial...

1H and 31P nuclear magnetic resonance investigation of the interaction between 2,3-diphosphoglycerate and human normal adult hemoglobin

International Nuclear Information System (INIS)

Russu, I.M.; Wu, S.S.; Bupp, K.A.; Ho, N.T.; Ho, C.

1990-01-01

High-resolution 1 H and 31 P nuclear magnetic resonance spectroscopy has been used to investigate the binding of 2,3-diphosphoglycerate to human normal adult hemoglobin and the molecular interactions involved in the allosteric effect of the 2,3-diphosphoglycerate molecule on hemoglobin. Individual hydrogen ion NMR titration curves have been obtained for 22-26 histidyl residues of hemoglobin and for each phosphate group of 2,3-diphosphoglycerate with hemoglobin in both the deoxy and carbonmonoxy forms. The results indicate that 2,3-diphosphoglycerate binds to deoxyhemoglobin at the central cavity between the two β chains and the binding involves the β2-histidyl residues. Moreover, the results suggest that the binding site of 2,3-diphosphoglycerate to carbonmonoxyhemoglobin contains the same (or at least some of the same) amino acid residues responsible for binding in the deoxy form. As a result of the specific interactions with 2,3-diphosphoglycerate, the β2-histidyl residues make a significant contribution to the alkaline Bohr effect under these experimental conditions. These results give the first experimental demonstration that long-range electrostatic and/or conformation effects of the binding could play an important role in the allosteric effect of 2,3-diphosphoglycerate on hemoglobin. The 31 P nuclear magnetic resonance titration data for each phosphate group of 2,3-diphosphoglycerate have been used to calculate the pK values of the phosphate groups in 2,3-diphosphoglycerate bound to deoxy- and carbon-monoxyhemoglobin and the proton uptake by 2,3-diphosphoglycerate upon ligand binding to hemoglobin

Bioenergy from agro-industrial residues in the East African region. Summary report

Energy Technology Data Exchange (ETDEWEB)

Jungersen, G. [Dansk Teknologisk Inst. (Denmark); Kivaisi, A.; Rubindamayugi, M. [Univ. of Dar es Salaam (Tanzania, United Republic of)

1998-05-01

Tanzania has recently developed a comprehensive environmental policy which has put high priority on several specific environmental issues. One of the issues is the quality of waste water. A special priority is given to the pollution from the sisal industry. The East-African agro-industries generate very large quantities of organic residues from production and processing of different crops. These residues form a major contribution to the pollution of air, soil and waterways, but, at the same time they constitute a large potential for production of bioenergy through anaerobic digestion as well as potential substrate for other biological fermentation processes. Generally, these residues are regarded as having no or very little value and the different disposal methods are mainly a matter of getting rid of the waste. The generation of residues are very often concentrated on few large units, which makes the exploitation of these resources feasible in large scale biogas systems. Typically the units will have a potential of a daily methane generation of 1,000-20,000 m{sup 3} CH{sub 4}, equivalent to a potential electricity production of 0.2-3.2 MW. The future utilization of these resources for production of valuable products is described in this report. This report consists of 3 volumes. This summary report including the main objectives and findings from the different project report: Mapping and Quantification of Organic Agro-Industrial Residues in East Africa; Biogas - Bioenergy Potential in East Africa, Seminar Proceedings, Siler Sands, Dar es Salaam 22-23 September 1997; Bioenergy from Sisal residues - Experimental results and Capacity Building Activities. (EG)

The n→π* Interaction.

Science.gov (United States)

Newberry, Robert W; Raines, Ronald T

2017-08-15

groups, demonstrating unequivocally that a dipolar mechanism is insufficient to describe these interactions. Rather, these interactions have important quantum-mechanical character that can be evaluated through careful experimental analysis and judicious use of computation. Although individual n→π* interactions are relatively weak (∼0.3-0.7 kcal/mol), the ubiquity of carbonyl groups across chemistry and biology gives the n→π* interaction broad impact. In particular, the n→π* interaction is likely to play an important role in dictating protein structure. Indeed, bioinformatics analysis suggests that approximately one-third of residues in folded proteins satisfy the geometric requirements to engage in an n→π* interaction, which is likely to be of particular importance for the α-helix. Other carbonyl-dense polymeric materials like polyesters and peptoids are also influenced by n→π* interactions, as are a variety of small molecules, some with particular medicinal importance. Research will continue to identify molecules whose conformation and activity are affected by the n→π* interaction and will clarify their specific contributions to the structures of biomacromolecules.

Repaglinide-gemfibrozil drug interaction: inhibition of repaglinide glucuronidation as a potential additional contributing mechanism.

Science.gov (United States)

Gan, Jinping; Chen, Weiqi; Shen, Hong; Gao, Ling; Hong, Yang; Tian, Yuan; Li, Wenying; Zhang, Yueping; Tang, Yuwei; Zhang, Hongjian; Humphreys, William Griffith; Rodrigues, A David

2010-12-01

To further explore the mechanism underlying the interaction between repaglinide and gemfibrozil, alone or in combination with itraconazole. Repaglinide metabolism was assessed in vitro (human liver subcellular fractions, fresh human hepatocytes, and recombinant enzymes) and the resulting incubates were analyzed, by liquid chromatography-mass spectrometry (LC-MS) and radioactivity counting, to identify and quantify the different metabolites therein. Chemical inhibitors, in addition to a trapping agent, were also employed to elucidate the importance of each metabolic pathway. Finally, a panel of human liver microsomes (genotyped for UGT1A1*28 allele status) was used to determine the importance of UGT1A1 in the direct glucuronidation of repaglinide. The results of the present study demonstrate that repaglinide can undergo direct glucuronidation, a pathway that can possibly contribute to the interaction with gemfibrozil. For example, [³H]-repaglinide formed glucuronide and oxidative metabolites (M2 and M4) when incubated with primary human hepatocytes. Gemfibrozil effectively inhibited (∼78%) both glucuronide and M4 formation, but had a minor effect on M2 formation. Concomitantly, the overall turnover of repaglinide was also inhibited (∼80%), and was completely abolished when gemfibrozil was co-incubated with itraconazole. These observations are in qualitative agreement with the in vivo findings. UGT1A1 plays a significant role in the glucuronidation of repaglinide. In addition, gemfibrozil and its glucuronide inhibit repaglinide glucuronidation and the inhibition by gemfibrozil glucuronide is time-dependent. Inhibition of UGT enzymes, especially UGT1A1, by gemfibrozil and its glucuronide is an additional mechanism to consider when rationalizing the interaction between repaglinide and gemfibrozil. © 2010 The Authors. British Journal of Clinical Pharmacology © 2010 The British Pharmacological Society.

Nitrogen recycling from fuel-extracted algal biomass: residuals as the sole nitrogen source for culturing Scenedesmus acutus.

Science.gov (United States)

Gu, Huiya; Nagle, Nick; Pienkos, Philip T; Posewitz, Matthew C

2015-05-01

In this study, the reuse of nitrogen from fuel-extracted algal residues was investigated. The alga Scenedesmus acutus was found to be able to assimilate nitrogen contained in amino acids, yeast extracts, and proteinaceous alga residuals. Moreover, these alternative nitrogen resources could replace nitrate in culturing media. The ability of S. acutus to utilize the nitrogen remaining in processed algal biomass was unique among the promising biofuel strains tested. This alga was leveraged in a recycling approach where nitrogen is recovered from algal biomass residuals that remain after lipids are extracted and carbohydrates are fermented to ethanol. The protein-rich residuals not only provided an effective nitrogen resource, but also contributed to a carbon "heterotrophic boost" in subsequent culturing, improving overall biomass and lipid yields relative to the control medium with only nitrate. Prior treatment of the algal residues with Diaion HP20 resin was required to remove compounds inhibitory to algal growth. Copyright © 2014 Elsevier Ltd. All rights reserved.

Investigation of the possibility of using residual heat reactor energy

Science.gov (United States)

Aminov, R. Z.; Yurin, V. E.; Bessonov, V. N.

2017-11-01

The largest contribution to the probable frequency of core damage is blackout events. The main component of the heat capacity at each reactor within a few minutes following a blackout is the heat resulting from the braking of beta-particles and the transfer of gamma-ray energy by the fission fragments and their decay products, which is known as the residual heat. The power of the residual heat changes gradually over a long period of time and for a VVER-1000 reactor is about 15-20 MW of thermal power over 72 hours. Current cooldown systems increase the cost of the basic nuclear power plants (NPP) funds without changing the amount of electricity generated. Such systems remain on standby, accelerating the aging of the equipment and accordingly reducing its reliability. The probability of system failure increases with the duration of idle time. Furthermore, the reactor residual heat energy is not used. A proposed system for cooling nuclear power plants involves the use of residual thermal power to supply the station’s own needs in emergency situations accompanied by a complete blackout. The thermal power of residual heat can be converted to electrical energy through an additional low power steam turbine. In normal mode, the additional steam turbine generates electricity, which makes it possible to ensure spare NPP and a return on the investment in the reservation system. In this work, experimental data obtained from a Balakovo NPP was analyzed to determine the admissibility of cooldown of the reactors through the 2nd circuit over a long time period, while maintaining high-level parameters for the steam generated by the steam generators.

Geochemical, hydrological, and biological cycling of energy residual. Research plan

International Nuclear Information System (INIS)

Wobber, F.J.

1983-03-01

Proposed research goals and specific research areas designed to provide a base of fundamental scientific information so that the geochemical, hydrological, and biophysical mechanisms that contribute to the transport and long term fate of energy residuals in natural systems can be understood are described. Energy development and production have resulted in a need for advanced scientific information on the geochemical transformations, transport rates, and potential for bioaccumulation of contaminants in subsurface environments

P-matrix description of charged particles interaction

International Nuclear Information System (INIS)

Babenko, V.A.; Petrov, N.M.

1992-01-01

The paper deals with formalism of the P-matrix description of two charged particles interaction. Separation in the explicit form of the background part corresponding to the purely Coulomb interaction in the P-matrix is proposed. Expressions for the purely Coulomb P-matrix, its poles, residues and purely Coulomb P-matrix approach eigenfunctions are obtained. (author). 12 refs

Salt bridges: geometrically specific, designable interactions.

Science.gov (United States)

Donald, Jason E; Kulp, Daniel W; DeGrado, William F

2011-03-01

Salt bridges occur frequently in proteins, providing conformational specificity and contributing to molecular recognition and catalysis. We present a comprehensive analysis of these interactions in protein structures by surveying a large database of protein structures. Salt bridges between Asp or Glu and His, Arg, or Lys display extremely well-defined geometric preferences. Several previously observed preferences are confirmed, and others that were previously unrecognized are discovered. Salt bridges are explored for their preferences for different separations in sequence and in space, geometric preferences within proteins and at protein-protein interfaces, co-operativity in networked salt bridges, inclusion within metal-binding sites, preference for acidic electrons, apparent conformational side chain entropy reduction on formation, and degree of burial. Salt bridges occur far more frequently between residues at close than distant sequence separations, but, at close distances, there remain strong preferences for salt bridges at specific separations. Specific types of complex salt bridges, involving three or more members, are also discovered. As we observe a strong relationship between the propensity to form a salt bridge and the placement of salt-bridging residues in protein sequences, we discuss the role that salt bridges might play in kinetically influencing protein folding and thermodynamically stabilizing the native conformation. We also develop a quantitative method to select appropriate crystal structure resolution and B-factor cutoffs. Detailed knowledge of these geometric and sequence dependences should aid de novo design and prediction algorithms. Copyright © 2010 Wiley-Liss, Inc.

PENETAPAN RESIDU DAN PERKIRAAN PENETAPAN BATAS MAKSIMUM RESIDU (BMR ORGANOKLORIN PADA SIMPLISIA

Directory of Open Access Journals (Sweden)

Ani Isnawati

2012-10-01

Full Text Available Penggunaaan bahan obat tradisional (simplisia untuk skala industri dan peningkatan produksi tanaman obat dalam skala besar menjadi tidak ekonomis tanpa pestisida. Disatu sisi penggunaan pestisida dapat menguntungkan yaitu menyebabkan toksis pada hama namun disisi lain toksisitas dapat terjadi juga pada manusia, sehingga residu pestisida dalam tanaman obat yang dikonsumsi dalam jangka panjang akan merugikan kesehatan. Batas maksimum Residu (BMR pestisida dalam simplisia baik di Indonesia maupun di negara lain belum ditetapkan. Sehingga untuk itu untuk mengetahui adanya residu pestisida jenis organoklorin yang telah dilarang penggunaannya melalui Permentan No.434.1/kpts/TP.270/7/2001 dan untuk mengetahui batas keamanannya, maka perlu dilakukan penetapan residu organoklorin dalam simplisia dan menetapkan batas keamanan berdasarkan perhitungan secara teoritis. Pengujian residu dilakukan terhadap golongan pestisida organoklorin pada 4 jenis simplisia (daun wungu (Graptophyllum pictum (L Grifl, daun sambiloto Andrographis paniculata Ness, herba pegagan (Centella  asiatica (L Urban, daun tempuyung (Sonchus arvensis (L yang berasal dari 3 lokasi penanaman, yaitu : perkebunan Tanaman Obat Manako (Jawa Barat, Balai Penelitian Tanaman Obat Tawangmangu (BPTO di Jawa Tengah dan Perkebunan Tanaman Obat Purwodadi (Jawa Timur. Pemeriksaan residu pestisida organoklorin menggunakan kromatografi gas dan perhitungan batas keamanan dihitung dengan adanya nilai ADI (Acceptable daily intake yang telah ditetapkan bersama antara JAO dan WHO serta perkiraan banyaknya konsumsi simplisia. Hasil Pengujian residu pestisida organoklorin diperoleh bahwa simplisia daun Wungu (Tawangmangu mengandung residu lindan dengan kadar 0,24 mg/kg, pegagan (Purwodadi, mengandung lindan 0,36 mg/kg dan aldrin 0,31 mg/kg serta pegagan (Manako mengandung heptaklor 0,15 mg/kg dan op-DDE 0,11 mg/kg. Adapun penghitungan BMR heptaklor dan lindan secara teoritis dengan asumsi rata

Interacting vegetative and thermal contributions to water movement in desert soil

Science.gov (United States)

Garcia, C.A.; Andraski, Brian J.; Stonestrom, David A.; Cooper, C.A.; Šimůnek, J.; Wheatcraft, S.W.

2011-01-01

Thermally driven water-vapor flow can be an important component of total water movement in bare soil and in deep unsaturated zones, but this process is often neglected when considering the effects of soil–plant–atmosphere interactions on shallow water movement. The objectives of this study were to evaluate the coupled and separate effects of vegetative and thermal-gradient contributions to soil water movement in desert environments. The evaluation was done by comparing a series of simulations with and without vegetation and thermal forcing during a 4.7-yr period (May 2001–December 2005). For vegetated soil, evapotranspiration alone reduced root-zone (upper 1 m) moisture to a minimum value (25 mm) each year under both isothermal and nonisothermal conditions. Variations in the leaf area index altered the minimum storage values by up to 10 mm. For unvegetated isothermal and nonisothermal simulations, root-zone water storage nearly doubled during the simulation period and created a persistent driving force for downward liquid fluxes below the root zone (total net flux ~1 mm). Total soil water movement during the study period was dominated by thermally driven vapor fluxes. Thermally driven vapor flow and condensation supplemented moisture supplies to plant roots during the driest times of each year. The results show how nonisothermal flow is coupled with plant water uptake, potentially influencing ecohydrologic relations in desert environments.

Research items regarding seismic residual risk evaluation

Energy Technology Data Exchange (ETDEWEB)

NONE

2013-08-15

After learning the Fukushima Dai-ichi NPP severe accidents in 2011, the government investigation committee proposed the effective use of probabilistic safety assessment (PSA), and now it is required to establish new safety rules reflecting the results of probabilistic risk assessment (PRA) and proposed severe accident measures. Since the Seismic Design Guide has been revised on September 19, 2006, JNES has been discussing seismic PRA (Levels 1-3) methods to review licensees' residual risk assessment while preparing seismic PRA models. Meanwhile, new safety standards for light water reactors are to be issued and enforced on July 2013, which require the residual risk of tsunami, in addition to earthquakes, should be lowered as much as possible. The Fukushima accidents raised the problems related to risk assessment, e.g. approaches based on multi-hazard (earthquake and tsunami), multi-unit, multi-site, and equipment's common cause failure. This fiscal year, while performing seismic and/or tsunami PRA to work on these problems, JNES picked up the equipment whose failure greatly contribute to core damage, surveyed accident management measures on those equipment as well as effectiveness to reduce core damage probability. (author)

Residual magnetic field in rotary machines; Campo magnetico residual en maquinas rotatorias

Energy Technology Data Exchange (ETDEWEB)

Gonzalez V, Esteban A; Apanco R, Marcelino [Instituto de Investigaciones Electricas, Cuernavaca, Morelos (Mexico)

2007-07-01

The residual magnetism is a phenomenon in which the magnetic dipoles of a substance are oriented in a certain degree. On the other hand, when internal forces exist capable of aligning elementary magnetic dipoles of a material, a permanent magnet is obtained. Just as in a conductor or in a material, in the elements of a rotary electrical machine magnetic fields can be induced that produce a residual magnetism or magnetization. In the rotary electrical machines, the magnetization phenomenon causes serious problems, such as the generation of induced currents that propitiate the mechanical wear in bearings, collars, trunnions and inclusive in the shaft, by effects known as pitting, frosting and spark tracks, as well as erroneous readings in vibration and temperature sensors, that in some cases can cause the shut down of the machine. In this article are presented the general concepts on the residual magnetism in rotary electrical machines, the causes that originate it and the problems that arises, as well as the demagnetization of the components that have residual magnetic field. The results obtained by the area of Electrical Equipment of the Instituto de Investigaciones Electricas are revised, during the execution of activities related to the measurement and elimination of the residual magnetic field in rotary electrical machines. [Spanish] El magnetismo residual es un fenomeno en el que los dipolos magneticos de una sustancia se encuentran orientados en un grado determinado. Por otro lado, cuando existen fuerzas internas capaces de alinear los dipolos magneticos elementales de un material, se tiene un iman permanente. Al igual que en un conductor o un material, en los elementos de una maquina electrica rotatoria se pueden inducir campos magneticos que producen un magnetismo residual o magnetizacion. En las maquinas electricas rotatorias, el fenomeno de magnetizacion causa graves problemas, como la generacion de corrientes inducidas que propician el desgaste mecanico

Maternal Dispositional Empathy and Electrodermal Reactivity: Interactive Contributions to Maternal Sensitivity with Toddler-Aged Children

Science.gov (United States)

Emery, Helen T.; McElwain, Nancy L.; Groh, Ashley M.; Haydon, Katherine C.; Roisman, Glenn I.

2015-01-01

The present study investigated maternal dispositional empathy and skin conductance level (SCL) reactivity to infant emotional cues as joint predictors of maternal sensitivity. Sixty-four mother-toddler dyads (31 boys) were observed across a series of interaction tasks during a laboratory visit, and maternal sensitivity was coded from approximately 55 minutes of observation per family. In a second, mother-only laboratory visit, maternal SCL reactivity to infant cues was assessed using a cry-laugh audio paradigm. Mothers reported on their dispositional empathy via a questionnaire. As hypothesized, mothers with greater dispositional empathy exhibited more sensitive behavior at low, but not high, levels of SCL reactivity to infant cues. Analyses examining self-reported emotional reactivity to the cry-laugh audio paradigm yielded a similar finding: dispositional empathy was related to greater sensitivity when mothers reported low, but not high, negative emotional reactivity. Results provide support for Dix’s (1991) affective model of parenting that underscores the combined contribution of the parent’s empathic tendencies and his/her own emotional experience in response to child emotions. Specificity of the Empathy × Reactivity interaction is discussed with respect to the context in which reactivity was assessed (infant cry versus laugh) and the type of sensitivity examined (sensitivity to the child’s distress versus non-distress). PMID:24955589

Biomass Residues from Agriculture and Potential Contribution towards Modern Energy Supply in West Africa