WorldWideScience

Sample records for residual secondary structure

  1. Residual structure of Streptococcus mutans biofilm following complete disinfection favors secondary bacterial adhesion and biofilm re-development.

    Directory of Open Access Journals (Sweden)

    Tatsuya Ohsumi

    Full Text Available Chemical disinfection of oral biofilms often leaves biofilm structures intact. This study aimed to examine whether the residual structure promotes secondary bacterial adhesion. Streptococcus mutans biofilms generated on resin-composite disks in a rotating disc reactor were disinfected completely with 70% isopropyl alcohol, and were again cultured in the same reactor after resupplying with the same bacterial solution. Specimens were subjected to fluorescence confocal laser scanning microscopy, viable cell counts and PCR-Invader assay in order to observe and quantify secondarily adhered cells. Fluorescence microscopic analysis, particularly after longitudinal cryosectioning, demonstrated stratified patterns of viable cells on the disinfected biofilm structure. Viable cell counts of test specimens were significantly higher than those of controls, and increased according to the amount of residual structure and culture period. Linear regression analysis exhibited a high correlation between viable and total cell counts. It was concluded that disinfected biofilm structures favored secondary bacterial adhesion.

  2. Application of secondary and residual stresses to the assessment of the structural integrity of nuclear power-generating plant

    International Nuclear Information System (INIS)

    Banahan, B.D.

    2008-01-01

    Magnox nuclear power stations were built in the 1960s to design codes that, in general, required weldments to be subject to a post-weld heat treatment to remove residual stresses. Implicit in this was the assumption that the heat treatment reduced the stresses significantly such that as stated in the codes 'stresses caused by fabrication and welding are practically annulled'. However, it has since been realised that the stresses remaining, although small, could still be significant when incorporated into the subsequently developed failure avoidance methodologies such as R6. Moreover, either at the time of construction or during the operating life, repairs are undertaken to remove manufacturing or service-induced defects. These repairs can be put into service with or without a post-weld heat treatment. As a consequence of a paucity of data for the two- and three-dimensional distribution of the magnitude of these stresses, extremely conservative values of stresses have been adopted to ensure that the plant is secure against the design intent throughout the service life. In this paper, the requirements of the failure-avoidance methodology R6 Revision 4 are briefly reviewed with respect to the categorisation of secondary and residual stresses and the application of the three approaches for determining the as-welded residual stress distribution at room temperature. These three levels comprise, Level 1, simple estimates, Level 2, bounding profiles, and Level 3, detailed evaluation. Examples are presented where knowledge of the residual stresses has been an important component of the overall integrity assessment. The first relates to multi-pass weldments in superheater headers fabricated from a ferritic steel and the second to the weldments in the standpipes, both at Magnox power stations with concrete pressure vessels. Although in these cases the weldments had been subject to a post-weld heat treatment, the remaining residual stresses presented a significant challenge to

  3. Amino acid code of protein secondary structure.

    Science.gov (United States)

    Shestopalov, B V

    2003-01-01

    The calculation of protein three-dimensional structure from the amino acid sequence is a fundamental problem to be solved. This paper presents principles of the code theory of protein secondary structure, and their consequence--the amino acid code of protein secondary structure. The doublet code model of protein secondary structure, developed earlier by the author (Shestopalov, 1990), is part of this theory. The theory basis are: 1) the name secondary structure is assigned to the conformation, stabilized only by the nearest (intraresidual) and middle-range (at a distance no more than that between residues i and i + 5) interactions; 2) the secondary structure consists of regular (alpha-helical and beta-structural) and irregular (coil) segments; 3) the alpha-helices, beta-strands and coil segments are encoded, respectively, by residue pairs (i, i + 4), (i, i + 2), (i, i = 1), according to the numbers of residues per period, 3.6, 2, 1; 4) all such pairs in the amino acid sequence are codons for elementary structural elements, or structurons; 5) the codons are divided into 21 types depending on their strength, i.e. their encoding capability; 6) overlappings of structurons of one and the same structure generate the longer segments of this structure; 7) overlapping of structurons of different structures is forbidden, and therefore selection of codons is required, the codon selection is hierarchic; 8) the code theory of protein secondary structure generates six variants of the amino acid code of protein secondary structure. There are two possible kinds of model construction based on the theory: the physical one using physical properties of amino acid residues, and the statistical one using results of statistical analysis of a great body of structural data. Some evident consequences of the theory are: a) the theory can be used for calculating the secondary structure from the amino acid sequence as a partial solution of the problem of calculation of protein three

  4. Automatic prediction of catalytic residues by modeling residue structural neighborhood

    Directory of Open Access Journals (Sweden)

    Passerini Andrea

    2010-03-01

    Full Text Available Abstract Background Prediction of catalytic residues is a major step in characterizing the function of enzymes. In its simpler formulation, the problem can be cast into a binary classification task at the residue level, by predicting whether the residue is directly involved in the catalytic process. The task is quite hard also when structural information is available, due to the rather wide range of roles a functional residue can play and to the large imbalance between the number of catalytic and non-catalytic residues. Results We developed an effective representation of structural information by modeling spherical regions around candidate residues, and extracting statistics on the properties of their content such as physico-chemical properties, atomic density, flexibility, presence of water molecules. We trained an SVM classifier combining our features with sequence-based information and previously developed 3D features, and compared its performance with the most recent state-of-the-art approaches on different benchmark datasets. We further analyzed the discriminant power of the information provided by the presence of heterogens in the residue neighborhood. Conclusions Our structure-based method achieves consistent improvements on all tested datasets over both sequence-based and structure-based state-of-the-art approaches. Structural neighborhood information is shown to be responsible for such results, and predicting the presence of nearby heterogens seems to be a promising direction for further improvements.

  5. Prediction of the Secondary Structure of HIV-1 gp120

    DEFF Research Database (Denmark)

    Hansen, Jan; Lund, Ole; Nielsen, Jens O.

    1996-01-01

    Fourier transform infrared spectroscopy. The predicted secondary structure of gp120 compared well with data from NMR analysis of synthetic peptides from the V3 loop and the C4 region. As a first step towards modeling the tertiary structure of gp120, the predicted secondary structure may guide the design......The secondary structure of HIV-1 gp120 was predicted using multiple alignment and a combination of two independent methods based on neural network and nearest-neighbor algorithms. The methods agreed on the secondary structure for 80% of the residues in BH10 gp120. Six helices were predicted in HIV...

  6. Mapping Residual Structure in Intrinsically Disordered Proteins at Residue Resolution Using Millisecond Hydrogen/Deuterium Exchange and Residue Averaging

    Science.gov (United States)

    Keppel, Theodore R.; Weis, David D.

    2015-04-01

    Measurement of residual structure in intrinsically disordered proteins can provide insights into the mechanisms by which such proteins undergo coupled binding and folding. The present work describes an approach to measure residual structure in disordered proteins using millisecond hydrogen/deuterium (H/D) exchange in a conventional bottom-up peptide-based workflow. We used the exchange mid-point, relative to a totally deuterated control, to quantify the rate of H/D exchange in each peptide. A weighted residue-by-residue average of these midpoints was used to map the extent of residual structure at near single-residue resolution. We validated this approach both by simulating a disordered protein and experimentally using the p300 binding domain of ACTR, a model disordered protein already well-characterized by other approaches. Secondary structure elements mapped in the present work are in good agreement with prior nuclear magnetic resonance measurements. The new approach was somewhat limited by a loss of spatial resolution and subject to artifacts because of heterogeneities in intrinsic exchange. Approaches to correct these limitations are discussed.

  7. Protein structure based prediction of catalytic residues

    Science.gov (United States)

    2013-01-01

    Background 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. Results 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. Conclusions 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

  8. Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures

    Directory of Open Access Journals (Sweden)

    Bailey Timothy L

    2006-02-01

    Full Text Available Abstract Background The structure of proteins may change as a result of the inherent flexibility of some protein regions. We develop and explore probabilistic machine learning methods for predicting a continuum secondary structure, i.e. assigning probabilities to the conformational states of a residue. We train our methods using data derived from high-quality NMR models. Results Several probabilistic models not only successfully estimate the continuum secondary structure, but also provide a categorical output on par with models directly trained on categorical data. Importantly, models trained on the continuum secondary structure are also better than their categorical counterparts at identifying the conformational state for structurally ambivalent residues. Conclusion Cascaded probabilistic neural networks trained on the continuum secondary structure exhibit better accuracy in structurally ambivalent regions of proteins, while sustaining an overall classification accuracy on par with standard, categorical prediction methods.

  9. Residual strength evaluation of concrete structural components ...

    Indian Academy of Sciences (India)

    This paper presents methodologies for residual strength evaluation of concrete structural components using linear elastic and nonlinear fracture mechanics principles. The effect of cohesive forces due to aggregate bridging has been represented mathematically by employing tension softening models. Various tension ...

  10. Prediction of the secondary structure of HIV-1 gp120

    DEFF Research Database (Denmark)

    Hansen, J E; Lund, O; Nielsen, Jens Ole

    1996-01-01

    The secondary structure of HIV-1 gp120 was predicted using multiple alignment and a combination of two independent methods based on neural network and nearest-neighbor algorithms. The methods agreed on the secondary structure for 80% of the residues in BH10 gp120. Six helices were predicted in HIV...... strain BH10 gp120, as well as in 27 other HIV-1 strains examined. Two helical segments were predicted in regions displaying profound sequence variation, one in a region suggested to be critical for CD4 binding. The predicted content of helix, beta-strand, and coil was consistent with estimates from...... of future HIV subunit vaccine candidates....

  11. Nucleic acid secondary structure prediction and display.

    OpenAIRE

    Stüber, K

    1986-01-01

    A set of programs has been developed for the prediction and display of nucleic acid secondary structures. Information from experimental data can be used to restrict or enforce secondary structural elements. The predictions can be displayed either on normal line printers or on graphic devices like plotters or graphic terminals.

  12. On the Structural Context and Identification of Enzyme Catalytic Residues

    Science.gov (United States)

    Chien, Yu-Tung; Huang, Shao-Wei

    2013-01-01

    Enzymes play important roles in most of the biological processes. Although only a small fraction of residues are directly involved in catalytic reactions, these catalytic residues are the most crucial parts in enzymes. The study of the fundamental and unique features of catalytic residues benefits the understanding of enzyme functions and catalytic mechanisms. In this work, we analyze the structural context of catalytic residues based on theoretical and experimental structure flexibility. The results show that catalytic residues have distinct structural features and context. Their neighboring residues, whether sequence or structure neighbors within specific range, are usually structurally more rigid than those of noncatalytic residues. The structural context feature is combined with support vector machine to identify catalytic residues from enzyme structure. The prediction results are better or comparable to those of recent structure-based prediction methods. PMID:23484160

  13. Flexible Structures and Secondary Schools.

    Science.gov (United States)

    Dennison, W. F.

    1985-01-01

    Considers the problems inherent in British secondary school organization, the resistance to change built into the organizational systems, and possible organizational concepts that could serve the same general purposes (curricular oversight and student services) while adapting more successfully to changing needs and conditions. (PGD)

  14. Endrin in birds: Lethal residues and secondary poisoning

    Science.gov (United States)

    Stickel, W.H.; Reichel, W.L.; Hughes, D.L.

    1979-01-01

    Endrin residues in brains that are diagnostic of death were determined for several species of birds. Residues of 0.8 ppm or more of endrin in brain meant death; 0.6 ppm or less meant survival; between was a zone of overlap. These criteria indicate that some wild birds of the U.S., particularly white pelicans in the Northwest and two bald eagles, have been killed by endrin. Signs of endrin poisoning in experimental birds are described. The important and highly toxic metabolite in rodents, 12-ketoendrin, was sought but not found.

  15. Residuals and the Residual-Based Statistic for Testing Goodness of Fit of Structural Equation Models

    Science.gov (United States)

    Foldnes, Njal; Foss, Tron; Olsson, Ulf Henning

    2012-01-01

    The residuals obtained from fitting a structural equation model are crucial ingredients in obtaining chi-square goodness-of-fit statistics for the model. The authors present a didactic discussion of the residuals, obtaining a geometrical interpretation by recognizing the residuals as the result of oblique projections. This sheds light on the…

  16. Improving RNA secondary structure prediction with structure mapping data.

    Science.gov (United States)

    Sloma, Michael F; Mathews, David H

    2015-01-01

    Methods to probe RNA secondary structure, such as small molecule modifying agents, secondary structure-specific nucleases, inline probing, and SHAPE chemistry, are widely used to study the structure of functional RNA. Computational secondary structure prediction programs can incorporate probing data to predict structure with high accuracy. In this chapter, an overview of current methods for probing RNA secondary structure is provided, including modern high-throughput methods. Methods for guiding secondary structure prediction algorithms using these data are explained, and best practices for using these data are provided. This chapter concludes by listing a number of open questions about how to best use probing data, and what these data can provide. © 2015 Elsevier Inc. All rights reserved.

  17. Protein secondary structure: category assignment and predictability

    DEFF Research Database (Denmark)

    Andersen, Claus A.; Bohr, Henrik; Brunak, Søren

    2001-01-01

    In the last decade, the prediction of protein secondary structure has been optimized using essentially one and the same assignment scheme known as DSSP. We present here a different scheme, which is more predictable. This scheme predicts directly the hydrogen bonds, which stabilize the secondary......-forward neural network with one hidden layer on a data set identical to the one used in earlier work....

  18. Continuum secondary structure captures protein flexibility

    DEFF Research Database (Denmark)

    Anderson, C.A.F.; Palmer, A.G.; Brunak, Søren

    2002-01-01

    with different hydrogen bond thresholds. The final continuous assignment for a single NMR model successfully reflected the structural variations observed between all NMR models in the ensemble. The structural variations between NMR models were verified to correlate with thermal motion; these variations were...... captured by the continuous assignments. Because the continuous assignment reproduces the structural variation between many NMR models from one single model, functionally important variation can be extracted from a single X-ray structure. Thus, continuous assignments of secondary structure may affect future...

  19. RNAmute: RNA secondary structure mutation analysis tool

    Directory of Open Access Journals (Sweden)

    Barash Danny

    2006-04-01

    Full Text Available Abstract Background RNAMute is an interactive Java application that calculates the secondary structure of all single point mutations, given an RNA sequence, and organizes them into categories according to their similarity with respect to the wild type predicted structure. The secondary structure predictions are performed using the Vienna RNA package. Several alternatives are used for the categorization of single point mutations: Vienna's RNAdistance based on dot-bracket representation, as well as tree edit distance and second eigenvalue of the Laplacian matrix based on Shapiro's coarse grain tree graph representation. Results Selecting a category in each one of the processed tables lists all single point mutations belonging to that category. Selecting a mutation displays a graphical drawing of the single point mutation and the wild type, and includes basic information such as associated energies, representations and distances. RNAMute can be used successfully with very little previous experience and without choosing any parameter value alongside the initial RNA sequence. The package runs under LINUX operating system. Conclusion RNAMute is a user friendly tool that can be used to predict single point mutations leading to conformational rearrangements in the secondary structure of RNAs. In several cases of substantial interest, notably in virology, a point mutation may lead to a loss of important functionality such as the RNA virus replication and translation initiation because of a conformational rearrangement in the secondary structure.

  20. PEGylated nanoparticles: protein corona and secondary structure

    Science.gov (United States)

    Runa, Sabiha; Hill, Alexandra; Cochran, Victoria L.; Payne, Christine K.

    2014-09-01

    Nanoparticles have important biological and biomedical applications ranging from drug and gene delivery to biosensing. In the presence of extracellular proteins, a "corona" of proteins adsorbs on the surface of the nanoparticles, altering their interaction with cells, including immune cells. Nanoparticles are often functionalized with polyethylene glycol (PEG) to reduce this non-specific adsorption of proteins. To understand the change in protein corona that occurs following PEGylation, we first quantified the adsorption of blood serum proteins on bare and PEGylated gold nanoparticles using gel electrophoresis. We find a threefold decrease in the amount of protein adsorbed on PEGylated gold nanoparticles compared to the bare gold nanoparticles, showing that PEG reduces, but does not prevent, corona formation. To determine if the secondary structure of corona proteins was altered upon adsorption onto the bare and PEGylated gold nanoparticles, we use CD spectroscopy to characterize the secondary structure of bovine serum albumin following incubation with the nanoparticles. Our results show no significant change in protein secondary structure following incubation with bare or PEGylated nanoparticles. Further examination of the secondary structure of bovine serum albumin, α2-macroglobulin, and transferrin in the presence of free PEG showed similar results. These findings provide important insights for the use of PEGylated gold nanoparticles under physiological conditions.

  1. A Kernel for Protein Secondary Structure Prediction

    OpenAIRE

    Guermeur , Yann; Lifchitz , Alain; Vert , Régis

    2004-01-01

    http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid=10338&mode=toc; International audience; Multi-class support vector machines have already proved efficient in protein secondary structure prediction as ensemble methods, to combine the outputs of sets of classifiers based on different principles. In this chapter, their implementation as basic prediction methods, processing the primary structure or the profile of multiple alignments, is investigated. A kernel devoted to the task is in...

  2. 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 .

  3. Characterization of particulate residues from greenlandic mswi for use as secondary resources

    DEFF Research Database (Denmark)

    Kirkelund, Gunvor Marie; Dias-Ferreira, Célia; Jensen, Pernille Erland

    2016-01-01

    In Greenland, waste incineration is used in the larger towns to treat the municipal solid waste. The incineration reduces the amount of waste, but produces particulate incineration residues such as fly and bottom ash that are disposed of. Most construction materials are imported to Arctic areas....... The focus in this study is a characterisation of Greenlandic incineration residues to assess the potential as local secondary resources. In this study, fly ash samples from all the incinerators and bottom ash from two incinerators were collected and investigated for several physical-chemical properties...... as secondary material. The bottom ashes consisted of coarser particles and exhibited lower heavy metal leaching than the fly ash. All residue samples were different and evaluation of reuse should be made individually, however the fly ash shows potential as cement replacement and bottom ash as sand replacement...

  4. Residual strength evaluation of concrete structural components ...

    Indian Academy of Sciences (India)

    to failure. It is of interest to characterize the material behaviour subjected to such loading and study the crack propagation, remaining life and residual strength resulting from such loading. The current approaches used to evaluate fatigue performance of concrete members are mainly empirical. Fatigue equations based on ...

  5. Epimorphisms in Varieties of Residuated Structures

    Czech Academy of Sciences Publication Activity Database

    Bezhanishvili, G.; Moraschini, Tommaso; Raftery, J.G.

    2017-01-01

    Roč. 492, 15 December (2017), s. 185-211 ISSN 0021-8693 R&D Projects: GA ČR GA17-04630S Institutional support: RVO:67985807 Keywords : Epimorphism * Brouwerian algebra * Heyting algebra * Esakia space * Residuated lattice * Sugihara monoid * Substructural logic * Intuitionistic logic * Relevance logic * R-mingle * Beth definability Subject RIV: BA - General Mathematics OBOR OECD: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8) Impact factor: 0.610, year: 2016

  6. Predicting Protein Secondary Structure with Markov Models

    DEFF Research Database (Denmark)

    Fischer, Paul; Larsen, Simon; Thomsen, Claus

    2004-01-01

    we are considering here, is to predict the secondary structure from the primary one. To this end we train a Markov model on training data and then use it to classify parts of unknown protein sequences as sheets, helices or coils. We show how to exploit the directional information contained...... in the Markov model for this task. Classifications that are purely based on statistical models might not always be biologically meaningful. We present combinatorial methods to incorporate biological background knowledge to enhance the prediction performance....

  7. Detection of secondary structure elements in proteins by hydrophobic cluster analysis.

    Science.gov (United States)

    Woodcock, S; Mornon, J P; Henrissat, B

    1992-10-01

    Hydrophobic cluster analysis (HCA) is a protein sequence comparison method based on alpha-helical representations of the sequences where the size, shape and orientation of the clusters of hydrophobic residues are primarily compared. The effectiveness of HCA has been suggested to originate from its potential ability to focus on the residues forming the hydrophobic core of globular proteins. We have addressed the robustness of the bidimensional representation used for HCA in its ability to detect the regular secondary structure elements of proteins. Various parameters have been studied such as those governing cluster size and limits, the hydrophobic residues constituting the clusters as well as the potential shift of the cluster positions with respect to the position of the regular secondary structure elements. The following results have been found to support the alpha-helical bidimensional representation used in HCA: (i) there is a positive correlation (clearly above background noise) between the hydrophobic clusters and the regular secondary structure elements in proteins; (ii) the hydrophobic clusters are centred on the regular secondary structure elements; (iii) the pitch of the helical representation which gives the best correspondence is that of an alpha-helix. The correspondence between hydrophobic clusters and regular secondary structure elements suggests a way to implement variable gap penalties during the automatic alignment of protein sequences.

  8. A folding algorithm for extended RNA secondary structures.

    Science.gov (United States)

    Höner zu Siederdissen, Christian; Bernhart, Stephan H; Stadler, Peter F; Hofacker, Ivo L

    2011-07-01

    RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment. We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction. All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/.

  9. RNA-SSPT: RNA Secondary Structure Prediction Tools.

    Science.gov (United States)

    Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

    2013-01-01

    The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.

  10. Estimation of pharmaceutical residues in primary and secondary sewage sludge based on quantities of use and fugacity modelling.

    Science.gov (United States)

    Khan, S J; Ongerth, J E

    2002-01-01

    A general procedure was developed for estimating the concentrations of pharmaceutical residues in fresh primary and secondary sewage sludge. Prescribed quantities coupled with information on the various excretion ratios of 20 pharmaceuticals and 2 of their metabolites enabled prediction of the overall rates of excretion into Australian sewage. Fugacity modelling was applied to predict concentrations of these residues in fresh primary and secondary sludge. Predicted concentrations ranged from 10(-3)-884 microg/L in primary sludge and 10(-4)-36 microg/L in secondary sludge. Overall rates of removal to sludges ranged from 1-39%. The accuracy of the model was verified by comparison to analytical data.

  11. Prediction of the Secondary Structure of HIV-1 gp120

    DEFF Research Database (Denmark)

    Hansen, Jan; Lund, Ole; Nielsen, Jens O.

    1996-01-01

    Fourier transform infrared spectroscopy. The predicted secondary structure of gp120 compared well with data from NMR analysis of synthetic peptides from the V3 loop and the C4 region. As a first step towards modeling the tertiary structure of gp120, the predicted secondary structure may guide the design...

  12. Column imprints: a secondary index structure

    NARCIS (Netherlands)

    Sidirourgos, L.; Kersten, M.

    2013-01-01

    Large scale data warehouses rely heavily on secondary indexes, such as bitmaps and b-trees, to limit access to slow IO devices. However, with the advent of large main memory systems, cache conscious secondary indexes are needed to improve also the transfer bandwidth between memory and cpu. In this

  13. CING: an integrated residue-based structure validation program suite

    International Nuclear Information System (INIS)

    Doreleijers, Jurgen F.; Sousa da Silva, Alan W.; Krieger, Elmar; Nabuurs, Sander B.; Spronk, Christian A. E. M.; Stevens, Tim J.; Vranken, Wim F.; Vriend, Gert; Vuister, Geerten W.

    2012-01-01

    We present a suite of programs, named CING for Common Interface for NMR Structure Generation that provides for a residue-based, integrated validation of the structural NMR ensemble in conjunction with the experimental restraints and other input data. External validation programs and new internal validation routines compare the NMR-derived models with empirical data, measured chemical shifts, distance- and dihedral restraints and the results are visualized in a dynamic Web 2.0 report. A red–orange–green score is used for residues and restraints to direct the user to those critiques that warrant further investigation. Overall green scores below ∼20 % accompanied by red scores over ∼50 % are strongly indicative of poorly modelled structures. The publically accessible, secure iCing webserver (https://nmr.le.ac.ukhttps://nmr.le.ac.uk) allows individual users to upload the NMR data and run a CING validation analysis.

  14. Protein secondary structure assignment revisited: a detailed analysis of different assignment methods

    Directory of Open Access Journals (Sweden)

    de Brevern Alexandre G

    2005-09-01

    Full Text Available Abstract Background A number of methods are now available to perform automatic assignment of periodic secondary structures from atomic coordinates, based on different characteristics of the secondary structures. In general these methods exhibit a broad consensus as to the location of most helix and strand core segments in protein structures. However the termini of the segments are often ill-defined and it is difficult to decide unambiguously which residues at the edge of the segments have to be included. In addition, there is a "twilight zone" where secondary structure segments depart significantly from the idealized models of Pauling and Corey. For these segments, one has to decide whether the observed structural variations are merely distorsions or whether they constitute a break in the secondary structure. Methods To address these problems, we have developed a method for secondary structure assignment, called KAKSI. Assignments made by KAKSI are compared with assignments given by DSSP, STRIDE, XTLSSTR, PSEA and SECSTR, as well as secondary structures found in PDB files, on 4 datasets (X-ray structures with different resolution range, NMR structures. Results A detailed comparison of KAKSI assignments with those of STRIDE and PSEA reveals that KAKSI assigns slightly longer helices and strands than STRIDE in case of one-to-one correspondence between the segments. However, KAKSI tends also to favor the assignment of several short helices when STRIDE and PSEA assign longer, kinked, helices. Helices assigned by KAKSI have geometrical characteristics close to those described in the PDB. They are more linear than helices assigned by other methods. The same tendency to split long segments is observed for strands, although less systematically. We present a number of cases of secondary structure assignments that illustrate this behavior. Conclusion Our method provides valuable assignments which favor the regularity of secondary structure segments.

  15. Antimony and arsenic leaching from secondary lead smelter air-pollution-control residues.

    Science.gov (United States)

    Ettler, Vojtech; Mihaljevic, Martin; Sebek, Ondrej

    2010-07-01

    Environments in the vicinity of the lead (Pb) smelters are contaminated by emissions containing high concentrations of antimony (Sb) and arsenic (As). Air-pollution-control (APC) residues from bag-type filters from a secondary Pb smelter were subjected to leaching experiments to elucidate the controlling mechanisms of Sb and As release. Kinetic batch leaching tests at a liquid-to-solid (L/S) ratio of 10 L kg(- 1) within the time frame of 720 hours and batch leaching at various L/S ratios (ranging from 1 to 1000 L kg(-1)) were performed. In contrast to other inorganic contaminants (Pb, Cd, Zn), less than 1% of the total Sb and As content was leached from the residues. At a L/S ratio of 10, the As and Sb concentrations in the leachates exceeded the EU limit values for non-hazardous waste (0.2 and 0.07 mg L(-1) ). According to PHREEQC-2 calculations, the concentrations of As and Sb are controlled by the precipitation of complex arsenates and antimonates mainly at low L/S ratios. The washing and related chemical/mineralogical transformation of APC residues was suggested as a technological pre-treatment process before their re-smelting in a blast furnace. The Ferrox-like processing of the resulting contaminated process water/leachate was simulated using the PHREEQC-2 code. Significant reduction was obtained in the concentration of some key contaminants (As, Cu, Pb, Zn) related to sorption on newly formed hydrous ferric oxides, whereas Sb and Cd exhibited only limited attenuation.

  16. Combining neural networks for protein secondary structure prediction

    DEFF Research Database (Denmark)

    Riis, Søren Kamaric

    1995-01-01

    In this paper structured neural networks are applied to the problem of predicting the secondary structure of proteins. A hierarchical approach is used where specialized neural networks are designed for each structural class and then combined using another neural network. The submodels are designed...... by using a priori knowledge of the mapping between protein building blocks and the secondary structure and by using weight sharing. Since none of the individual networks have more than 600 adjustable weights over-fitting is avoided. When ensembles of specialized experts are combined the performance...... is better than most secondary structure prediction methods based on single sequences even though this model contains much fewer parameters...

  17. ncRNA consensus secondary structure derivation using grammar strings.

    Science.gov (United States)

    Achawanantakun, Rujira; Sun, Yanni; Takyar, Seyedeh Shohreh

    2011-04-01

    Many noncoding RNAs (ncRNAs) function through both their sequences and secondary structures. Thus, secondary structure derivation is an important issue in today's RNA research. The state-of-the-art structure annotation tools are based on comparative analysis, which derives consensus structure of homologous ncRNAs. Despite promising results from existing ncRNA aligning and consensus structure derivation tools, there is a need for more efficient and accurate ncRNA secondary structure modeling and alignment methods. In this work, we introduce a consensus structure derivation approach based on grammar string, a novel ncRNA secondary structure representation that encodes an ncRNA's sequence and secondary structure in the parameter space of a context-free grammar (CFG) and a full RNA grammar including pseudoknots. Being a string defined on a special alphabet constructed from a grammar, grammar string converts ncRNA alignment into sequence alignment. We derive consensus secondary structures from hundreds of ncRNA families from BraliBase 2.1 and 25 families containing pseudoknots using grammar string alignment. Our experiments have shown that grammar string-based structure derivation competes favorably in consensus structure quality with Murlet and RNASampler. Source code and experimental data are available at http://www.cse.msu.edu/~yannisun/grammar-string.

  18. Recovery of metal values from copper slag and reuse of residual secondary slag.

    Science.gov (United States)

    Sarfo, Prince; Das, Avimanyu; Wyss, Gary; Young, Courtney

    2017-12-01

    Resource and environmental factors have become major forces in mining and metallurgy sectors driving research for sustainability purposes. The concept of zero-waste processing has been gaining ground readily. The scant availability of high quality raw materials has forced the researchers to shift their focus to recycling while the exceedingly stringent environmental regulations have forced researchers to explore new frontiers of minimizing/eliminating waste generation. The present work is aimed at addressing both aspects by employing recycling to generate wealth from copper slag and producing utilizable materials at the same time thus restoring the ecosystem. Copper slag was characterized and processed. The pyro-metallurgical processing prospects to generate utilizable materials were arrived at through rigorous thermodynamic analysis. Carbothermal reduction at elevated temperature (near 1440°C) helped recover a majority of the metal values (e.g., Fe, Cu and Mo) into the iron-rich alloy product which can be a feed material for steel making. On the other hand, the non-metallic residue, the secondary slag, can be used in the glass and ceramic industries. Reduction time and temperature and carbon content were shown to be the most important process variables for the reaction which were optimized to identify the most favored operating regime that maximizes the metal recovery and simultaneously maximizes the hardness of the secondary slag and minimizes its density, the two major criteria for the secondary slag product to be utilizable. The flux addition level was shown to have relatively less impact on the process performance if these are maintained at an adequate level. The work established that the copper slag, a waste material, can be successfully processed to generate reusable products through pyrometallurgical processing. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Prediction of backbone dihedral angles and protein secondary structure using support vector machines

    Directory of Open Access Journals (Sweden)

    Hirst Jonathan D

    2009-12-01

    Full Text Available Abstract Background The prediction of the secondary structure of a protein is a critical step in the prediction of its tertiary structure and, potentially, its function. Moreover, the backbone dihedral angles, highly correlated with secondary structures, provide crucial information about the local three-dimensional structure. Results We predict independently both the secondary structure and the backbone dihedral angles and combine the results in a loop to enhance each prediction reciprocally. Support vector machines, a state-of-the-art supervised classification technique, achieve secondary structure predictive accuracy of 80% on a non-redundant set of 513 proteins, significantly higher than other methods on the same dataset. The dihedral angle space is divided into a number of regions using two unsupervised clustering techniques in order to predict the region in which a new residue belongs. The performance of our method is comparable to, and in some cases more accurate than, other multi-class dihedral prediction methods. Conclusions We have created an accurate predictor of backbone dihedral angles and secondary structure. Our method, called DISSPred, is available online at http://comp.chem.nottingham.ac.uk/disspred/.

  20. Use of secondary structural information and Cα-Cα distance ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    2007-06-21

    Jun 21, 2007 ... information, we end up predicting model structures much distant from their corresponding native structures. [Reddy B V B and Kaznessis Y N 2007 Use of secondary structural information and Cα-Cα distance restraints to model protein structures with. MODELLER; J. Biosci. 32 929–936] http://www.ias.ac.in/ ...

  1. CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures

    Directory of Open Access Journals (Sweden)

    Hamed Bostan

    2012-01-01

    Full Text Available Computational approaches to the disulphide bonding state and its connectivity pattern prediction are based on various descriptors. One descriptor is the amino acid sequence motifs flanking the cysteine residue motifs. Despite the existence of disulphide bonding information in many databases and applications, there is no complete reference and motif query available at the moment. Cysteine motif database (CMD is the first online resource that stores all cysteine residues, their flanking motifs with their secondary structure, and propensity values assignment derived from the laboratory data. We extracted more than 3 million cysteine motifs from PDB and UniProt data, annotated with secondary structure assignment, propensity value assignment, and frequency of occurrence and coefficiency of their bonding status. Removal of redundancies generated 15875 unique flanking motifs that are always bonded and 41577 unique patterns that are always nonbonded. Queries are based on the protein ID, FASTA sequence, sequence motif, and secondary structure individually or in batch format using the provided APIs that allow remote users to query our database via third party software and/or high throughput screening/querying. The CMD offers extensive information about the bonded, free cysteine residues, and their motifs that allows in-depth characterization of the sequence motif composition.

  2. Structural perfection and residual electric resistance of tungsten single crystals

    International Nuclear Information System (INIS)

    Tagirova, D.M.; Dyakina, V.P.; Startsev, V.E.; Esin, V.O.

    1997-01-01

    A study was made into residual relative resistance (RRR) and structural perfection (SP) of tungsten single crystals, grown by electron beam zone melting using seeding crystals of several orientations, namely, , , , . The single crystals were of 99.98 and 99.9995 wt.% purity. The RRR value is found to depend on crystallographic orientation of an axis of crystal growth and to correlate with SP. Single crystals of different purity are differ in the nature of orientational dependences. It is shown that the correlation between RRR and SP of crystals is mainly due to conduction electron scattering by subgrain boundaries (internal size effect)

  3. Prediction of Spontaneous Protein Deamidation from Sequence-Derived Secondary Structure and Intrinsic Disorder.

    Directory of Open Access Journals (Sweden)

    J Ramiro Lorenzo

    Full Text Available Asparagine residues in proteins undergo spontaneous deamidation, a post-translational modification that may act as a molecular clock for the regulation of protein function and turnover. Asparagine deamidation is modulated by protein local sequence, secondary structure and hydrogen bonding. We present NGOME, an algorithm able to predict non-enzymatic deamidation of internal asparagine residues in proteins in the absence of structural data, using sequence-based predictions of secondary structure and intrinsic disorder. Compared to previous algorithms, NGOME does not require three-dimensional structures yet yields better predictions than available sequence-only methods. Four case studies of specific proteins show how NGOME may help the user identify deamidation-prone asparagine residues, often related to protein gain of function, protein degradation or protein misfolding in pathological processes. A fifth case study applies NGOME at a proteomic scale and unveils a correlation between asparagine deamidation and protein degradation in yeast. NGOME is freely available as a webserver at the National EMBnet node Argentina, URL: http://www.embnet.qb.fcen.uba.ar/ in the subpage "Protein and nucleic acid structure and sequence analysis".

  4. A method for rapid similarity analysis of RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Liu Na

    2006-11-01

    Full Text Available Abstract Background Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolutionary analysis. Usually, the similarity of RNA secondary structures is evaluated based on tree models and dynamic programming algorithms. We present here a new method for the similarity analysis of RNA secondary structures. Results Three sets of real data have been used as input for the example applications. Set I includes the structures from 5S rRNAs. Set II includes the secondary structures from RNase P and RNase MRP. Set III includes the structures from 16S rRNAs. Reasonable phylogenetic trees are derived for these three sets of data by using our method. Moreover, our program runs faster as compared to some existing ones. Conclusion The famous Lempel-Ziv algorithm can efficiently extract the information on repeated patterns encoded in RNA secondary structures and makes our method an alternative to analyze the similarity of RNA secondary structures. This method will also be useful to researchers who are interested in evolutionary analysis.

  5. Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics

    Science.gov (United States)

    Hata, Hiroaki; Kitajima, Tetsuro

    2018-01-01

    Abstract Nucleic acid secondary structure plays an important role in nucleic acid–nucleic acid recognition/hybridization processes, and is also a vital consideration in DNA nanotechnology. Although the influence of stable secondary structures on hybridization kinetics has been characterized, unstable secondary structures, which show positive ΔG° with self-folding, can also form, and their effects have not been systematically investigated. Such thermodynamically unfavorable secondary structures should not be ignored in DNA hybridization kinetics, especially under isothermal conditions. Here, we report that positive ΔG° secondary structures can change the hybridization rate by two-orders of magnitude, despite the fact that their hybridization obeyed second-order reaction kinetics. The temperature dependence of hybridization rates showed non-Arrhenius behavior; thus, their hybridization is considered to be nucleation limited. We derived a model describing how ΔG° positive secondary structures affect hybridization kinetics in stopped-flow experiments with 47 pairs of oligonucleotides. The calculated hybridization rates, which were based on the model, quantitatively agreed with the experimental rate constant. PMID:29220504

  6. Predicting RNA secondary structures from sequence and probing data.

    Science.gov (United States)

    Lorenz, Ronny; Wolfinger, Michael T; Tanzer, Andrea; Hofacker, Ivo L

    2016-07-01

    RNA secondary structures have proven essential for understanding the regulatory functions performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success is in part due to the availability of efficient computational methods for predicting RNA secondary structures. Recent advances focus on dealing with the inherent uncertainty of prediction by considering the ensemble of possible structures rather than the single most stable one. Moreover, the advent of high-throughput structural probing has spurred the development of computational methods that incorporate such experimental data as auxiliary information. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  7. RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data.

    Science.gov (United States)

    Incarnato, Danny; Neri, Francesco; Anselmi, Francesca; Oliviero, Salvatore

    2016-02-01

    The rapidly increasing number of discovered non-coding RNAs makes the understanding of their structure a key feature toward a deeper comprehension of gene expression regulation. Various enzymatic- and chemically- based approaches have been recently developed to allow whole-genome studies of RNA secondary structures. Several methods have been recently presented that allow high-throughput RNA structure probing (CIRS-seq, Structure-seq, SHAPE-seq, PARS, etc.) and unbiased structural inference of residues within RNAs in their native conformation. We here present an analysis toolkit, named RNA Structure Framework (RSF), which allows fast and fully-automated analysis of high-throughput structure probing data, from data pre-processing to whole-transcriptome RNA structure inference. RSF is written in Perl and is freely available under the GPLv3 license from http://rsf.hugef-research.org. salvatore.oliviero@hugef-torino.org Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  8. Residual capacity estimation of bridges using structural health monitoring data

    Science.gov (United States)

    Baghaei, Reza; Feng, Maria Q.; Torbol, Marco

    2011-04-01

    In this study, a vibration-based procedure for residual capacity estimation of bridges after damaging earthquake events is proposed. The procedure starts with estimation of collapse capacity of the intact bridge using incremental dynamic analysis (IDA) curves. The collapse capacity is defined as the median intensity level of the earthquakes that cause global or local collapse within the structure. A database of post-earthquake modal properties is created by calculating the analytical modal properties of the bridge after each nonlinear response history analysis performed for generation IDA curves. After the damaging event, experimental modal properties of the bridge are identified from vibration measurements of the bridge. These properties along with the modal properties database are used to find ground motionintensity pairs that can drive nonlinear FE model of the structure to the current damage state of the bridge. The IDA curves corresponding to the damaged FE model of the bridge are subsequently used to estimate amount of loss in collapse capacity of the damaged structure. Estimated loss in capacity of the bridge besides the bridge-site-specific seismic hazard curves are used to update the functionality status of the bridge. Proposed procedure is applied to experimental data from a large-scale shake table test on a quarter-scale model of a short-span reinforced concrete bridge. The bridge was subjected to a series of earthquake ground motions introducing progressive seismic damage to the bridge which finally led to the failure of one of the bents. Residual collapse capacity and functionality status of the bridge are updated at different stages of the experiment using the proposed procedure.

  9. Secondary structural analyses of ITS1 in Paramecium.

    Science.gov (United States)

    Hoshina, Ryo

    2010-01-01

    The nuclear ribosomal RNA gene operon is interrupted by internal transcribed spacer (ITS) 1 and ITS2. Although the secondary structure of ITS2 has been widely investigated, less is known about ITS1 and its structure. In this study, the secondary structure of ITS1 sequences for Paramecium and other ciliates was predicted. Each Paramecium ITS1 forms an open loop with three helices, A through C. Helix B was highly conserved among Paramecium, and similar helices were found in other ciliates. A phylogenetic analysis using the ITS1 sequences showed high-resolution, implying that ITS1 is a good tool for species-level analyses.

  10. Original Paper Floristic and structural changes in secondary forests ...

    African Journals Online (AJOL)

    http://ajol.info/index.php/ijbcs http://indexmedicus.afro.who.int. Floristic and structural changes ... This study aims at providing quantitative information on floristic composition and structure of the Lama secondary forests (Benin), so as to contribute to ...... Seedling recruitment in a hurricane- driven tropical forest: light limitation,.

  11. RNA secondary structure diagrams for very large molecules: RNAfdl

    DEFF Research Database (Denmark)

    Hecker, Nikolai; Wiegels, Tim; Torda, Andrew E.

    2013-01-01

    There are many programs that can read the secondary structure of an RNA molecule and draw a diagram, but hardly any that can cope with 10 3 bases. RNAfdl is slow but capable of producing intersection-free diagrams for ribosome-sized structures, has a graphical user interface for adjustments...

  12. Use of secondary structural information and Cα-Cα distance ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    2007-06-21

    Jun 21, 2007 ... single domain protein structures of varied lengths. The results shows that it is very difficult to obtain ... This analysis further shows that MODELLER restrain optimization program can be useful only if we .... identifies largest set of residues deviating from the target by no more than a specified Cα distance cutoff.

  13. Prediction of RNA secondary structure using generalized centroid estimators.

    Science.gov (United States)

    Hamada, Michiaki; Kiryu, Hisanori; Sato, Kengo; Mituyama, Toutai; Asai, Kiyoshi

    2009-02-15

    Recent studies have shown that the methods for predicting secondary structures of RNAs on the basis of posterior decoding of the base-pairing probabilities has an advantage with respect to prediction accuracy over the conventionally utilized minimum free energy methods. However, there is room for improvement in the objective functions presented in previous studies, which are maximized in the posterior decoding with respect to the accuracy measures for secondary structures. We propose novel estimators which improve the accuracy of secondary structure prediction of RNAs. The proposed estimators maximize an objective function which is the weighted sum of the expected number of the true positives and that of the true negatives of the base pairs. The proposed estimators are also improved versions of the ones used in previous works, namely CONTRAfold for secondary structure prediction from a single RNA sequence and McCaskill-MEA for common secondary structure prediction from multiple alignments of RNA sequences. We clarify the relations between the proposed estimators and the estimators presented in previous works, and theoretically show that the previous estimators include additional unnecessary terms in the evaluation measures with respect to the accuracy. Furthermore, computational experiments confirm the theoretical analysis by indicating improvement in the empirical accuracy. The proposed estimators represent extensions of the centroid estimators proposed in Ding et al. and Carvalho and Lawrence, and are applicable to a wide variety of problems in bioinformatics. Supporting information and the CentroidFold software are available online at: http://www.ncrna.org/software/centroidfold/.

  14. Structural plasticity among glutathione transferase Phi members: natural combination of catalytic residues confers dual biochemical activities.

    Science.gov (United States)

    Pégeot, Henri; Mathiot, Sandrine; Perrot, Thomas; Gense, Frédéric; Hecker, Arnaud; Didierjean, Claude; Rouhier, Nicolas

    2017-08-01

    The glutathione transferase (GST) gene family is divided into 14 classes in photosynthetic organisms. Among them, the Phi class (GSTF) is composed of a large number of genes that are often induced in response to environmental constraints due to their ability to detoxify xenobiotics, to their peroxidase activity and to their involvement in the biosynthesis and/or transport of secondary metabolites. However, the exact functions of GSTFs from many plants including Populus trichocarpa are unknown. Here, following GSTF1 characterization, we have performed a comparative analysis of the seven other GSTFs found in poplar by systematically evaluating the biochemical and enzymatic properties of the corresponding recombinant proteins and of variants mutated for active site residues and by determining the three-dimensional structures of several representatives. Owing to the presence of a cysteine with a pK a value around 5 in their active site, GSTF3, F7, and F8 displayed a thiol transferase activity in addition to the usual glutathione transferase and peroxidase activities. From structural analyses, it appeared that these dual biochemical properties originate from the existence of a certain variability in the β1-α1 loop. This allows positioning of several active site residues at proximity of the glutathione molecule, which itself remains unchanged in GSTF three-dimensional structures. These results highlight the promiscuity of some GSTFs and that changes of active site residues in some isoforms during evolution generated functional diversity by modifying their activity profile. Structural data are available in the PDB under the accession numbers 5EY6, 5F05, 5F06, and 5F07. © 2017 Federation of European Biochemical Societies.

  15. Multiple coding and the evolutionary properties of RNA secondary structure.

    Science.gov (United States)

    Huynen, M A; Konings, D A; Hogeweg, P

    1993-11-21

    This article evaluates evolutionary properties of the transition from RNA primary sequence to RNA secondary structure. It focuses on the restrictions that the conservation of a protein code in an RNA sequence puts on its potential to evolve towards a specific secondary structure. Restricting the mutations to those that do not affect the coding for a protein restricts both the accessibility and the connectivity of the sequence space. The accessibility is restricted because only certain point mutations are allowed. The connectivity is restricted because no insertions and deletions are allowed. Simulating an evolutionary search process for a specific secondary structure shows that (i) the reduction of allowable point mutations allows for adaptation to some large-scale topology, but strongly reduces the possibility of small-scale adaptations, (ii) the abolition of insertions and deletions has very little effect on the results of the search process. During the evolutionary search process for a secondary structure with a specific topology and a high frequency of base-pairing the quasispecies moves into a subspace in which the similarity between secondary structures of neighboring sequences is relatively high. Increased similarity between second structures of neighboring sequences is also found in the Rev responsive element (RRE) in the lentiviruses Caprine arthritis-encephalitis virus and Visna virus. In these viruses a biased nucleotide frequency in the RRE region suggests that selection for the RRE RNA secondary structure affects the amino acid sequence of the env gene. Our results show a variation in the ruggedness of fitness landscapes which are based on a high degree of epistatic interactions. Fitness landscapes play an essential role, not only in biotic evolution, but also in all kinds of optimization processes (Hill Climbing, Simulated Annealing, Genetic Algorithms, etc). Variation in their ruggedness should therefore be taken into account in the analysis of these

  16. Active site studies of bovine alpha1-->3-galactosyltransferase and its secondary structure prediction.

    Science.gov (United States)

    Shah, P S; Bizik, F; Dukor, R K; Qasba, P K

    2000-07-14

    The catalytic domain of bovine alpha1-->3-galactosyltransferase (alpha3GalT), residues 80-368, have been cloned and expressed, in Escherichia coli. Using a sequential purification protocol involving a Ni(2+) affinity column followed by a UDP-hexanolamine affinity column, we have obtained a pure and active protein from the soluble fraction which catalyzes the transfer of galactose (Gal) from UDP-Gal to N-acetyllactosamine (LacNAc) with a specific activity of 0.69 pmol/min/ng. The secondary structural content of alpha3GalT protein was analyzed by Fourier transform infrared (FTIR) spectroscopy, which shows that the enzyme has about 35% beta-sheet and 22% alpha-helix. This predicted secondary structure content by FTIR spectroscopy was used in the protein sequence analysis algorithm, developed by the Biomolecular Engineering Research Center at Boston University and Tasc Inc., for the assignment of secondary structural elements to the amino acid sequence of alpha3GalT. The enzyme appears to have three major and three minor helices and five sheet-like structures. The studies on the acceptor substrate specificity of the enzyme, alpha3GalT, show that in addition to LacNAc, which is the natural substrate, the enzyme accepts various other disaccharides as substrates such as lactose and Gal derivatives, beta-O-methylgalactose and beta-D-thiogalactopyranoside, albeit with lower specific activities. There is an absolute requirement for Gal to be at the non-reducing end of the acceptor molecule which has to be beta1-->4-linked to a second residue that can be more diverse in structure. The kinetic parameters for four acceptor molecules were determined. Lactose binds and functions in a similar way as LacNAc. However, beta-O-methylgalactose and Gal do not bind as tightly as LacNAc or lactose, as their K(ia) and K(A) values indicate, suggesting that the second monosaccharide is critical for holding the acceptor molecule in place. The 2' and 4' hydroxyl groups of the receiving Gal

  17. Atomic structure of recombinant thaumatin II reveals flexible conformations in two residues critical for sweetness and three consecutive glycine residues.

    Science.gov (United States)

    Masuda, Tetsuya; Mikami, Bunzo; Tani, Fumito

    2014-11-01

    Thaumatin, an intensely sweet-tasting protein used as a sweetener, elicits a sweet taste at 50 nM. Although two major variants designated thaumatin I and thaumatin II exist in plants, there have been few dedicated thaumatin II structural studies and, to date, data beyond atomic resolution had not been obtained. To identify the detailed structural properties explaining why thaumatin elicits a sweet taste, the structure of recombinant thaumatin II was determined at the resolution of 0.99 Å. Atomic resolution structural analysis with riding hydrogen atoms illustrated the differences in the direction of the side-chains more precisely and the electron density maps of the C-terminal regions were markedly improved. Though it had been suggested that the three consecutive glycine residues (G142-G143-G144) have highly flexible conformations, G143, the central glycine residue was successfully modelled in two conformations for the first time. Furthermore, the side chain r.m.s.d. values for two residues (R67 and R82) critical for sweetness exhibited substantially higher values, suggesting that these residues are highly disordered. These results demonstrated that the flexible conformations in two critical residues favoring their interaction with sweet taste receptors are prominent features of the intensely sweet taste of thaumatin. Copyright © 2014 Elsevier B.V. and Société française de biochimie et biologie Moléculaire (SFBBM). All rights reserved.

  18. BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

    Directory of Open Access Journals (Sweden)

    Julien Allali

    2012-01-01

    Full Text Available The pairwise comparison of RNA secondary structures is a fundamental problem, with direct application in mining databases for annotating putative noncoding RNA candidates in newly sequenced genomes. An increasing number of software tools are available for comparing RNA secondary structures, based on different models (such as ordered trees or forests, arc annotated sequences, and multilevel trees and computational principles (edit distance, alignment. We describe here the website BRASERO that offers tools for evaluating such software tools on real and synthetic datasets.

  19. Approaches to link RNA secondary structures with splicing regulation

    DEFF Research Database (Denmark)

    Plass, Mireya; Eyras, Eduardo

    2014-01-01

    by facilitating or hindering the interaction with factors and small nuclear ribonucleoproteins (snRNPs) that regulate splicing. Moreover, the secondary structure could play a fundamental role in the splicing of yeast species, which lack many of the regulatory splicing factors present in metazoans. This chapter......In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either...

  20. Predicting protein-protein interface residues using local surface structural similarity

    Directory of Open Access Journals (Sweden)

    Jordan Rafael A

    2012-03-01

    Full Text Available Abstract Background Identification of the residues in protein-protein interaction sites has a significant impact in problems such as drug discovery. Motivated by the observation that the set of interface residues of a protein tend to be conserved even among remote structural homologs, we introduce PrISE, a family of local structural similarity-based computational methods for predicting protein-protein interface residues. Results We present a novel representation of the surface residues of a protein in the form of structural elements. Each structural element consists of a central residue and its surface neighbors. The PrISE family of interface prediction methods uses a representation of structural elements that captures the atomic composition and accessible surface area of the residues that make up each structural element. Each of the members of the PrISE methods identifies for each structural element in the query protein, a collection of similar structural elements in its repository of structural elements and weights them according to their similarity with the structural element of the query protein. PrISEL relies on the similarity between structural elements (i.e. local structural similarity. PrISEG relies on the similarity between protein surfaces (i.e. general structural similarity. PrISEC, combines local structural similarity and general structural similarity to predict interface residues. These predictors label the central residue of a structural element in a query protein as an interface residue if a weighted majority of the structural elements that are similar to it are interface residues, and as a non-interface residue otherwise. The results of our experiments using three representative benchmark datasets show that the PrISEC outperforms PrISEL and PrISEG; and that PrISEC is highly competitive with state-of-the-art structure-based methods for predicting protein-protein interface residues. Our comparison of PrISEC with PredUs, a recently

  1. Knowledge base and neural network approach for protein secondary structure prediction.

    Science.gov (United States)

    Patel, Maulika S; Mazumdar, Himanshu S

    2014-11-21

    Protein structure prediction is of great relevance given the abundant genomic and proteomic data generated by the genome sequencing projects. Protein secondary structure prediction is addressed as a sub task in determining the protein tertiary structure and function. In this paper, a novel algorithm, KB-PROSSP-NN, which is a combination of knowledge base and modeling of the exceptions in the knowledge base using neural networks for protein secondary structure prediction (PSSP), is proposed. The knowledge base is derived from a proteomic sequence-structure database and consists of the statistics of association between the 5-residue words and corresponding secondary structure. The predicted results obtained using knowledge base are refined with a Backpropogation neural network algorithm. Neural net models the exceptions of the knowledge base. The Q3 accuracy of 90% and 82% is achieved on the RS126 and CB396 test sets respectively which suggest improvement over existing state of art methods. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. On the Structure of Finite Integral Commutative Residuated Chains

    Czech Academy of Sciences Publication Activity Database

    Horčík, Rostislav

    2011-01-01

    Roč. 21, č. 5 (2011), s. 717-728 ISSN 0955-792X Institutional research plan: CEZ:AV0Z10300504 Keywords : residuated lattice * ordered residuated monoid * nucleus * conucleus,Abelian lattice-ordered group * free commutative monoid Subject RIV: BA - General Mathematics Impact factor: 0.611, year: 2011

  3. Protein secondary structure prediction for a single-sequence using hidden semi-Markov models

    Directory of Open Access Journals (Sweden)

    Borodovsky Mark

    2006-03-01

    Full Text Available Abstract Background The accuracy of protein secondary structure prediction has been improving steadily towards the 88% estimated theoretical limit. There are two types of prediction algorithms: Single-sequence prediction algorithms imply that information about other (homologous proteins is not available, while algorithms of the second type imply that information about homologous proteins is available, and use it intensively. The single-sequence algorithms could make an important contribution to studies of proteins with no detected homologs, however the accuracy of protein secondary structure prediction from a single-sequence is not as high as when the additional evolutionary information is present. Results In this paper, we further refine and extend the hidden semi-Markov model (HSMM initially considered in the BSPSS algorithm. We introduce an improved residue dependency model by considering the patterns of statistically significant amino acid correlation at structural segment borders. We also derive models that specialize on different sections of the dependency structure and incorporate them into HSMM. In addition, we implement an iterative training method to refine estimates of HSMM parameters. The three-state-per-residue accuracy and other accuracy measures of the new method, IPSSP, are shown to be comparable or better than ones for BSPSS as well as for PSIPRED, tested under the single-sequence condition. Conclusions We have shown that new dependency models and training methods bring further improvements to single-sequence protein secondary structure prediction. The results are obtained under cross-validation conditions using a dataset with no pair of sequences having significant sequence similarity. As new sequences are added to the database it is possible to augment the dependency structure and obtain even higher accuracy. Current and future advances should contribute to the improvement of function prediction for orphan proteins inscrutable

  4. A phase transition in energy-filtered RNA secondary structures

    DEFF Research Database (Denmark)

    Han, Hillary Siwei; reidys, Christian

    2012-01-01

    In this paper we study the effect of energy parameters on minimum free energy (mfe) RNA secondary structures. Employing a simplified combinatorial energy model, that is only dependent on the diagram representation and that is not sequence specific, we prove the following dichotomy result. Mfe str...

  5. Secondary Structures Associated With Alkaline Transition of Horse ...

    African Journals Online (AJOL)

    acer

    ABSTRACT: The spectra of amide I region (1700-1600cm-1) of horse heart ferricytochrome c at. 20oC are reported at low ionic strength at of pH values between 7.0 and 11.5 encompassing the alkaline transition. The mid-infrared spectra can probe the protein secondary structures. The Fourier transform infrared ...

  6. Secondary Structures Associated With Alkaline Transition of Horse ...

    African Journals Online (AJOL)

    acer

    Wasagu et al.; Secondary Structures Associated With Alkaline Transition of Horse Heart Ferricytochrome C: An FTIR Study. 251 above mentioned enhancement techniques. In contrast with single band observed in the primary spectrum, second derivative in the amide I region (1700 and 1600 cm-1), was characterized by ...

  7. Secondary Structures Associated With Alkaline Transition of Horse ...

    African Journals Online (AJOL)

    The spectra of amide I region (1700-1600cm-1) of horse heart ferricytochrome c at 20oC are reported at low ionic strength at of pH values between 7.0 and 11.5 encompassing the alkaline transition. The mid-infrared spectra can probe the protein secondary structures. The Fourier transform infrared spectroscopic technique ...

  8. A combinatorial enumeration problem of RNA secondary structures

    African Journals Online (AJOL)

    use

    2011-12-21

    Dec 21, 2011 ... connection between Discrete Mathematics and Compu- tational Molecular Biology (Chen et al, 2005; Hofacker et ... in Computational Molecular Biology. An RNA molecule is described by its sequences of bases ... Here, a mathematical definition of secondary structure is given (Stein and Waterman 1978).

  9. General enumeration of RNA secondary structures based on new ...

    African Journals Online (AJOL)

    Crick base pairs between AU and GC. Based on the new representation, this paper also computes the number of various types of constrained secondary structures taking the minimum stack length 1 and minimum size m for each bonding loop as ...

  10. A combinatorial enumeration problem of RNA secondary structures

    African Journals Online (AJOL)

    use

    2011-12-21

    Dec 21, 2011 ... interesting combinatorial questions (Chen et al., 2005;. Liu, 2006; Schmitt and Waterman 1994; Stein and. Waterman 1978). The research on the enumeration of. RNA secondary structures becomes one of the hot topics in Computational Molecular Biology. An RNA molecule is described by its sequences of.

  11. Synonymous codon usage in different protein secondary structural ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    2007-06-21

    Jun 21, 2007 ... However, when the genes were classified according to their GC3 levels there was an increase in non-randomness in high GC3 ... each of the protein secondary structural unit there exist some synonymous family that shows class specific codon- ... class by SCOP database are removed from our analysis.

  12. Quantitative DMS mapping for automated RNA secondary structure inference

    OpenAIRE

    Cordero, Pablo; Kladwang, Wipapat; VanLang, Christopher C.; Das, Rhiju

    2012-01-01

    For decades, dimethyl sulfate (DMS) mapping has informed manual modeling of RNA structure in vitro and in vivo. Here, we incorporate DMS data into automated secondary structure inference using a pseudo-energy framework developed for 2'-OH acylation (SHAPE) mapping. On six non-coding RNAs with crystallographic models, DMS- guided modeling achieves overall false negative and false discovery rates of 9.5% and 11.6%, comparable or better than SHAPE-guided modeling; and non-parametric bootstrappin...

  13. RNA secondary structure image - fRNAdb | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us fRNA...db RNA secondary structure image Data detail Data name RNA secondary structure image DOI... 10.18908/lsdba.nbdc00452-005 Description of data contents RNA secondary structure images - png.zip: RNA sec...ondary structure images (PNG) - pdf.zip: RNA secondary structure images (PDF) - thumbnail.zip: Thumbnails of RNA... secondary structure images Data file File name: RNA_secondary_structure_imag

  14. Prediction of RNA secondary structure with pseudoknots using integer programming.

    Science.gov (United States)

    Poolsap, Unyanee; Kato, Yuki; Akutsu, Tatsuya

    2009-01-30

    RNA secondary structure prediction is one major task in bioinformatics, and various computational methods have been proposed so far. Pseudoknot is one of the typical substructures appearing in several RNAs, and plays an important role in some biological processes. Prediction of RNA secondary structure with pseudoknots is still challenging since the problem is NP-hard when arbitrary pseudoknots are taken into consideration. We introduce a new method of predicting RNA secondary structure with pseudoknots based on integer programming. In our formulation, we aim at minimizing the value of the objective function that reflects free energy of a folding structure of an input RNA sequence. We focus on a practical class of pseudoknots by setting constraints appropriately. Experimental results for a set of real RNA sequences show that our proposed method outperforms several existing methods in sensitivity. Furthermore, for a set of sequences of small length, our approach achieved good performance in both sensitivity and specificity. Our integer programming-based approach for RNA structure prediction is flexible and extensible.

  15. Modeling RNA secondary structure folding ensembles using SHAPE mapping data.

    Science.gov (United States)

    Spasic, Aleksandar; Assmann, Sarah M; Bevilacqua, Philip C; Mathews, David H

    2018-01-09

    RNA secondary structure prediction is widely used for developing hypotheses about the structures of RNA sequences, and structure can provide insight about RNA function. The accuracy of structure prediction is known to be improved using experimental mapping data that provide information about the pairing status of single nucleotides, and these data can now be acquired for whole transcriptomes using high-throughput sequencing. Prior methods for using these experimental data focused on predicting structures for sequences assuming that they populate a single structure. Most RNAs populate multiple structures, however, where the ensemble of strands populates structures with different sets of canonical base pairs. The focus on modeling single structures has been a bottleneck for accurately modeling RNA structure. In this work, we introduce Rsample, an algorithm for using experimental data to predict more than one RNA structure for sequences that populate multiple structures at equilibrium. We demonstrate, using SHAPE mapping data, that we can accurately model RNA sequences that populate multiple structures, including the relative probabilities of those structures. This program is freely available as part of the RNAstructure software package. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Absence of residual structure in the intrinsically disordered regulatory protein CP12 in its reduced state

    International Nuclear Information System (INIS)

    Launay, Hélène; Barré, Patrick; Puppo, Carine; Manneville, Stéphanie; Gontero, Brigitte; Receveur-Bréchot, Véronique

    2016-01-01

    The redox switch protein CP12 is a key player of the regulation of the Benson–Calvin cycle. Its oxidation state is controlled by the formation/dissociation of two intramolecular disulphide bridges during the day/night cycle. CP12 was known to be globally intrinsically disordered on a large scale in its reduced state, while being partly ordered in the oxidised state. By combining Nuclear Magnetic Resonance and Small Angle X-ray Scattering experiments, we showed that, contrary to secondary structure or disorder predictions, reduced CP12 is fully disordered, with no transient or local residual structure likely to be precursor of the structures identified in the oxidised active state and/or in the bound state with GAPDH or PRK. These results highlight the diversity of the mechanisms of regulation of conditionally disordered redox switches, and question the stability of oxidised CP12 scaffold. - Highlights: • CP12 is predicted to form two helices in its N-terminal sequence. • Reduced CP12 is disordered as a random coil according to SAXS. • Limited or no transient structures are observed in reduced CP12 by NMR.

  17. Absence of residual structure in the intrinsically disordered regulatory protein CP12 in its reduced state

    Energy Technology Data Exchange (ETDEWEB)

    Launay, Hélène; Barré, Patrick [Laboratory of integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix-Marseille Universités, Marseille 13009 (France); Puppo, Carine [Aix-Marseille Université, Centre National de la Recherche Scientifique, UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20 (France); Manneville, Stéphanie [Laboratory of integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix-Marseille Universités, Marseille 13009 (France); Gontero, Brigitte [Aix-Marseille Université, Centre National de la Recherche Scientifique, UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20 (France); Receveur-Bréchot, Véronique, E-mail: veronique.brechot@inserm.fr [Laboratory of integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix-Marseille Universités, Marseille 13009 (France)

    2016-08-12

    The redox switch protein CP12 is a key player of the regulation of the Benson–Calvin cycle. Its oxidation state is controlled by the formation/dissociation of two intramolecular disulphide bridges during the day/night cycle. CP12 was known to be globally intrinsically disordered on a large scale in its reduced state, while being partly ordered in the oxidised state. By combining Nuclear Magnetic Resonance and Small Angle X-ray Scattering experiments, we showed that, contrary to secondary structure or disorder predictions, reduced CP12 is fully disordered, with no transient or local residual structure likely to be precursor of the structures identified in the oxidised active state and/or in the bound state with GAPDH or PRK. These results highlight the diversity of the mechanisms of regulation of conditionally disordered redox switches, and question the stability of oxidised CP12 scaffold. - Highlights: • CP12 is predicted to form two helices in its N-terminal sequence. • Reduced CP12 is disordered as a random coil according to SAXS. • Limited or no transient structures are observed in reduced CP12 by NMR.

  18. Residual stress alleviation of aircraft metal structures reinforced with filamentary composites

    Science.gov (United States)

    Kelly, J. B.; June, R. R.

    1973-01-01

    Methods to eliminate or reduce residual stresses in aircraft metal structures reinforced by filamentary composites are discussed. Residual stress level reductions were achieved by modifying the manufacturing procedures used during adhesive bonding. The residual stress alleviation techniques involved various forms of mechanical constraint which were applied to the components during bonding. Nine methods were evaluated, covering a wide range in complexity. All methods investigated during the program affected the residual stress level. In general, residual stresses were reduced by 70 percent or more from the stress level produced by conventional adhesive bonding procedures.

  19. Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure

    Directory of Open Access Journals (Sweden)

    Bilmes Jeff

    2011-05-01

    Full Text Available Abstract Background Protein secondary structure prediction provides insight into protein function and is a valuable preliminary step for predicting the 3D structure of a protein. Dynamic Bayesian networks (DBNs and support vector machines (SVMs have been shown to provide state-of-the-art performance in secondary structure prediction. As the size of the protein database grows, it becomes feasible to use a richer model in an effort to capture subtle correlations among the amino acids and the predicted labels. In this context, it is beneficial to derive sparse models that discourage over-fitting and provide biological insight. Results In this paper, we first show that we are able to obtain accurate secondary structure predictions. Our per-residue accuracy on a well established and difficult benchmark (CB513 is 80.3%, which is comparable to the state-of-the-art evaluated on this dataset. We then introduce an algorithm for sparsifying the parameters of a DBN. Using this algorithm, we can automatically remove up to 70-95% of the parameters of a DBN while maintaining the same level of predictive accuracy on the SD576 set. At 90% sparsity, we are able to compute predictions three times faster than a fully dense model evaluated on the SD576 set. We also demonstrate, using simulated data, that the algorithm is able to recover true sparse structures with high accuracy, and using real data, that the sparse model identifies known correlation structure (local and non-local related to different classes of secondary structure elements. Conclusions We present a secondary structure prediction method that employs dynamic Bayesian networks and support vector machines. We also introduce an algorithm for sparsifying the parameters of the dynamic Bayesian network. The sparsification approach yields a significant speed-up in generating predictions, and we demonstrate that the amino acid correlations identified by the algorithm correspond to several known features of

  20. Random generation of RNA secondary structures according to native distributions

    Directory of Open Access Journals (Sweden)

    Nebel Markus E

    2011-10-01

    Full Text Available Abstract Background Random biological sequences are a topic of great interest in genome analysis since, according to a powerful paradigm, they represent the background noise from which the actual biological information must differentiate. Accordingly, the generation of random sequences has been investigated for a long time. Similarly, random object of a more complicated structure like RNA molecules or proteins are of interest. Results In this article, we present a new general framework for deriving algorithms for the non-uniform random generation of combinatorial objects according to the encoding and probability distribution implied by a stochastic context-free grammar. Briefly, the framework extends on the well-known recursive method for (uniform random generation and uses the popular framework of admissible specifications of combinatorial classes, introducing weighted combinatorial classes to allow for the non-uniform generation by means of unranking. This framework is used to derive an algorithm for the generation of RNA secondary structures of a given fixed size. We address the random generation of these structures according to a realistic distribution obtained from real-life data by using a very detailed context-free grammar (that models the class of RNA secondary structures by distinguishing between all known motifs in RNA structure. Compared to well-known sampling approaches used in several structure prediction tools (such as SFold ours has two major advantages: Firstly, after a preprocessing step in time O(n2 for the computation of all weighted class sizes needed, with our approach a set of m random secondary structures of a given structure size n can be computed in worst-case time complexity Om⋅n⋅ log(n while other algorithms typically have a runtime in O(m⋅n2. Secondly, our approach works with integer arithmetic only which is faster and saves us from all the discomforting details of using floating point arithmetic with

  1. Improving the accuracy of protein secondary structure prediction using structural alignment

    Directory of Open Access Journals (Sweden)

    Gallin Warren J

    2006-06-01

    Full Text Available Abstract Background The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3 of about 75%. We believe this accuracy could be further improved by including structure (as opposed to sequence database comparisons as part of the prediction process. Indeed, given the large size of the Protein Data Bank (>35,000 sequences, the probability of a newly identified sequence having a structural homologue is actually quite high. Results We have developed a method that performs structure-based sequence alignments as part of the secondary structure prediction process. By mapping the structure of a known homologue (sequence ID >25% onto the query protein's sequence, it is possible to predict at least a portion of that query protein's secondary structure. By integrating this structural alignment approach with conventional (sequence-based secondary structure methods and then combining it with a "jury-of-experts" system to generate a consensus result, it is possible to attain very high prediction accuracy. Using a sequence-unique test set of 1644 proteins from EVA, this new method achieves an average Q3 score of 81.3%. Extensive testing indicates this is approximately 4–5% better than any other method currently available. Assessments using non sequence-unique test sets (typical of those used in proteome annotation or structural genomics indicate that this new method can achieve a Q3 score approaching 88%. Conclusion By using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called PROTEUS, that performs these secondary structure predictions is accessible at http://wishart.biology.ualberta.ca/proteus. For high throughput or batch sequence analyses, the PROTEUS programs

  2. LBA-ECO ND-04 Secondary Forest Recovery, Structure, and LAI, Central Amazonia, Brazil

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: This data set reports measurements of the canopy and structure of secondary forests regenerating from abandoned pastures. These secondary forests are...

  3. STUDYING THE SECONDARY STRUCTURE OF ACCESSION NUMBER USING CETD MATRIX

    Directory of Open Access Journals (Sweden)

    Anamika Dutta

    2016-10-01

    Full Text Available This paper, we have tried to analyze about the Secondary Structure of nucleotide sequences of rice. The data have been collected from NCBI (National Centre for Biotechnology Information using Nucleotide as data base. All the programs were developed using R programming language using “sequinr” package. Here, we have used CETD matrix method to study the prediction. The conclusions are drawn accordingly.

  4. Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements

    Directory of Open Access Journals (Sweden)

    Sze Sing-Hoi

    2008-07-01

    Full Text Available Abstract Background Since experimental determination of protein folding pathways remains difficult, computational techniques are often used to simulate protein folding. Most current techniques to predict protein folding pathways are computationally intensive and are suitable only for small proteins. Results By assuming that the native structure of a protein is known and representing each intermediate conformation as a collection of fully folded structures in which each of them contains a set of interacting secondary structure elements, we show that it is possible to significantly reduce the conformation space while still being able to predict the most energetically favorable folding pathway of large proteins with hundreds of residues at the mesoscopic level, including the pig muscle phosphoglycerate kinase with 416 residues. The model is detailed enough to distinguish between different folding pathways of structurally very similar proteins, including the streptococcal protein G and the peptostreptococcal protein L. The model is also able to recognize the differences between the folding pathways of protein G and its two structurally similar variants NuG1 and NuG2, which are even harder to distinguish. We show that this strategy can produce accurate predictions on many other proteins with experimentally determined intermediate folding states. Conclusion Our technique is efficient enough to predict folding pathways for both large and small proteins at the mesoscopic level. Such a strategy is often the only feasible choice for large proteins. A software program implementing this strategy (SSFold is available at http://faculty.cs.tamu.edu/shsze/ssfold.

  5. Electrodialytic upgrading of MSWI APC residue from hazardous waste to secondary resource

    DEFF Research Database (Denmark)

    Jensen, Pernille Erland; Kirkelund, Gunvor Marie; Parés Viader, Raimon

    The aim of this project was to contribute to the development of electrodialytic treatment technology of air pollution control residues (APC) from municipal solid waste incineration (MSWI) to obtain maximal leaching reduction by optimization of treatment time and current density for different type...... of MSWI APC residues. The concept idea was in a pilot scale unit to reduce the mobility of toxic elements and salts by electrodialytic treatment enough for the residual product to constitute an environmentally safe resource for substitution of virgin resources in construction material e.......g. for substitution of cement or fillers in concrete. In general leaching could not be reduced by optimizing current density and treatment time in the pilot scale stack treatment unit, as hypothesized, even though there was evidence of dependency on current density for e.g. zinc, this was not true for most elements......, and it was clear that experimental conditions and pre-treatments affected different target elements differently. Statistical analysis of the results revealed that the final pH was the major parameter determining leachability. The robustness of the stack setup proved to be very limited. At several occasions during...

  6. Study on distribution and optimization of residual stress inside plate-fin structure after braze welding

    International Nuclear Information System (INIS)

    Zhou Guoyan; Tu Shandong; Xuan Fuzhen; Wang Zhengdong

    2010-01-01

    The residual stress inside the plate-fin structure has been analyzed by the finite element method under different operation conditions. The calculated results show that a large scale of residual stress will occur in the plate-fin structure and the maximum value is found at the braze corner. The rapid cooling process and the pressured assembly technology have a significant effect on the distribution of the residual stress. The brazed material owns a better performance with a quicker cooling rate. However, the quicker cooling rate also leads to a tensile residual stress near the brazed seam, which is deleterious to the whole structure. The pressure assembly technology can change the residual stress from a tensile state to the compressed state which can improve the safety and extend the service life of the plate-fin structure effectively. (authors)

  7. Evolutionary rate variation and RNA secondary structure prediction

    DEFF Research Database (Denmark)

    Knudsen, B.; Andersen, E.S.; Damgaard, C.

    2004-01-01

    Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type...... by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions...

  8. Why are Papers about Filters on Residuated Structures (Usually) Trivial?

    Czech Academy of Sciences Publication Activity Database

    Víta, Martin

    2014-01-01

    Roč. 276, 20 August (2014), s. 387-391 ISSN 0020-0255 R&D Projects: GA ČR GAP202/10/1826 Institutional support: RVO:67985807 Keywords : residuated lattice * filter * t-Filter Subject RIV: BA - General Mathematics Impact factor: 4.038, year: 2014

  9. Computational RNA secondary structure design: empirical complexity and improved methods

    Directory of Open Access Journals (Sweden)

    Condon Anne

    2007-01-01

    Full Text Available Abstract Background We investigate the empirical complexity of the RNA secondary structure design problem, that is, the scaling of the typical difficulty of the design task for various classes of RNA structures as the size of the target structure is increased. The purpose of this work is to understand better the factors that make RNA structures hard to design for existing, high-performance algorithms. Such understanding provides the basis for improving the performance of one of the best algorithms for this problem, RNA-SSD, and for characterising its limitations. Results To gain insights into the practical complexity of the problem, we present a scaling analysis on random and biologically motivated structures using an improved version of the RNA-SSD algorithm, and also the RNAinverse algorithm from the Vienna package. Since primary structure constraints are relevant for designing RNA structures, we also investigate the correlation between the number and the location of the primary structure constraints when designing structures and the performance of the RNA-SSD algorithm. The scaling analysis on random and biologically motivated structures supports the hypothesis that the running time of both algorithms scales polynomially with the size of the structure. We also found that the algorithms are in general faster when constraints are placed only on paired bases in the structure. Furthermore, we prove that, according to the standard thermodynamic model, for some structures that the RNA-SSD algorithm was unable to design, there exists no sequence whose minimum free energy structure is the target structure. Conclusion Our analysis helps to better understand the strengths and limitations of both the RNA-SSD and RNAinverse algorithms, and suggests ways in which the performance of these algorithms can be further improved.

  10. Strategies for measuring evolutionary conservation of RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Hofacker Ivo L

    2008-02-01

    Full Text Available Abstract Background Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential. Results We systematically assessed the ability of various measures to detect conserved RNA structures in multiple sequence alignments. We tested three existing and eight novel strategies that are based on metrics of folding energies, metrics of single optimal structure predictions, and metrics of structure ensembles. We find that the folding energy based SCI score used in the RNAz program and a simple base-pair distance metric are by far the most accurate. The use of more complex metrics like for example tree editing does not improve performance. A variant of the SCI performed particularly well on highly conserved alignments and is thus a viable alternative when only little evolutionary information is available. Surprisingly, ensemble based methods that, in principle, could benefit from the additional information contained in sub-optimal structures, perform particularly poorly. As a general trend, we observed that methods that include a consensus structure prediction outperformed equivalent methods that only consider pairwise comparisons. Conclusion Structural conservation can be measured accurately with relatively simple and intuitive metrics. They have the potential to form the basis of future RNA gene finders, that face new challenges like finding lineage specific structures or detecting mis-aligned sequences.

  11. Data-directed RNA secondary structure prediction using probabilistic modeling.

    Science.gov (United States)

    Deng, Fei; Ledda, Mirko; Vaziri, Sana; Aviran, Sharon

    2016-08-01

    Structure dictates the function of many RNAs, but secondary RNA structure analysis is either labor intensive and costly or relies on computational predictions that are often inaccurate. These limitations are alleviated by integration of structure probing data into prediction algorithms. However, existing algorithms are optimized for a specific type of probing data. Recently, new chemistries combined with advances in sequencing have facilitated structure probing at unprecedented scale and sensitivity. These novel technologies and anticipated wealth of data highlight a need for algorithms that readily accommodate more complex and diverse input sources. We implemented and investigated a recently outlined probabilistic framework for RNA secondary structure prediction and extended it to accommodate further refinement of structural information. This framework utilizes direct likelihood-based calculations of pseudo-energy terms per considered structural context and can readily accommodate diverse data types and complex data dependencies. We use real data in conjunction with simulations to evaluate performances of several implementations and to show that proper integration of structural contexts can lead to improvements. Our tests also reveal discrepancies between real data and simulations, which we show can be alleviated by refined modeling. We then propose statistical preprocessing approaches to standardize data interpretation and integration into such a generic framework. We further systematically quantify the information content of data subsets, demonstrating that high reactivities are major drivers of SHAPE-directed predictions and that better understanding of less informative reactivities is key to further improvements. Finally, we provide evidence for the adaptive capability of our framework using mock probe simulations. © 2016 Deng et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  12. Origins of coevolution between residues distant in protein 3D structures

    OpenAIRE

    Anishchenko, Ivan; Ovchinnikov, Sergey; Kamisetty, Hetunandan; Baker, David

    2017-01-01

    Coevolution-derived contact predictions are enabling accurate protein structure modeling. However, coevolving residues are not always in contact, and this is a potential source of error in such modeling efforts. To investigate the sources of such errors and, more generally, the origins of coevolution in protein structures, we provide a global overview of the contributions to the “exceptions” to the general rule that coevolving residues are close in protein three-dimensional structures.

  13. PCI-SS: MISO dynamic nonlinear protein secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Aboul-Magd Mohammed O

    2009-07-01

    Full Text Available Abstract Background Since the function of a protein is largely dictated by its three dimensional configuration, determining a protein's structure is of fundamental importance to biology. Here we report on a novel approach to determining the one dimensional secondary structure of proteins (distinguishing α-helices, β-strands, and non-regular structures from primary sequence data which makes use of Parallel Cascade Identification (PCI, a powerful technique from the field of nonlinear system identification. Results Using PSI-BLAST divergent evolutionary profiles as input data, dynamic nonlinear systems are built through a black-box approach to model the process of protein folding. Genetic algorithms (GAs are applied in order to optimize the architectural parameters of the PCI models. The three-state prediction problem is broken down into a combination of three binary sub-problems and protein structure classifiers are built using 2 layers of PCI classifiers. Careful construction of the optimization, training, and test datasets ensures that no homology exists between any training and testing data. A detailed comparison between PCI and 9 contemporary methods is provided over a set of 125 new protein chains guaranteed to be dissimilar to all training data. Unlike other secondary structure prediction methods, here a web service is developed to provide both human- and machine-readable interfaces to PCI-based protein secondary structure prediction. This server, called PCI-SS, is available at http://bioinf.sce.carleton.ca/PCISS. In addition to a dynamic PHP-generated web interface for humans, a Simple Object Access Protocol (SOAP interface is added to permit invocation of the PCI-SS service remotely. This machine-readable interface facilitates incorporation of PCI-SS into multi-faceted systems biology analysis pipelines requiring protein secondary structure information, and greatly simplifies high-throughput analyses. XML is used to represent the input

  14. Evaluation of Pentachlorophenol Residues in Some Hygienic Papers Prepared from Virgin and Secondary Pulp by Electron Capture Gas Chromatographic Method

    Directory of Open Access Journals (Sweden)

    Behrouz Akbari-adergani

    2016-01-01

    Full Text Available In this study, residual amount of pentachlorophenol (PCP as the most important paper preservative, which is extremely hazardous pollutant, was determined in some tissue papers and napkins. Twenty-five samples of two producing hygienic paper factories prepared from virgin and secondary pulp were analyzed for the presence of trace amount of PCP. The analytical procedure involved direct extraction of PCP from hygienic paper and its determination by gas chromatography with electron capture detection. The statistical results for the analysis of all samples revealed that there were significant differences between mean of PCP in hygienic papers prepared from virgin and secondary pulp (P<0.05. This method gave recoveries of 86-98% for hygienic paper made from virgin pulp and 79-92% for hygienic paper made from secondary pulp. The limit of detection (LOD and limit of quantification (LOQ for PCP were 6.3 and 21.0 mg/kg, respectively. The analytical method has the requisite sensitivity, accuracy, precision and specificity to assay PCP in hygienic papers. This study demonstrates a concern with exposition to PCP considering that hygienic paper is largely consumed in the society.

  15. Structure, microstructure and residual stresses in borided steels

    Czech Academy of Sciences Publication Activity Database

    Pala, Z.; Mušálek, Radek; Kyncl, J.; Harcuba, P.; Stráský, J.; Kolařík, K.

    2013-01-01

    Roč. 20, č. 2 (2013), s. 93-95 ISSN 1211-5894. [Struktura 2013 - Kolokvium Krystalografické společnosti. Češkovice (Blansko), 09.09.2013-13.09.2013] Institutional support: RVO:61389021 Keywords : boriding * surface hardening * iron borides * tooth-shaped microstructure * residual stresses Subject RIV: JK - Corrosion ; Surface Treatment of Materials http://www.xray.cz/ms/bul2013-2/s6.pdf

  16. An adjoint method of sensitivity analysis for residual vibrations of structures subject to impacts

    Science.gov (United States)

    Yan, Kun; Cheng, Gengdong

    2018-03-01

    For structures subject to impact loads, the residual vibration reduction is more and more important as the machines become faster and lighter. An efficient sensitivity analysis of residual vibration with respect to structural or operational parameters is indispensable for using a gradient based optimization algorithm, which reduces the residual vibration in either active or passive way. In this paper, an integrated quadratic performance index is used as the measure of the residual vibration, since it globally measures the residual vibration response and its calculation can be simplified greatly with Lyapunov equation. Several sensitivity analysis approaches for performance index were developed based on the assumption that the initial excitations of residual vibration were given and independent of structural design. Since the resulting excitations by the impact load often depend on structural design, this paper aims to propose a new efficient sensitivity analysis method for residual vibration of structures subject to impacts to consider the dependence. The new method is developed by combining two existing methods and using adjoint variable approach. Three numerical examples are carried out and demonstrate the accuracy of the proposed method. The numerical results show that the dependence of initial excitations on structural design variables may strongly affects the accuracy of sensitivities.

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

    Science.gov (United States)

    Sengupta, Dhriti; Kundu, Sudip

    2012-06-21

    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. 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 higher interaction strength between amino acids

  18. Secondary metabolites of Mirabilis jalapa structurally inhibit Lactate Dehydrogenase A in silico: a potential cancer treatment

    Science.gov (United States)

    Kusumawati, R.; Nasrullah, A. H.; Pesik, R. N.; Muthmainah; Indarto, D.

    2018-03-01

    Altered energy metabolism from phosphorylated oxidation to aerobic glycolysis is one of the cancer hallmarks. Lactate dehydrogenase A (LDHA) is a major enzyme that catalyses pyruvate to lactate in such condition. The aim of this study was to explore LDHA inhibitors derived from Indonesian herbal plants. In this study, LDHA and oxamate molecular structures were obtained from protein data bank. As a standard ligand inhibitor, oxamate was molecularly re-validated using Autodock Vina 1.1.2 software and showed binding energy -4.26 ± 0.006 kcal/mol and interacted with LDHA at Gln99, Arg105, Asn137, Arg168, His192, and Thr247 residues. Molecular docking was used to visualize interaction between Indonesian phytochemicals and LDHA. Indonesian phytochemicals with the lowest binding energy and similar residues with standard ligand was Miraxanthin-III (-8.53 ± 0.006 kcal/mol), Vulgaxanthin-I (-8.46 ± 0.006 kcal/mol), Miraxanthin-II (-7.9 ± 0.2 kcal/mol) and Miraxanthin-V (-7.96 ± kcal/mol). Lower energy binding to LDHA and binding site at these residues was predicted to inhibit LDHA activity better than standard ligand. All phytochemicals were found in Mirabilis jalapa plant. Secondary metabolites in Mirabilis jalapa have LDHA inhibitor property in silico. Further in vitro study should be performed to confirm this result.

  19. Resonance assignments and secondary structure of a phytocystatin from Sesamum indicum.

    Science.gov (United States)

    Hu, Yu-Jun; Irene, Deli; Lo, Chi-Jen; Cai, Yong-Liang; Tzen, T-C; Lin, Ta-Hsien; Chyan, Chia-Lin

    2015-10-01

    A cDNA encoding a cysteine protease inhibitor, cystatin was cloned from sesame (Sesamum indicum L.) seed. This clone was constructed into an expression vector and expressed in E. coli and purified to homogeneous. The recombinant sesame cystatin (SiCYS) showed effectively inhibitory activity toward C1 cysteine proteases. In order to unravel its inhibitory action from structural point of view, multidimensional heteronuclear NMR techniques were used to characterize the structure of SiCYS. The full (1)H, (15)N, and (13)C resonances of SiCYS were assigned. The secondary structure of SiCYS was identified by using the assigned chemical shifts of (1)H(α), (13)C(α), (13)C(β), and (13)CO through the consensus chemical shift index (CSI). The results of CSI analysis of SiCYS suggest eight β-strands (residues 33-46, 51-61, 63-75, 80-87, 150-155, 157-169, 172-183, and 192-195) and two α-helices (residues 16-30, and 120-135).

  20. X ray measurement of residual stresses on metallic structures

    International Nuclear Information System (INIS)

    Barbarin, P.; Convert, M.; Miege

    1983-01-01

    The principle of measuring residual stresses by X ray diffraction (the famous Bragg'law is used) may be applied at an industrial level. CETIM has perfected an outfit adjusted to measurements on the spot, which can be used on metallic parts of a large size. This paper describes this equipment, giving its advantages towards previous devices, and assessing measurements errors. Some actual cases for results obtained are given. This paper starts with a brief historical account and theoretical backgrounds of the method [fr

  1. Detecting Local Residue Environment Similarity for Recognizing Near-Native Structure Models

    Science.gov (United States)

    Kim, Hyungrae; Kihara, Daisuke

    2014-01-01

    We developed a new representation of local amino acid environments in protein structures called the Side-chain Depth Environment (SDE). An SDE defines a local structural environment of a residue considering the coordinates and the depth of amino acids that locate in the vicinity of the side-chain centroid of the residue. SDEs are general enough that similar SDEs are found in protein structures with globally different folds. Using SDEs, we developed a procedure called PRESCO (Protein Residue Environment SCOre) for selecting native or near-native models from a pool of computational models. The procedure searches similar residue environments observed in a query model against a set of representative native protein structures to quantify how native-like SDEs in the model are. When benchmarked on commonly used computational model datasets, our PRESCO compared favorably with the other existing scoring functions in selecting native and near-native models. PMID:25132526

  2. Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis.

    Science.gov (United States)

    Du, Yushen; Wu, Nicholas C; Jiang, Lin; Zhang, Tianhao; Gong, Danyang; Shu, Sara; Wu, Ting-Ting; Sun, Ren

    2016-11-01

    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. To fully comprehend the diverse functions of a protein, it is essential to understand the functionality of individual residues. Current methods are highly dependent on evolutionary sequence conservation, which is

  3. Bi-Metallic Composite Structures With Designed Internal Residual Stress Field

    Science.gov (United States)

    Brice, Craig A.

    2014-01-01

    Shape memory alloys (SMA) have a unique ability to recover small amounts of plastic strain through a temperature induced phase change. For these materials, mechanical displacement can be accomplished by heating the structure to induce a phase change, through which some of the plastic strain previously introduced to the structure can be reversed. This paper introduces a concept whereby an SMA phase is incorporated into a conventional alloy matrix in a co-continuous reticulated arrangement forming a bi-metallic composite structure. Through memory activation of the mechanically constrained SMA phase, a controlled residual stress field is developed in the interior of the structure. The presented experimental data show that the memory activation of the SMA composite component significantly changes the residual stress distribution in the overall structure. Designing the structural arrangement of the two phases to produce a controlled residual stress field could be used to create structures that have much improved durability and damage tolerance properties.

  4. 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

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

    Science.gov (United States)

    2012-01-01

    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 higher interaction

  6. Effect of pretreatment on biomass residue structure and the application of pyrolysed and composted biomass residues in soilless culture.

    Directory of Open Access Journals (Sweden)

    Linna Suo

    Full Text Available The changes in the structural characteristics of biomass residues during pyrolysis and composting were investigated. The biomass residues particles were prepared by pyrolysing at temperatures ranging from 350 to 400. For soilless production of the ornamental plant Anthurium andraeanum, pure sphagnum peat moss (P has traditionally been used as the growing medium. This use of P must be reduced, however, because P is an expensive and nonrenewable resource. The current study investigated the use of biomass residues as substitutes for P in A. andraeanum production. Plants were grown for 15 months in 10 soilless media that contained different proportions of pyrolysed corn cobs (PC, composted corn cobs (C, pyrolysed garden wastes (PG, and P. Although the media altered the plant nutrient content, A. andraeanum growth, development, and yield were similar with media consisting of 50% P+50% PC, 50% P+35% PC+15% PG, and 100% P. This finding indicates that, when pyrolysed, organic wastes, which are otherwise an environmental problem, can be used to reduce the requirement for peat in the soilless culture of A. andraeanum.

  7. Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: combining GOR V and Fragment Database Mining (FDM).

    Science.gov (United States)

    Cheng, Haitao; Sen, Taner Z; Jernigan, Robert L; Kloczkowski, Andrzej

    2007-10-01

    One of the challenges in protein secondary structure prediction is to overcome the cross-validated 80% prediction accuracy barrier. Here, we propose a novel approach to surpass this barrier. Instead of using a single algorithm that relies on a limited data set for training, we combine two complementary methods having different strengths: Fragment Database Mining (FDM) and GOR V. FDM harnesses the availability of the known protein structures in the Protein Data Bank and provides highly accurate secondary structure predictions when sequentially similar structural fragments are identified. In contrast, the GOR V algorithm is based on information theory, Bayesian statistics, and PSI-BLAST multiple sequence alignments to predict the secondary structure of residues inside a sliding window along a protein chain. A combination of these two different methods benefits from the large number of structures in the PDB and significantly improves the secondary structure prediction accuracy, resulting in Q3 ranging from 67.5 to 93.2%, depending on the availability of highly similar fragments in the Protein Data Bank.

  8. Approaches for Modelling the Residual Service Life of Marine Concrete Structures

    Directory of Open Access Journals (Sweden)

    Amir Rahimi

    2014-01-01

    Full Text Available This paper deals with the service life design of existing reinforced concrete structures in a marine environment. The general procedure of condition assessment for estimating the residual service life of structures before a repair measure is illustrated. For assessment of the residual service life of structures which have undergone a repair measure a simplified mathematical model of chloride diffusion in a 2-layer system is presented. Preliminary probabilistic calculations demonstrate the effect of various conditions on the residual service life. First studies of the chloride diffusion in a 2-layer system have been conducted using the finite element method. Results of a long-term exposure test are presented to illustrate the performance of two different repair materials. The distribution of residual chlorides after application of a repair material is being studied in laboratory investigations. The residual chlorides migrate from the concrete layer into the new layer immediately after the repair material has been applied to the concrete member. The content and gradient of residual chlorides, along with the thickness and the chloride ingress resistance of both the remaining and the new layer of cover, will determine the residual service life of the repaired structures.

  9. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts

    International Nuclear Information System (INIS)

    Labudde, D.; Leitner, D.; Krueger, M.; Oschkinat, H.

    2003-01-01

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the α-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely α-helix, β-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time

  10. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts.

    Science.gov (United States)

    Labudde, D; Leitner, D; Krüger, M; Oschkinat, H

    2003-01-01

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the alpha-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely alpha-helix, beta-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

  11. RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data.

    Science.gov (United States)

    Wu, Yang; Qu, Rihao; Huang, Yiming; Shi, Binbin; Liu, Mengrong; Li, Yang; Lu, Zhi John

    2016-07-08

    Several high-throughput technologies have been developed to probe RNA base pairs and loops at the transcriptome level in multiple species. However, to obtain the final RNA secondary structure, extensive effort and considerable expertise is required to statistically process the probing data and combine them with free energy models. Therefore, we developed an RNA secondary structure prediction server that is enhanced by experimental data (RNAex). RNAex is a web interface that enables non-specialists to easily access cutting-edge structure-probing data and predict RNA secondary structures enhanced by in vivo and in vitro data. RNAex annotates the RNA editing, RNA modification and SNP sites on the predicted structures. It provides four structure-folding methods, restrained MaxExpect, SeqFold, RNAstructure (Fold) and RNAfold that can be selected by the user. The performance of these four folding methods has been verified by previous publications on known structures. We re-mapped the raw sequencing data of the probing experiments to the whole genome for each species. RNAex thus enables users to predict secondary structures for both known and novel RNA transcripts in human, mouse, yeast and Arabidopsis The RNAex web server is available at http://RNAex.ncrnalab.org/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. RNA secondary structure diagrams for very large molecules: RNAfdl.

    Science.gov (United States)

    Hecker, Nikolai; Wiegels, Tim; Torda, Andrew E

    2013-11-15

    There are many programs that can read the secondary structure of an RNA molecule and draw a diagram, but hardly any that can cope with 10(3) bases. RNAfdl is slow but capable of producing intersection-free diagrams for ribosome-sized structures, has a graphical user interface for adjustments and produces output in common formats. Source code is available under the GNU General Public License v3.0 at http://sourceforge.net/projects/rnafdl for Linux and similar systems or Windows using MinGW. RNAfdl is implemented in C, uses the Cairo 2D graphics library and offers both command line and graphical user interfaces. hecker@rth.dk

  13. 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.

  14. RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

    Science.gov (United States)

    Ellington, Roni; Wachira, James; Nkwanta, Asamoah

    2010-01-01

    The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses…

  15. Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings

    International Nuclear Information System (INIS)

    Montalvao, Rinaldo W.; De Simone, Alfonso; Vendruscolo, Michele

    2012-01-01

    Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural restraints in molecular dynamics simulations we show that it is possible to extract effectively the information provided by RDCs about the conformational fluctuations in the native states of proteins. The approach that we present can be used in a wide range of alignment media, including Pf1, charged bicelles and gels. The accuracy of the method is demonstrated by the analysis of the Q factors for RDCs not used as restraints in the calculations, which are significantly lower than those corresponding to existing high-resolution structures and structural ensembles, hence showing that we capture effectively the contributions to RDCs from conformational fluctuations.

  16. Secondary structural entropy in RNA switch (Riboswitch) identification.

    Science.gov (United States)

    Manzourolajdad, Amirhossein; Arnold, Jonathan

    2015-04-28

    RNA regulatory elements play a significant role in gene regulation. Riboswitches, a widespread group of regulatory RNAs, are vital components of many bacterial genomes. These regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in RNA. Riboswitch-mediated mechanisms are ubiquitous across bacterial genomes. A typical class of riboswitch has its own unique structural and biological complexity, making de novo riboswitch identification a formidable task. Traditionally, riboswitches have been identified through comparative genomics based on sequence and structural homology. The limitations of structural-homology-based approaches, coupled with the assumption that there is a great diversity of undiscovered riboswitches, suggests the need for alternative methods for riboswitch identification, possibly based on features intrinsic to their structure. As of yet, no such reliable method has been proposed. We used structural entropy of riboswitch sequences as a measure of their secondary structural dynamics. Entropy values of a diverse set of riboswitches were compared to that of their mutants, their dinucleotide shuffles, and their reverse complement sequences under different stochastic context-free grammar folding models. Significance of our results was evaluated by comparison to other approaches, such as the base-pairing entropy and energy landscapes dynamics. Classifiers based on structural entropy optimized via sequence and structural features were devised as riboswitch identifiers and tested on Bacillus subtilis, Escherichia coli, and Synechococcus elongatus as an exploration of structural entropy based approaches. The unusually long untranslated region of the cotH in Bacillus subtilis, as well as upstream regions of certain genes, such as the sucC genes were associated with significant structural entropy values in genome-wide examinations. Various tests show that there

  17. Self-contacts in Asx and Glx residues of high-resolution protein structures: role of local environment and tertiary interactions.

    Science.gov (United States)

    Pal, Tuhin Kumar; Sankararamakrishnan, Ramasubbu

    2008-08-01

    In protein structures, side-chains of asparagine and aspartic acid (Asx) and glutamine and glutamic acid (Glx) can approach their own backbone nitrogen or carbonyl group. We have systematically analyzed intra-residue contacts in Asx and Glx residues and their secondary structure preferences in two different datasets consisting of 500 and 1506 high-resolution structures. Intra-residue contact in an Asx/Glx residue between the heavy atoms of side-chain and main-chain functional groups of the same residue was investigated irrespective of whether such contacts are due to hydrogen bonding or not. Our search yielded 563 and 1462 cases of self-contacting Asx and Glx residues from the two datasets. Two important observations have been made in this analysis. First, self-contacts involving side-chain oxygen and backbone nitrogen atoms in majority of Asx residues are not due to hydrogen bonds. In the second instance, surprisingly, side-chain and backbone carbonyl oxygens of a significant number of Asx and Glx residues approach each other. For a wide-range of accessible surface areas, self-contacting residues are surrounded by less number of polar groups compared to all other Asx/Glx residues. In buried and partially buried regions, side-chain and main-chain functional groups of these residues together participate in simultaneous interactions with the available polar groups or water molecules. Asx/Glx residues with self-contacts are rarely observed in the middle of an alpha-helix or a beta-strand. Asx/Glx side-chain having contact with its own backbone nitrogen shows different capping preferences compared to those having contact with its backbone oxygen. Examples of proteins with multiple self-contacting Asx/Glx residues are found. We speculate that mutation of a self-contacting residue in the buried or partially buried region of a protein will destabilize the structure. The results of this analysis will help in engineering protein structures and site-directed mutagenesis

  18. A semi-supervised learning approach for RNA secondary structure prediction.

    Science.gov (United States)

    Yonemoto, Haruka; Asai, Kiyoshi; Hamada, Michiaki

    2015-08-01

    RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because of the difficulty of determining RNA secondary structures by experimental procedures, such as NMR or X-ray crystal structural analyses, there are still many RNA sequences that could be useful for training whose secondary structures have not been experimentally determined. In this paper, we introduce a novel semi-supervised learning approach for training parameters in a probabilistic model of RNA secondary structures in which we employ not only RNA sequences with annotated secondary structures but also ones with unknown secondary structures. Our model is based on a hybrid of generative (stochastic context-free grammars) and discriminative models (conditional random fields) that has been successfully applied to natural language processing. Computational experiments indicate that the accuracy of secondary structure prediction is improved by incorporating RNA sequences with unknown secondary structures into training. To our knowledge, this is the first study of a semi-supervised learning approach for RNA secondary structure prediction. This technique will be useful when the number of reliable structures is limited. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Influence of the fluctuations of the alignment tensor on the analysis of the structure and dynamics of proteins using residual dipolar couplings

    Energy Technology Data Exchange (ETDEWEB)

    Salvatella, X., E-mail: xs210@cam.ac.uk; Richter, B.; Vendruscolo, M. [University of Cambridge, Department of Chemistry (United Kingdom)], E-mail: mv245@cam.ac.uk

    2008-01-15

    It has been suggested that the fluctuations of the alignment tensor can affect the results of procedures for characterizing the structure and the dynamics of proteins using residual dipolar couplings. We show here that the very significant fluctuations of the steric alignment tensor caused by the dynamics of proteins can be safely ignored when they do not correlate with those of the bond vectors. A detailed analysis of these correlations in the protein ubiquitin reveals that their effects are negligible for the analysis of backbone motions within secondary structure elements, but also that they may be significant in turns, loops and side chains, especially for bond vectors that have small residual dipolar couplings. Our results suggest that methods that explicitly consider the motions of the alignment tensor will be needed to study the large-scale structural fluctuations that take place on the millisecond timescale, which are often important for the biological function of proteins, from residual dipolar coupling measurements.

  20. 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.

  1. Secondary Structure of Huntingtin Amino-Terminal Region

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Mee Whi; Chelliah, Yogarany; Kim, Sang Woo; Otwinowski, Zbyszek; Bezprozvanny, Ilya; (UTSMC)

    2010-09-21

    Huntington's disease is a genetic neurodegenerative disorder resulting from polyglutamine (polyQ) expansion (>36Q) within the first exon of Huntingtin (Htt) protein. We applied X-ray crystallography to determine the secondary structure of the first exon (EX1) of Htt17Q. The structure of Htt17Q-EX1 consists of an amino-terminal {alpha} helix, poly17Q region, and polyproline helix formed by the proline-rich region. The poly17Q region adopts multiple conformations in the structure, including {alpha} helix, random coil, and extended loop. The conformation of the poly17Q region is influenced by the conformation of neighboring protein regions, demonstrating the importance of the native protein context. We propose that the conformational flexibility of the polyQ region observed in our structure is a common characteristic of many amyloidogenic proteins. We further propose that the pathogenic polyQ expansion in the Htt protein increases the length of the random coil, which promotes aggregation and facilitates abnormal interactions with other proteins in cells.

  2. Sequence-specific H NMR assignments and secondary structure in the sea anemone polypeptide Stichodactyla helianthus neurotoxin I

    International Nuclear Information System (INIS)

    Fogh, R.H.; Mabbutt, B.C.; Kem, W.R.; Norton, R.S.

    1989-01-01

    Sequence-specific assignments are reported for the 500-MHz H nuclear magnetic resonance (NMR) spectrum of the 48-residue polypeptide neurotoxin I from the sea anemone Stichodactyla helianthus (Sh I). Spin systems were first identified by using two-dimensional relayed or multiple quantum filtered correlation spectroscopy, double quantum spectroscopy, and spin lock experiments. Specific resonance assignments were then obtained from nuclear Overhauser enhancement (NOE) connectivities between protons from residues adjacent in the amino acid sequence. Of a total of 265 potentially observable resonances, 248 (i.e., 94%) were assigned, arising from 39 completely and 9 partially assigned amino acid spin systems. The secondary structure of Sh I was defined on the basis of the pattern of sequential NOE connectivities. NOEs between protons on separate strands of the polypeptide backbone, and backbone amide exchange rates. Sh I contains a four-stranded antiparallel β-sheet encompassing residues 1-5, 16-24, 30-33, and 40-46, with a β-bulge at residues 17 and 18 and a reverse turn, probably a type II β-turn, involving residues 27-30. No evidence of α-helical structure was found

  3. Rapid NMR screening of RNA secondary structure and binding

    Energy Technology Data Exchange (ETDEWEB)

    Helmling, Christina; Keyhani, Sara; Sochor, Florian; Fürtig, Boris; Hengesbach, Martin; Schwalbe, Harald, E-mail: schwalbe@nmr.uni-frankfurt.de [Johann Wolfgang Goethe-Universität, Institut für Organische Chemie und Chemische Biologie, Center for Biomolecular Magnetic Resonance (BMRZ) (Germany)

    2015-09-15

    Determination of RNA secondary structures by NMR spectroscopy is a useful tool e.g. to elucidate RNA folding space or functional aspects of regulatory RNA elements. However, current approaches of RNA synthesis and preparation are usually time-consuming and do not provide analysis with single nucleotide precision when applied for a large number of different RNA sequences. Here, we significantly improve the yield and 3′ end homogeneity of RNA preparation by in vitro transcription. Further, by establishing a native purification procedure with increased throughput, we provide a shortcut to study several RNA constructs simultaneously. We show that this approach yields μmol quantities of RNA with purities comparable to PAGE purification, while avoiding denaturation of the RNA.

  4. Efficient identification of critical residues based only on protein structure by network analysis.

    Directory of Open Access Journals (Sweden)

    Michael P Cusack

    2007-05-01

    Full Text Available Despite the increasing number of published protein structures, and the fact that each protein's function relies on its three-dimensional structure, there is limited access to automatic programs used for the identification of critical residues from the protein structure, compared with those based on protein sequence. Here we present a new algorithm based on network analysis applied exclusively on protein structures to identify critical residues. Our results show that this method identifies critical residues for protein function with high reliability and improves automatic sequence-based approaches and previous network-based approaches. The reliability of the method depends on the conformational diversity screened for the protein of interest. We have designed a web site to give access to this software at http://bis.ifc.unam.mx/jamming/. In summary, a new method is presented that relates critical residues for protein function with the most traversed residues in networks derived from protein structures. A unique feature of the method is the inclusion of the conformational diversity of proteins in the prediction, thus reproducing a basic feature of the structure/function relationship of proteins.

  5. High-resolution NMR reveals secondary structure and folding of amino acid transporter from outer chloroplast membrane.

    Directory of Open Access Journals (Sweden)

    James D Zook

    Full Text Available Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16, an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the (13C, (15N, (2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, Cα, and Cβ chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T 1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein.

  6. Normal linear models with genetically structured residual variance heterogeneity: a case study

    DEFF Research Database (Denmark)

    Sorensen, Daniel; Waagepetersen, Rasmus Plenge

    2003-01-01

    Normal mixed models with different levels of heterogeneity in the residual variance are fitted to pig litter size data. Exploratory analysis and model assessment is based on examination of various posterior predictive distributions. Comparisons based on Bayes factors and related criteria favour...... models with a genetically structured residual variance heterogeneity. There is, moreover, strong evidence of a negative correlation between the additive genetic values affecting litter size and those affecting residual variance. The models are also compared according to the purposes for which they might...... be used, such as prediction of 'future' data, inference about response to selection and ranking candidates for selection. A brief discussion is given of some implications for selection of the genetically structured residual variance model....

  7. Dynamic changes in the secondary structure of ECE-1 and XCE account for their different substrate specificities

    Directory of Open Access Journals (Sweden)

    Ul-Haq Zaheer

    2012-11-01

    Full Text Available Abstract Background X-converting enzyme (XCE involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet. In contrast, it’s well characterized homologue endothelin-converting enzyme-1 (ECE-1 showed broad substrate specificity and acts as endopeptidase as well as dipeptidase. To explore the structural differences between XCE and ECE-1, homology model of XCE was built using the complex structure of ECE-1 with phosphoramidon (pdb-id: 3DWB as template. Phosphoramidon was docked into the binding site of XCE whereas phosphate oxygen of the inhibitor was used as water molecule to design the apo forms of both enzymes. Molecular dynamics simulation of both enzymes was performed to analyze the dynamic nature of their active site residues in the absence and presence of the inhibitor. Results Homology model of XCE explained the role of non-conserved residues of its S2’ subsite. Molecular dynamics (MD simulations identified the flexible transitions of F149/I150, N566/N571, W714/W719, and R145/R723 residues of ECE-1/XCE for the strong binding of the inhibitor. Secondary structure calculations using DSSP method reveals the folding of R145/R723 residue of ECE-1/XCE into β-sheet structure while unfolding of the S2’ subsite residues in aECE-1 and sustained compact folding of that of aXCE. The results evaluated are in good agreement with available experimental data, thus providing detailed molecular models which can explain the structural and specificities differences between both zinc peptidases. Conclusions Secondary structure changes of both enzymes during the simulation time revealed the importance of β-sheet structure of R145/R723 for its binding with the terminal carboxylate group of the inhibitor. Unfolding of the α-helix comprising the S2’ subsite residues in aECE-1 correlate well with its endopeptidase activity while their compact folding in aXCE may

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

    Directory of Open Access Journals (Sweden)

    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.

  9. STAGS Developments for Residual Strength Analysis Methods for Metallic Fuselage Structures

    Science.gov (United States)

    Young, Richard D.; Rose, Cheryl A.

    2014-01-01

    A summary of advances in the Structural Analysis of General Shells (STAGS) finite element code for the residual strength analysis of metallic fuselage structures, that were realized through collaboration between the structures group at NASA Langley, and Dr. Charles Rankin is presented. The majority of the advancements described were made in the 1990's under the NASA Airframe Structural Integrity Program (NASIP). Example results from studies that were conducted using the STAGS code to develop improved understanding of the nonlinear response of cracked fuselage structures subjected to combined loads are presented. An integrated residual strength analysis methodology for metallic structure that models crack growth to predict the effect of cracks on structural integrity is demonstrated

  10. Relating secondary structure to the mechanical properties of polypeptide hydrogels

    Science.gov (United States)

    Hagan, Sharon Anne

    Biomimetic hydrogels are being developed for use in medicine as drug delivery devices and tissue engineering matrices, and the mechanical properties of the materials play an important role in their performance. For example, in tissue engineering, gene expression and cell adhesion have been closely linked to the mechanical properties of the surrounding hydrogel matrix. In poly-L-lysine hydrogels, a five-fold increase in storage modulus, a 50% increase in equilibrium modulus, and a 62% decrease in swelling degree are shown to occur as the hydrogel network chains transition from an alpha-helix to a beta-sheet conformation. The manipulation of the network's mechanical behavior through changes in the secondary structure of the polymer chains offers an additional design variable in the development of biosynthetic materials. Analogous to poly-L-lysine, elastin-mimetic proteins based on the consensus repeat sequence of elastin (VPGVG) undergo a temperature-dependent secondary structure transition from a random coil to a beta-spiral. In this research, chemically-crosslinked poly[(VPGVG)4(VPGKG)] hydrogels are shown to possess temperature- and pH-dependent swelling. Following scaling law predictions (G ˜ φ2n), the hydrogels have been shown to behave as ideal elastic networks when the crosslink density is varied at synthesis (theory: n = 9/4, experimental: n = 2.0 +/- 0.1), and behave as flexible networks above and below their structural transition temperature of 35°C (theory: n = 1/3, experimental: n = 0.45 +/- 0.06). Evaluation of published data on elastin-mimetic hydrogels shows that the hydrogels behave as ideal elastic networks for all crosslinking techniques, crosslink spacings, and crosslink functionalities reported. As a contrast to chemically-crosslinked hydrogels, a novel elastin-mimetic triblock (EMT) copolymer was evaluated because of its potential use in cell encapsulation without potentially harmful side reactions. Unlike other thermally gelling copolymers

  11. LBA-ECO ND-04 Secondary Forest Recovery, Structure, and LAI, Central Amazonia, Brazil

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set reports measurements of the canopy and structure of secondary forests regenerating from abandoned pastures. These secondary forests are located in the...

  12. Distortion and residual stresses in structures reinforced with titanium straps for improved damage tolerance

    International Nuclear Information System (INIS)

    Liljedahl, C.D.M.; Fitzpatrick, M.E.; Edwards, L.

    2008-01-01

    Distortion and residual stresses induced during the manufacturing process of bonded crack retarders have been investigated. Titanium alloy straps were adhesively bonded to an aluminium alloy SENT specimen to promote fatigue crack growth retardation. The effect of three different strap dimensions was investigated. The spring-back of a component when released from the autoclave and the residual stresses are important factors to take into account when designing a selective reinforcement, as this may alter the local aerodynamic characteristics and reduce the crack bridging effect of the strap. The principal problem with residual stresses is that the tensile nature of the residual stresses in the primary aluminium structure has a negative impact on the crack initiation and crack propagation behaviour in the aluminium. The residual stresses were measured with neutron diffraction and the distortion of the specimens was measured with a contour measurement machine. The bonding process was simulated with a three-dimensional FE model. The residual stresses were found to be tensile close to the strap and slightly compressive on the un-bonded side. Both the distortion and the residual stresses increased with the thickness and the width of the strap. Very good agreement between the measured stresses and the measured distortion and the FE simulation was found

  13. Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

    Directory of Open Access Journals (Sweden)

    Aparecido R. Silva

    2008-05-01

    Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

  14. 1H and 15N NMR resonance assignments and secondary structure of titin type I domains

    Energy Technology Data Exchange (ETDEWEB)

    Muhle-Goll, Claudia; Nilges, Michael; Pastore, Annalisa [European Molecular Biology Laboratory (Germany)

    1997-01-15

    Titin/connect in is a giant muscle protein with a highly modular architecture consisting of multiple repeats of two sequence motifs, named type I and type II. Type I modules have been suggested to be intracellular members of the fibronectin type III (Fn3) domain family. Along the titin sequence they are exclusively present in the region of the molecule located in the sarcomere A-band. This region has been shown to interact with myosin and C-protein. One of the most noticeable features of type I modules is that they are particularly rich in semiconserved prolines, since these residues account for about 8% of their sequence. We have determined the secondary structure of a representative type I domain (A71) by 15N and 1HNMR. We show that the type I domains of titin have the Fn3 fold as proposed, consisting of a three- and a four-stranded {beta}-sheet. When the two sheets are placed on top of each other to form the {beta}-sandwich characteristic of the Fn3 fold, 8 out of 10 prolines are found on the same side of the molecule and form an exposed hydrophobic patch. This suggests that the semiconserved prolines might be relevant for the function of type I modules, providing a surface for binding to other A-band proteins. The secondary structure of A71 was structurally aligned to other extracellular Fn3 modules of known 3D structure. The alignment shows that titin type I modules have closest similarity to the first Fn3 domain of Drosophila neuroglian.

  15. Prediction of welding residual distortions of large structures using a local/global approach

    International Nuclear Information System (INIS)

    Duan, Y. G.; Bergheau, J. M.; Vincent, Y.; Boitour, F.; Leblond, J. B.

    2007-01-01

    Prediction of welding residual distortions is more difficult than that of the microstructure and residual stresses. On the one hand, a fine mesh (often 3D) has to be used in the heat affected zone for the sake of the sharp variations of thermal, metallurgical and mechanical fields in this region. On the other hand, the whole structure is required to be meshed for the calculation of residual distortions. But for large structures, a 3D mesh is inconceivable caused by the costs of the calculation. Numerous methods have been developed to reduce the size of models. A local/global approach has been proposed to determine the welding residual distortions of large structures. The plastic strains and the microstructure due to welding are supposed can be determined from a local 3D model which concerns only the weld and its vicinity. They are projected as initial strains into a global 3D model which consists of the whole structure and obviously much less fine in the welded zone than the local model. The residual distortions are then calculated using a simple elastic analysis, which makes this method particularly effective in an industrial context. The aim of this article is to present the principle of the local/global approach then show the capacity of this method in an industrial context and finally study the definition of the local model

  16. Effects of interface edge configuration on residual stress in the bonded structures for a divertor application

    International Nuclear Information System (INIS)

    Kitamura, K.; Nagata, K.; Shibui, M.; Tachikawa, N.; Araki, M.

    1998-01-01

    Residual stresses in the interface region, that developed at the cool down during the brazing, were evaluated for several bonded structures to assess the mechanical strength of the bonded interface, using thermoelasto-plastic stress analysis. Normal stress components of the residual stresses around the interface edge of graphite-copper (C-Cu) bonded structures were compared for three types of bonded features such as flat-type, monoblock-type and saddle-type. The saddle-type structure was found to be favorable for its relatively low residual stress, easy fabrication accuracy on bonded interface and armor replacement. Residual stresses around the interface edge in three armor materials/copper bonded structures for a divertor plate were also examined for the C-Cu, tungsten-copper (W-Cu) and molybdenum alloy-copper (TZM-Cu), varying the interface wedge angle from 45 to 135 . An optimal bonded configuration for the least value of residual stress was found to have a wedge angle of 45 for the C-Cu, and 135 for both the W-Cu and TZM-Cu bonded ones. (orig.)

  17. Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data.

    Science.gov (United States)

    Montaseri, Soheila; Ganjtabesh, Mohammad; Zare-Mirakabad, Fatemeh

    2016-01-01

    Non-coding RNAs perform a wide range of functions inside the living cells that are related to their structures. Several algorithms have been proposed to predict RNA secondary structure based on minimum free energy. Low prediction accuracy of these algorithms indicates that free energy alone is not sufficient to predict the functional secondary structure. Recently, the obtained information from the SHAPE experiment greatly improves the accuracy of RNA secondary structure prediction by adding this information to the thermodynamic free energy as pseudo-free energy. In this paper, a new method is proposed to predict RNA secondary structure based on both free energy and SHAPE pseudo-free energy. For each RNA sequence, a population of secondary structures is constructed and their SHAPE data are simulated. Then, an evolutionary algorithm is used to improve each structure based on both free and pseudo-free energies. Finally, a structure with minimum summation of free and pseudo-free energies is considered as the predicted RNA secondary structure. Computationally simulating the SHAPE data for a given RNA sequence requires its secondary structure. Here, we overcome this limitation by employing a population of secondary structures. This helps us to simulate the SHAPE data for any RNA sequence and consequently improves the accuracy of RNA secondary structure prediction as it is confirmed by our experiments. The source code and web server of our proposed method are freely available at http://mostafa.ut.ac.ir/ESD-Fold/.

  18. Residual stress distribution of the soldered structure with Kovar alloy and Al2O3 ceramics

    Directory of Open Access Journals (Sweden)

    Qile Gao

    2017-03-01

    Full Text Available Residual stress distribution in soldered structure of Kovar alloy and Al2O3 ceramics was determined using XRD analyses. In order to measure the residual stress, position of the characteristic diffraction peak and stress constant were obtained using several versatile/advanced techniques after calibration. Residual stress of soldered structure was measured based on the diffraction patterns obtained for the distribution of residual stress in the soldered joint. Only diffraction peak at 149° for Kovar alloy and two diffraction peaks ranging from 140–170° for Al2O3 ceramics were found to be appropriate for the residual stress determination. It was also confirmed that for Al2O3 ceramics the XRD peak at 152° reflects the changes of stress more precisely than the one at 146°. The stress constant K of Kovar alloy and Al2O3 ceramics was found to be −197 MPa/° and −654 MPa/°, respectively. After soldering, the maximum residual stress of the soldered joint of both materials developed at 1 mm from the soldering seam, and the values within 3 mm from the soldering seam are generally significant. Thus, it is important to pay attention to the area of 3 mm from the soldering seam in practical application.

  19. Systematic Identification of Machine-Learning Models Aimed to Classify Critical Residues for Protein Function from Protein Structure.

    Science.gov (United States)

    Corral-Corral, Ricardo; Beltrán, Jesús A; Brizuela, Carlos A; Del Rio, Gabriel

    2017-10-09

    Protein structure and protein function should be related, yet the nature of this relationship remains unsolved. Mapping the critical residues for protein function with protein structure features represents an opportunity to explore this relationship, yet two important limitations have precluded a proper analysis of the structure-function relationship of proteins: (i) the lack of a formal definition of what critical residues are and (ii) the lack of a systematic evaluation of methods and protein structure features. To address this problem, here we introduce an index to quantify the protein-function criticality of a residue based on experimental data and a strategy aimed to optimize both, descriptors of protein structure (physicochemical and centrality descriptors) and machine learning algorithms, to minimize the error in the classification of critical residues. We observed that both physicochemical and centrality descriptors of residues effectively relate protein structure and protein function, and that physicochemical descriptors better describe critical residues. We also show that critical residues are better classified when residue criticality is considered as a binary attribute (i.e., residues are considered critical or not critical). Using this binary annotation for critical residues 8 models rendered accurate and non-overlapping classification of critical residues, confirming the multi-factorial character of the structure-function relationship of proteins.

  20. Secondary use of structured patient data: interim results of a systematic review.

    Science.gov (United States)

    Vuokko, Riikka; Mäkelä-Bengs, Päivi; Hyppönen, Hannele; Doupi, Persephone

    2015-01-01

    In addition to patient care, EHR data are increasingly in demand for secondary purposes, e.g. administration, research and enterprise resource planning. We conducted a systematic literature review and subsequent analysis of 85 articles focusing on the secondary use of structured patient records. We grounded the analysis on how patient records have been structured, how these structures have been evaluated and what are the main results achieved from the secondary use viewpoint. We conclude that secondary use requires complete and interoperable patient records, which in turn depend on better alignment of primary and secondary users' needs and benefits.

  1. α-Aminoxy Oligopeptides: Synthesis, Secondary Structure, and Cytotoxicity of a New Class of Anticancer Foldamers.

    Science.gov (United States)

    Diedrich, Daniela; Moita, Ana J Rodrigues; Rüther, Anja; Frieg, Benedikt; Reiss, Guido J; Hoeppner, Astrid; Kurz, Thomas; Gohlke, Holger; Lüdeke, Steffen; Kassack, Matthias U; Hansen, Finn K

    2016-12-05

    α-Aminoxy peptides are peptidomimetic foldamers with high proteolytic and conformational stability. To gain an improved synthetic access to α-aminoxy oligopeptides we used a straightforward combination of solution- and solid-phase-supported methods and obtained oligomers that showed a remarkable anticancer activity against a panel of cancer cell lines. We solved the first X-ray crystal structure of an α-aminoxy peptide with multiple turns around the helical axis. The crystal structure revealed a right-handed 2 8 -helical conformation with precisely two residues per turn and a helical pitch of 5.8 Å. By 2D ROESY experiments, molecular dynamics simulations, and CD spectroscopy we were able to identify the 2 8 -helix as the predominant conformation in organic solvents. In aqueous solution, the α-aminoxy peptides exist in the 2 8 -helical conformation at acidic pH, but exhibit remarkable changes in the secondary structure with increasing pH. The most cytotoxic α-aminoxy peptides have an increased propensity to take up a 2 8 -helical conformation in the presence of a model membrane. This indicates a correlation between the 2 8 -helical conformation and the membranolytic activity observed in mode of action studies, thereby providing novel insights in the folding properties and the biological activity of α-aminoxy peptides. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA.

    Science.gov (United States)

    Fahim, Arjang; Mukhopadhyay, Rishi; Yandle, Ryan; Prestegard, James H; Valafar, Homayoun

    2013-08-22

    More than 90% of protein structures submitted to the PDB each year are homologous to some previously characterized protein structure. The extensive resources that are required for structural characterization of proteins can be justified for the 10% of the novel structures, but not for the remaining 90%. This report presents the 2D-PDPA method, which utilizes unassigned residual dipolar coupling in order to address the economics of structure determination of routine proteins by reducing the data acquisition and processing time. 2D-PDPA has been demonstrated to successfully identify the correct structure of an array of proteins that range from 46 to 445 residues in size from a library of 619 decoy structures by using unassigned simulated RDC data. When using experimental data, 2D-PDPA successfully identified the correct NMR structures from the same library of decoy structures. In addition, the most homologous X-ray structure was also identified as the second best structural candidate. Finally, success of 2D-PDPA in identifying and evaluating the most appropriate structure from a set of computationally predicted structures in the case of a previously uncharacterized protein Pf2048.1 has been demonstrated. This protein exhibits less than 20% sequence identity to any protein with known structure and therefore presents a compelling and practical application of our proposed work.

  3. Protein Structure Validation and Identification from Unassigned Residual Dipolar Coupling Data Using 2D-PDPA

    Science.gov (United States)

    Fahim, Arjang; Mukhopadhyay, Rishi; Yandle, Ryan; Prestegard, James H.; Valafar, Homayoun

    2014-01-01

    More than 90% of protein structures submitted to the PDB each year are homologous to some previously characterized protein structure. The extensive resources that are required for structural characterization of proteins can be justified for the 10% of the novel structures, but not for the remaining 90%. This report presents the 2D-PDPA method, which utilizes unassigned residual dipolar coupling in order to address the economics of structure determination of routine proteins by reducing the data acquisition and processing time. 2D-PDPA has been demonstrated to successfully identify the correct structure of an array of proteins that range from 46 to 445 residues in size from a library of 619 decoy structures by using unassigned simulated RDC data. When using experimental data, 2D-PDPA successfully identified the correct NMR structures from the same library of decoy structures. In addition, the most homologous X-ray structure was also identified as the second best structural candidate. Finally, success of 2D-PDPA in identifying and evaluating the most appropriate structure from a set of computationally predicted structures in the case of a previously uncharacterized protein Pf2048.1 has been demonstrated. This protein exhibits less than 20% sequence identity to any protein with known structure and therefore presents a compelling and practical application of our proposed work. PMID:23973992

  4. StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.

    Science.gov (United States)

    Tang, Yin; Bouvier, Emil; Kwok, Chun Kit; Ding, Yiliang; Nekrutenko, Anton; Bevilacqua, Philip C; Assmann, Sarah M

    2015-08-15

    RNAs fold into complex structures that are integral to the diverse mechanisms underlying RNA regulation of gene expression. Recent development of transcriptome-wide RNA structure profiling through the application of structure-probing enzymes or chemicals combined with high-throughput sequencing has opened a new field that greatly expands the amount of in vitro and in vivo RNA structural information available. The resultant datasets provide the opportunity to investigate RNA structural information on a global scale. However, the analysis of high-throughput RNA structure profiling data requires considerable computational effort and expertise. We present a new platform, StructureFold, that provides an integrated computational solution designed specifically for large-scale RNA structure mapping and reconstruction across any transcriptome. StructureFold automates the processing and analysis of raw high-throughput RNA structure profiling data, allowing the seamless incorporation of wet-bench structural information from chemical probes and/or ribonucleases to restrain RNA secondary structure prediction via the RNAstructure and ViennaRNA package algorithms. StructureFold performs reads mapping and alignment, normalization and reactivity derivation, and RNA structure prediction in a single user-friendly web interface or via local installation. The variation in transcript abundance and length that prevails in living cells and consequently causes variation in the counts of structure-probing events between transcripts is accounted for. Accordingly, StructureFold is applicable to RNA structural profiling data obtained in vivo as well as to in vitro or in silico datasets. StructureFold is deployed via the Galaxy platform. StructureFold is freely available as a component of Galaxy available at: https://usegalaxy.org/. yxt148@psu.edu or sma3@psu.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights

  5. Conserved residues and their role in the structure, function, and stability of acyl-coenzyme A binding protein

    DEFF Research Database (Denmark)

    Kragelund, B B; Poulsen, K; Andersen, K V

    1999-01-01

    for stability of the structure have likewise been identified and are Phe5, Ala9, Val12, Leu15, Leu25, Tyr28, Lys32, Gln33, Tyr73, Val77, and Leu80. Essentially, all of the conserved residues that maintain the stability are hydrophobic residues at the interface of the helices. Only one conserved polar residue...

  6. Distortion and Residual Stress Control in Integrally Stiffened Structure Produced by Direct Metal Deposition

    Science.gov (United States)

    Lin, Shih-Yung; Hoffman, Eric K.; Domack, Marcia S.

    2007-01-01

    2-D thermo-mechanical model developed to characterize distortion and residual stresses in integral structure produced by DMD. Demonstrated as a tool to guide experimental development of DMD fabrication process for aero structures. Distortion and residual stresses are local to deposit. Most distortion develops during deposition of the first few layers; Little change in distortion or residual stresses after fifth deposit layer Most of distortion is localized just beneath the build. Thicker build plates and the use of build lands results in greatest decrease in levels of distortion. Pre-straining shown to reduce distortion. Difficult to implement, particularly for complex stiffener arrays. Clamp position has complex effect on distortion and stresses. Overall distortion reduced with decreasing clamp clearance. Larger clamp clearances induce bending. Use of pre-heat and active cooling show minor influence on panel distortion. Generate changes in thermal gradients in the build plate.

  7. Floristic and structural changes in secondary forests following ...

    African Journals Online (AJOL)

    The results showed that the forests were less diversified with few species very common in the forest stands; the most dominant were Lonchocarpus sericeus and Anogeissus leiocarpa in the secondary forests, and Dialium guineense, Diospyros mespiliformis and Afzelia africana in the old-growth forests. The secondary ...

  8. Residual dent in locally loaded foam core sandwich structures – Analysis and use for NDI

    NARCIS (Netherlands)

    Koysin, V.; Shipsha, Andrey

    2008-01-01

    This paper addresses the residual denting in the face sheet and corresponding core damage in a locally loaded flat sandwich structure with foam core. The problem is analytically considered in the context of elastic bending of the face sheet accompanied by non-linear deformation of the crushed foam

  9. Enhanced measurement of residual chemical shift anisotropy for small molecule structure elucidation.

    Science.gov (United States)

    Liu, Yizhou; Cohen, Ryan D; Gustafson, Kirk R; Martin, Gary E; Williamson, R Thomas

    2018-03-05

    A method is introduced to measure residual chemical shift anisotropies conveniently and accurately in the mesophase of poly-γ-(benzyl-l-glutamate). The alignment amplitude is substantially enhanced over common methods which greatly benefits measurements particularly on sp 3 carbons. The approach offers significant improvements in data accuracy and utility for small molecule structure determination.

  10. Residual dipolar couplings : a new technique for structure determination of proteins in solution

    NARCIS (Netherlands)

    van Lune, Frouktje Sapke

    2004-01-01

    The aim of the work described in this thesis was to investigate how residual dipolar couplings can be used to resolve or refine the three-dimensional structure of one of the proteins of the phosphoenol-pyruvate phosphotransferase system (PTS), the main transport system for carbohydrates in

  11. Deamidation of asparagine and glutamine residues in proteins and peptides: structural determinants and analytical methodology

    NARCIS (Netherlands)

    Bischoff, Rainer; Kolbe, H.V.

    1994-01-01

    Non-enzymatic deamidation of asparagine and glutamine residues in proteins and peptides are reviewed by first outlining the well-described reaction mechanism involving cyclic imide intermediates, followed by a discussion of structural features which influence the reaction rate. The second and major

  12. Protein structure prediction using residue- and fragment-environment potentials in CASP11.

    Science.gov (United States)

    Kim, Hyungrae; Kihara, Daisuke

    2016-09-01

    An accurate scoring function that can select near-native structure models from a pool of alternative models is key for successful protein structure prediction. For the critical assessment of techniques for protein structure prediction (CASP) 11, we have built a protocol of protein structure prediction that has novel coarse-grained scoring functions for selecting decoys as the heart of its pipeline. The score named PRESCO (Protein Residue Environment SCOre) developed recently by our group evaluates the native-likeness of local structural environment of residues in a structure decoy considering positions and the depth of side-chains of spatially neighboring residues. We also introduced a helix interaction potential as an additional scoring function for selecting decoys. The best models selected by PRESCO and the helix interaction potential underwent structure refinement, which includes side-chain modeling and relaxation with a short molecular dynamics simulation. Our protocol was successful, achieving the top rank in the free modeling category with a significant margin of the accumulated Z-score to the subsequent groups when the top 1 models were considered. Proteins 2016; 84(Suppl 1):105-117. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  13. The Role of the Local Conformation of a Cyclically Constrained β-AMINO Acid in the Secondary Structures of a Mixed α/β Diastereomer Pair

    Science.gov (United States)

    Blodgett, Karl N.; Zwier, Timothy S.

    2017-06-01

    Synthetic foldamers are non-natural polymers designed to fold into unique secondary structures that either mimic nature's preferred secondary structures, or expand their possibilities. Among the most studied synthetic foldamers are β-peptides, which lengthen the distance between amide groups from the single substituted carbon spacer in α-peptides by one (β) additional carbon. Cyclically constrained β-amino acids can impart rigidity to the secondary structure of oligomers by locking in a particular conformation. The β-residue cis-2-aminocyclohexanecarboxylic acid (cis-ACHC) is one such amino acid which has been shown to drive vastly different secondary structures as a function of the local conformation of the cyclohexane ring. We present data on two diastereomers of the mixed α/β tri-peptide Ac-Ala-β_{ACHC}-Ala-NHBn which differ from one another by the chirality along the ACHC residue (SRSS vs. SSRS). The first oligomer is known to crystallize to a 9/11 mixed helix while the second forms no intramolecular hydrogen bonds in the crystal state. This talk will describe the conformation-specific IR and UV spectroscopy of the above two diastereomers under jet cooled conditions in the gas phase. Assignments based on comparison with calculations show the presence of incipient 9/11 mixed helices and competing structures containing more tightly folded hydrogen-bonded networks. The calculated global minimum structures are observed in each case, and in each case these folded structures are reminiscent of a β-turn.

  14. Evaluation of the information content of RNA structure mapping data for secondary structure prediction.

    Science.gov (United States)

    Quarrier, Scott; Martin, Joshua S; Davis-Neulander, Lauren; Beauregard, Arthur; Laederach, Alain

    2010-06-01

    Structure mapping experiments (using probes such as dimethyl sulfate [DMS], kethoxal, and T1 and V1 RNases) are used to determine the secondary structures of RNA molecules. The process is iterative, combining the results of several probes with constrained minimum free-energy calculations to produce a model of the structure. We aim to evaluate whether particular probes provide more structural information, and specifically, how noise in the data affects the predictions. Our approach involves generating "decoy" RNA structures (using the sFold Boltzmann sampling procedure) and evaluating whether we are able to identify the correct structure from this ensemble of structures. We show that with perfect information, we are always able to identify the optimal structure for five RNAs of known structure. We then collected orthogonal structure mapping data (DMS and RNase T1 digest) under several solution conditions using our high-throughput capillary automated footprinting analysis (CAFA) technique on two group I introns of known structure. Analysis of these data reveals the error rates in the data under optimal (low salt) and suboptimal solution conditions (high MgCl(2)). We show that despite these errors, our computational approach is less sensitive to experimental noise than traditional constraint-based structure prediction algorithms. Finally, we propose a novel approach for visualizing the interaction of chemical and enzymatic mapping data with RNA structure. We project the data onto the first two dimensions of a multidimensional scaling of the sFold-generated decoy structures. We are able to directly visualize the structural information content of structure mapping data and reconcile multiple data sets.

  15. RANDOM FUNCTIONS AND INTERVAL METHOD FOR PREDICTING THE RESIDUAL RESOURCE OF BUILDING STRUCTURES

    Directory of Open Access Journals (Sweden)

    Shmelev Gennadiy Dmitrievich

    2017-11-01

    Full Text Available Subject: possibility of using random functions and interval prediction method for estimating the residual life of building structures in the currently used buildings. Research objectives: coordination of ranges of values to develop predictions and random functions that characterize the processes being predicted. Materials and methods: when performing this research, the method of random functions and the method of interval prediction were used. Results: in the course of this work, the basic properties of random functions, including the properties of families of random functions, are studied. The coordination of time-varying impacts and loads on building structures is considered from the viewpoint of their influence on structures and representation of the structures’ behavior in the form of random functions. Several models of random functions are proposed for predicting individual parameters of structures. For each of the proposed models, its scope of application is defined. The article notes that the considered approach of forecasting has been used many times at various sites. In addition, the available results allowed the authors to develop a methodology for assessing the technical condition and residual life of building structures for the currently used facilities. Conclusions: we studied the possibility of using random functions and processes for the purposes of forecasting the residual service lives of structures in buildings and engineering constructions. We considered the possibility of using an interval forecasting approach to estimate changes in defining parameters of building structures and their technical condition. A comprehensive technique for forecasting the residual life of building structures using the interval approach is proposed.

  16. Engineered, highly reactive substrates of microbial transglutaminase enable protein labeling within various secondary structure elements.

    Science.gov (United States)

    Rachel, Natalie M; Quaglia, Daniela; Lévesque, Éric; Charette, André B; Pelletier, Joelle N

    2017-11-01

    Microbial transglutaminase (MTG) is a practical tool to enzymatically form isopeptide bonds between peptide or protein substrates. This natural approach to crosslinking the side-chains of reactive glutamine and lysine residues is solidly rooted in food and textile processing. More recently, MTG's tolerance for various primary amines in lieu of lysine have revealed its potential for site-specific protein labeling with aminated compounds, including fluorophores. Importantly, MTG can label glutamines at accessible positions in the body of a target protein, setting it apart from most labeling enzymes that react exclusively at protein termini. To expand its applicability as a labeling tool, we engineered the B1 domain of Protein G (GB1) to probe the selectivity and enhance the reactivity of MTG toward its glutamine substrate. We built a GB1 library where each variant contained a single glutamine at positions covering all secondary structure elements. The most reactive and selective variants displayed a >100-fold increase in incorporation of a recently developed aminated benzo[a]imidazo[2,1,5-cd]indolizine-type fluorophore, relative to native GB1. None of the variants were destabilized. Our results demonstrate that MTG can react readily with glutamines in α-helical, β-sheet, and unstructured loop elements and does not favor one type of secondary structure. Introducing point mutations within MTG's active site further increased reactivity toward the most reactive substrate variant, I6Q-GB1, enhancing MTG's capacity to fluorescently label an engineered, highly reactive glutamine substrate. This work demonstrates that MTG-reactive glutamines can be readily introduced into a protein domain for fluorescent labeling. © 2017 The Protein Society.

  17. Enzyme stability, thermodynamics and secondary structures of α-amylase as probed by the CD spectroscopy.

    Science.gov (United States)

    Kikani, B A; Singh, S P

    2015-11-01

    An amylase of a thermophilic bacterium, Bacillus sp. TSSC-3 (GenBank Number, EU710557) isolated from the Tulsi Shyam hot spring reservoir (Gujarat, India) was purified to the homogeneity in a single step on phenyl sepharose 6FF. The molecular weight of the enzyme was 25kD, while the temperature and pH optima for the enzyme catalysis were 80°C and 7, respectively. The purified enzyme was highly thermostable with broad pH stability and displayed remarkable resistance against surfactants, chelators, urea, guanidine HCl and various solvents as well. The stability and changes in the secondary structure of the enzyme under various extreme conditions were determined by the circular dichroism (CD) spectroscopy. The stability trends and the changes in the α-helices and β-sheets were analyzed by Mean Residual Ellipticity (MRE) and K2D3. The CD data confirmed the structural stability of the enzyme under various harsh conditions, yet it indicated reduced α-helix content and increased β-sheets upon denaturation. The thermodynamic parameters; deactivation rate constant, half-life, changes in entropy, enthalpy, activation energy and Gibb's free energy indicated that the enzyme-substrate reactions were highly stable. The overall profile of the enzyme: high thermostability, alkalitolerance, calcium independent nature, dextrose equivalent values and resistance against chemical denaturants, solvents and surfactants suggest its commercial applications. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA.

    Science.gov (United States)

    Xia, Fei; Dou, Yong; Zhou, Xingming; Yang, Xuejun; Xu, Jiaqing; Zhang, Yang

    2009-01-30

    In the field of RNA secondary structure prediction, the RNAalifold algorithm is one of the most popular methods using free energy minimization. However, general-purpose computers including parallel computers or multi-core computers exhibit parallel efficiency of no more than 50%. Field Programmable Gate-Array (FPGA) chips provide a new approach to accelerate RNAalifold by exploiting fine-grained custom design. RNAalifold shows complicated data dependences, in which the dependence distance is variable, and the dependence direction is also across two dimensions. We propose a systolic array structure including one master Processing Element (PE) and multiple slave PEs for fine grain hardware implementation on FPGA. We exploit data reuse schemes to reduce the need to load energy matrices from external memory. We also propose several methods to reduce energy table parameter size by 80%. To our knowledge, our implementation with 16 PEs is the only FPGA accelerator implementing the complete RNAalifold algorithm. The experimental results show a factor of 12.2 speedup over the RNAalifold (ViennaPackage - 1.6.5) software for a group of aligned RNA sequences with 2981-residue running on a Personal Computer (PC) platform with Pentium 4 2.6 GHz CPU.

  19. JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures.

    Directory of Open Access Journals (Sweden)

    Jieming Shi

    Full Text Available Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html.

  20. JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures.

    Science.gov (United States)

    Shi, Jieming; Li, Xi; Dong, Min; Graham, Mitchell; Yadav, Nehul; Liang, Chun

    2017-01-01

    Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html.

  1. JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

    Science.gov (United States)

    Dong, Min; Graham, Mitchell; Yadav, Nehul

    2017-01-01

    Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html. PMID:28582416

  2. The secondary and aggregation structural changes of BSA induced by trivalent chromium: A biophysical study

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Mingmao [Institute of Biomedical and Pharmaceutical Technology, Fuzhou University, Fuzhou 350002, Fujian (China); Liu, Yan, E-mail: liuyan@fjirsm.ac.cn [The State Key Lab of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian (China); Cao, Huan [Institute of Biomedical and Pharmaceutical Technology, Fuzhou University, Fuzhou 350002, Fujian (China); Song, Ling [The State Key Lab of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian (China); Zhang, Qiqing, E-mail: zhangqiq@126.com [Institute of Biomedical and Pharmaceutical Technology, Fuzhou University, Fuzhou 350002, Fujian (China)

    2015-02-15

    Trivalent chromium Cr(III), which was originally considered to be innocuous as a nutriment, has been suspected to induce some abnormalities in human body recently. In the present work, the effects of Cr(III) on the structural state of BSA were comprehensively investigated through a series of appropriate methods in combination, including X-ray photoelectron spectroscopy (XPS), fourier transform infrared spectroscopy (FTIR), circular dichroism (CD), UV–vis absorption, synchronous fluorescence, fluorescence lifetime analysis, resonance light scattering (RLS), dynamic light scattering (DLS) and excitation–emission matrix spectroscopy (EEMS) methods. XPS accurately described the binding activity of Cr(III) with protein C, N and O atoms. The structural analysis according to FTIR and CD methods showed that the Cr(III) binding altered BSA conformation with a major reduction of α-helix. RLS and DLS analyses demonstrated that the presence of Cr(III) with low concentration could induce the aggregation structural changes of BSA. UV–vis absorption, EEMS and synchronous fluorescence suggested that the interaction between Cr(III) and BSA induced a slight unfolding of the polypeptide backbone and altered the microenvironments of Trp and Tyr residues in BSA. This research is helpful for understanding the structure-function relationship involved in metal ion-protein bioconjugate process. - Highlights: • The effect of Cr(III) on the conformational state of BSA was comprehensively studied. • XPS described the binding activity of Cr(III) with protein C, N and O atoms. • FTIR and CD data revealed secondary structural alteration in BSA. • Cr(III) complexation induced microenvironmental changes of Trp and Tyr. • RLS, DLS and EEMS presented the aggregational states of Cr(III)–BSA complex.

  3. Structural transformations in Mn2NiGa due to residual stress

    International Nuclear Information System (INIS)

    Singh, Sanjay; Maniraj, M.; D'Souza, S. W.; Barman, S. R.; Ranjan, R.

    2010-01-01

    Powder x-ray diffraction study of Mn 2 NiGa ferromagnetic shape memory alloy shows the existence of a 7M monoclinic modulated structure at room temperature (RT). The structure of Mn 2 NiGa is found to be highly dependent on residual stress. For higher stress, the structure is tetragonal at RT, and for intermediate stress it is 7M monoclinic. However, only when the stress is considerably relaxed, the structure is cubic, as is expected at RT since the martensitic transition temperature is 230 K.

  4. Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes.

    Science.gov (United States)

    Lavender, Christopher A; Gorelick, Robert J; Weeks, Kevin M

    2015-05-01

    HIV and related primate lentiviruses possess single-stranded RNA genomes. Multiple regions of these genomes participate in critical steps in the viral replication cycle, and the functions of many RNA elements are dependent on the formation of defined structures. The structures of these elements are still not fully understood, and additional functional elements likely exist that have not been identified. In this work, we compared three full-length HIV-related viral genomes: HIV-1NL4-3, SIVcpz, and SIVmac (the latter two strains are progenitors for all HIV-1 and HIV-2 strains, respectively). Model-free RNA structure comparisons were performed using whole-genome structure information experimentally derived from nucleotide-resolution SHAPE reactivities. Consensus secondary structures were constructed for strongly correlated regions by taking into account both SHAPE probing structural data and nucleotide covariation information from structure-based alignments. In these consensus models, all known functional RNA elements were recapitulated with high accuracy. In addition, we identified multiple previously unannotated structural elements in the HIV-1 genome likely to function in translation, splicing and other replication cycle processes; these are compelling targets for future functional analyses. The structure-informed alignment strategy developed here will be broadly useful for efficient RNA motif discovery.

  5. Two-dimensional NMR studies of squash family inhibitors. Sequence-specific proton assignments and secondary structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III.

    Science.gov (United States)

    Krishnamoorthi, R; Gong, Y X; Lin, C L; VanderVelde, D

    1992-01-28

    The solution structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III*) was investigated by two-dimensional proton nuclear magnetic resonance (2D NMR) spectroscopy. CMTI-III*, prepared by reacting CMTI-III with trypsin which cleaved the Arg5-Ile6 peptide bond, had the two fragments held together by a disulfide linkage. Sequence-specific 1H NMR resonance assignments were made for all the 29 amino acid residues of the protein. The secondary structure of CMTI-III*, as deduced from NOESY cross peaks and identification of slowly exchanging hydrogens, contains two turns (residues 8-12 and 24-27), a 3(10)-helix (residues 13-16), and a triple-stranded beta-sheet (residues 8-10, 29-27, and 21-25). This secondary structure is similar to that of CMTI-I [Holak, T. A., Gondol, D., Otlewski, J., & Wilusz, T. (1989) J. Mol. Biol. 210, 635-648], which has a Glu instead of a Lys at position 9. Sequential proton assignments were also made for the virgin inhibitor, CMTI-III, at pH 4.71, 30 degrees C. Comparison of backbone hydrogen chemical shifts of CMTI-III and CMTI-III* revealed significant changes for residues located far away from the reactive-site region as well as for those located near it, indicating tertiary structural changes that are transmitted through most of the 29 residues of the inhibitor protein. Many of these residues are functionally important in that they make contact with atoms of the enzyme in the trypsin-inhibitor complex, as revealed by X-ray crystallography [Bode, W., Greyling, H. J., Huber, R., Otlewski, J., & Wilusz, T. (1989) FEBS Lett. 242, 285-292].(ABSTRACT TRUNCATED AT 250 WORDS)

  6. Structural implications of conserved aspartate residues located in tropomyosin's coiled-coil core.

    Science.gov (United States)

    Moore, Jeffrey R; Li, Xiaochuan; Nirody, Jasmine; Fischer, Stefan; Lehman, William

    2011-09-01

    Polar residues lying between adjacent α-helical chains of coiled-coils often contribute to coiled-coil curvature and flexibility, while more typical core hydrophobic residues anneal the chains together. In tropomyosins, ranging from smooth and skeletal muscle to cytoplasmic isoforms, a highly conserved Asp at residue 137 places negative charges within the tropomyosin coiled-coil core in a position which may affect the conformation needed for tropomyosin binding and regulatory movements on actin. Proteolytic susceptibility suggested that substituting a canonical Leu for the naturally occurring Asp at residue 137 increases inter-chain rigidity by stabilizing the tropomyosin coiled-coil. Using molecular dynamics, we now directly assess changes in coiled-coil curvature and flexibility caused by such mutants. Although the coiled-coil flexibility is modestly diminished near the residue 137 mutation site, as expected, a delocalized increase in flexibility along the overall coiled-coil is observed. Even though the average shape of the D137L tropomyosin is straighter than that of wild-type tropomyosin, it is still capable of binding actin due to this increase in flexibility. We conclude that the conserved, non-canonical Asp-137 destabilizes the local structure resulting in a local flexible region in the middle of tropomyosin that normally is important for tropomyosin steady-state equilibrium position on actin.

  7. Fitting correlated residual error structures in nonlinear mixed-effects models using SAS PROC NLMIXED.

    Science.gov (United States)

    Harring, Jeffrey R; Blozis, Shelley A

    2014-06-01

    Nonlinear mixed-effects (NLME) models remain popular among practitioners for analyzing continuous repeated measures data taken on each of a number of individuals when interest centers on characterizing individual-specific change. Within this framework, variation and correlation among the repeated measurements may be partitioned into interindividual variation and intraindividual variation components. The covariance structure of the residuals are, in many applications, consigned to be independent with homogeneous variances, [Formula: see text], not because it is believed that intraindividual variation adheres to this structure, but because many software programs that estimate parameters of such models are not well-equipped to handle other, possibly more realistic, patterns. In this article, we describe how the programmatic environment within SAS may be utilized to model residual structures for serial correlation and variance heterogeneity. An empirical example is used to illustrate the capabilities of the module.

  8. An Analysis of Central Residues Between Ligand-Bound and Ligand-Free Protein Structures Based on Network Approach.

    Science.gov (United States)

    Amala, Arumugam; Emerson, Isacc Arnold

    2017-08-01

    Depiction of protein structures as networks of interacting residues has enabled us to understand the structure and function of the protein. Previous investigations on closeness centrality have identified protein functional sites from three- dimensional structures. It is well recognized that ligand binding to a receptor protein induces a wide range of structural changes. An interesting question is how central residues function during conformational changes triggered during ligand binding? The aim of this study is to comprehend at what extent central residues change during ligand binding to receptor proteins. To determine this, we examined 37 pairs of protein structures consisting of ligand-bound and ligand-free forms. These protein structures were modelled as an undirected network and significant central residues were obtained using residue centrality measures. In addition to these, the basic network parameters were also analysed. On analysing the residue centrality measures, we observed that 60% of central residues were common in both the ligand-bound and ligand-free states. The geometry of the central residues revealed that they were situated closer to the protein center of the mass. Finally, we demonstrated the effectiveness of central residues in amino acids substitutions and in the evolution itself. The closeness centrality was also analyzed among different protein domain sizes and the values gradually declined from single-domains to multi-domain proteins suggesting that the network has potential for hierarchical organization. Betweenness centrality measure was also used to determine the central residues and 31% of these residues were common between the holo/apo states. Findings reveal that central residues play a significant role in determining the functional properties of proteins. These results have implications in predicting binding/active site residues, specifically in the context of drug designing, if additional information concerning ligand binding is

  9. Residual stress measurements in thick structural weldments by means of neutron diffraction

    International Nuclear Information System (INIS)

    Ohms, C.; Youtsos, A.G.; Idsert, P. v.d.; Timke, T.

    2000-01-01

    Welding residual stresses in large structural components are a major concern with respect to their performance and lifetime. In large structures reasonable thermal stress relief treatment is usually impossible due to the component size. On the other hand, prediction of welding stresses by numerical modelling has not yet proven to be generally reliable, while the experimental determination of such stresses remains a demanding task. At the high flux reactor (HFR), Petten, a new residual stress diffractometer has been installed recently capable of handling of components up to 1000 kg - the large component neutron diffraction facility (LCNDF). It has facilitated residual stress measurements in two large welded components, of which results are presented here. The first component represents a bi-metallic weld in form of a pipe of 25 mm wall thickness. Three dimensional measurements of residual stress are discussed in detail. The second specimen is a 66 mm wall thickness austenitic steel nuclear piping weld. Results on relief of strain within the weld through post weld heat treatment (PWHT) are presented. Additionally results obtained earlier at former CRNL (CAN) on a section of a thick nuclear piping weld are presented in order to illustrate the variation in the reference lattice parameter trough the weld and the heat affected zone (HAZ). These results clearly show the necessity to determine the reference parameters for each location in all measurement directions by means of measurements in small coupons free of macro-stresses. (orig.)

  10. Catalytic residues and a predicted structure of tetrahydrobiopterin-dependent alkylglycerol mono-oxygenase

    Science.gov (United States)

    Watschinger, Katrin; Fuchs, Julian E.; Yarov-Yarovoy, Vladimir; Keller, Markus A.; Golderer, Georg; Hermetter, Albin; Werner-Felmayer, Gabriele; Hulo, Nicolas; Werner, Ernst R.

    2012-01-01

    Alkylglycerol mono-oxygenase (EC 1.14.16.5) forms a third, distinct, class among tetrahydrobiopterin-dependent enzymes in addition to aromatic amino acid hydroxylases and nitric oxide synthases. Its protein sequence contains the fatty acid hydroxylase motif, a signature indicative of a di-iron centre, which contains eight conserved histidine residues. Membrane enzymes containing this motif, including alkylglycerol mono-oxygenase, are especially labile and so far have not been purified to homogeneity in active form. To obtain a first insight into structure–function relationships of this enzyme, we performed site-directed mutagenesis of 26 selected amino acid residues and expressed wild-type and mutant proteins containing a C-terminal Myc tag together with fatty aldehyde dehydrogenase in Chinese-hamster ovary cells. Among all of the acidic residues within the eight-histidine motif, only mutation of Glu137 to alanine led to an 18-fold increase in the Michaelis–Menten constant for tetrahydrobiopterin, suggesting a role in tetrahydrobiopterin interaction. A ninth additional histidine residue essential for activity was also identified. Nine membrane domains were predicted by four programs: ESKW, TMHMM, MEMSAT and Phobius. Prediction of a part of the structure using the Rosetta membrane ab initio method led to a plausible suggestion for a structure of the catalytic site of alkylglycerol mono-oxygenase. PMID:22220568

  11. Mathematical and Biological Modelling of RNA Secondary Structure and Its Effects on Gene Expression

    Directory of Open Access Journals (Sweden)

    T. A. Hughes

    2006-01-01

    Full Text Available Secondary structures within the 5′ untranslated regions of messenger RNAs can have profound effects on the efficiency of translation of their messages and thereby on gene expression. Consequently they can act as important regulatory motifs in both physiological and pathological settings. Current approaches to predicting the secondary structure of these RNA sequences find the structure with the global-minimum free energy. However, since RNA folds progressively from the 5′ end when synthesised or released from the translational machinery, this may not be the most probable structure. We discuss secondary structure prediction based on local-minimisation of free energy with thermodynamic fluctuations as nucleotides are added to the 3′ end and show that these can result in different secondary structures. We also discuss approaches for studying the extent of the translational inhibition specified by structures within the 5′ untranslated region.

  12. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees.

    Science.gov (United States)

    Keller, Alexander; Förster, Frank; Müller, Tobias; Dandekar, Thomas; Schultz, Jörg; Wolf, Matthias

    2010-01-15

    In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.

  13. Structural and functional characterization of Rpn12 identifies residues required for Rpn10 proteasome incorporation.

    Science.gov (United States)

    Boehringer, Jonas; Riedinger, Christiane; Paraskevopoulos, Konstantinos; Johnson, Eachan O D; Lowe, Edward D; Khoudian, Christina; Smith, Dominique; Noble, Martin E M; Gordon, Colin; Endicott, Jane A

    2012-11-15

    The ubiquitin-proteasome system targets selected proteins for degradation by the 26S proteasome. Rpn12 is an essential component of the 19S regulatory particle and plays a role in recruiting the extrinsic ubiquitin receptor Rpn10. In the present paper we report the crystal structure of Rpn12, a proteasomal PCI-domain-containing protein. The structure helps to define a core structural motif for the PCI domain and identifies potential sites through which Rpn12 might form protein-protein interactions. We demonstrate that mutating residues at one of these sites impairs Rpn12 binding to Rpn10 in vitro and reduces Rpn10 incorporation into proteasomes in vivo.

  14. Recovery and residual stress of SMA wires and applications for concrete structures

    International Nuclear Information System (INIS)

    Choi, Eunsoo; Cho, Sung-Chul; Park, Taehyo; Hu, Jong Wan; Chung, Young-Soo

    2010-01-01

    In general, NiTi shape memory alloys are used for applications in civil structures. NiTi SMAs show good superelasticity and shape memory effect properties. However, for application of the shape memory effect, it is desirable for SMAs to show a wide temperature hysteresis, especially for civil structures which are exposed to severe environmental conditions. NiTiNb SMAs, in general, show a wider temperature hysteresis than NiTi SMAs and are more applicable for civil structures. This study examines the temperature hysteresis of NiTiNb and NiTi SMAs, and their recovery and residual stress are investigated. In addition, the tensile behaviors of SMA wires under residual stress are evaluated. This study explains the possible applications for concrete structures with the shape memory effect and illustrates two experimental results of concrete cylinders and reinforced concrete columns. For both tests, SMA wires of NiTiNb and NiTi are used to confine concrete using residual stress. The SMA wire jackets on the concrete cylinders increase the peak strength and the ductility compared to the plain concrete cylinders. In addition, the SMA wire jackets on reinforced concrete columns increase the ductility greatly without flexural strength degradation

  15. A comparative method for finding and folding RNA secondary structures within protein-coding regions

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Meyer, Irmtraud Margret; Forsberg, Roald

    2004-01-01

    that RNA-DECODER's parameters can be automatically trained to successfully fold known secondary structures within the HCV genome. We scan the genomes of HCV and polio virus for conserved secondary-structure elements, and analyze performance as a function of available evolutionary information. On known...... secondary structures, RNA-DECODER shows a sensitivity similar to the programs MFOLD, PFOLD and RNAALIFOLD. When scanning the entire genomes of HCV and polio virus for structure elements, RNA-DECODER's results indicate a markedly higher specificity than MFOLD, PFOLD and RNAALIFOLD....

  16. Influence of secondary water supply systems on microbial community structure and opportunistic pathogen gene markers.

    Science.gov (United States)

    Li, Huan; Li, Shang; Tang, Wei; Yang, Yang; Zhao, Jianfu; Xia, Siqing; Zhang, Weixian; Wang, Hong

    2018-06-01

    Secondary water supply systems (SWSSs) refer to the in-building infrastructures (e.g., water storage tanks) used to supply water pressure beyond the main distribution systems. The purpose of this study was to investigate the influence of SWSSs on microbial community structure and the occurrence of opportunistic pathogens, the latter of which are an emerging public health concern. Higher numbers of bacterial 16S rRNA genes, Legionella and mycobacterial gene markers were found in public building taps served by SWSSs relative to the mains, regardless of the flushing practice (P < 0.05). In residential buildings, genes of L. pneumomhila, Acanthamoeba and Vermamoeba vermiformis were primarily detected in tanks and taps compared to the mains. Long water retention time, warm temperature and loss of disinfectant residuals promoted microbial growth and colonization of potential pathogens in SWSSs. Varied levels of microbial community shifts were found in different types of SWSSs during water transportation from the distribution main to taps, highlighting the critical role of SWSSs in shaping the drinking water microbiota. Overall, the results provided insight to factors that might aid in controlling pathogen proliferation in real-world water systems using SWSSs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  17. Deciphering the shape and deformation of secondary structures through local conformation analysis

    Directory of Open Access Journals (Sweden)

    Camproux Anne-Claude

    2011-02-01

    Full Text Available Abstract Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

  18. REAL STRUCTURE AND RESIDUAL STRESSES IN ADVANCED WELDS DETERMINED BY X-RAY AND NEUTRON DIFFRACTION

    Directory of Open Access Journals (Sweden)

    Karel Trojan

    2017-07-01

    Full Text Available The paper outlines the capability of X-ray diffraction (XRD for evaluation of real structure changes and residual stresses (RS on cross-section of advanced thick welds due to the welding of ferromagnetic plates. The results of neutron diffraction describe a three-dimensional state of RS and also verify previous assumptions of RS redistribution as a result of the surface preparation for determination 2D maps measured by XRD.

  19. Evolving stochastic context-free grammars for RNA secondary structure prediction

    DEFF Research Database (Denmark)

    Anderson, James WJ; Tataru, Paula Cristina; Stains, Joe

    2012-01-01

    to structure prediction as has been previously suggested. Results These search techniques were applied to predict RNA secondary structure on a maximal data set and revealed new and interesting grammars, though none are dramatically better than classic grammars. In general, results showed that many grammars......Background Stochastic Context-Free Grammars (SCFGs) were applied successfully to RNA secondary structure prediction in the early 90s, and used in combination with comparative methods in the late 90s. The set of SCFGs potentially useful for RNA secondary structure prediction is very large, but a few...... with quite different structure could have very similar predictive ability. Many ambiguous grammars were found which were at least as effective as the best current unambiguous grammars. Conclusions Overall the method of evolving SCFGs for RNA secondary structure prediction proved effective in finding many...

  20. Structural Characterisation of Asphaltenes during Residue Hydrotreatment with Light Cycle Oil as an Additive

    Directory of Open Access Journals (Sweden)

    Yong-Jun Liu

    2015-01-01

    Full Text Available Several atmospheric residues (AR of Kuwaiti crude, in the absence, or in the presence, of light cycle oil (LCO as an aromatic additive, were hydrotreated in an experimental plant. Asphaltenes (precipitated from Kuwaiti AR, a hydrotreated AR, and a hydrotreated blend of AR and LCO were characterised by chemical structure and changes during residue hydrotreatment. The average structural parameters of these asphaltenes, obtained from a combined method of element analysis, average molecular weight, X-ray diffraction, and NMR, demonstrate that, after hydrotreatment, the aromatic cores of the asphaltenes become more compact and smaller whereas the peripheral alkyl branches are decreased in number and shortened. The influence of LCO on residue hydrotreating is also studied in terms of structural changes in the asphaltenes. The findings imply that LCO added to AR during hydrotreating improves the degree of aromatic substitution, the total hydrogen/carbon atomic ratio per average molecule, the distance between aromatic sheets and aliphatic chains, and so forth, by modifying the colloidal nature and microstructure of asphaltene: this is beneficial for the further hydroprocessing of AR. Three hypothetical average molecules are proposed to represent the changes undergone by such asphaltenes during hydrotreatment as well as the effects of additive LCO.

  1. PAIRpred: partner-specific prediction of interacting residues from sequence and structure.

    Science.gov (United States)

    Minhas, Fayyaz ul Amir Afsar; Geiss, Brian J; Ben-Hur, Asa

    2014-07-01

    We present a novel partner-specific protein-protein interaction site prediction method called PAIRpred. Unlike most existing machine learning binding site prediction methods, PAIRpred uses information from both proteins in a protein complex to predict pairs of interacting residues from the two proteins. PAIRpred captures sequence and structure information about residue pairs through pairwise kernels that are used for training a support vector machine classifier. As a result, PAIRpred presents a more detailed model of protein binding, and offers state of the art accuracy in predicting binding sites at the protein level as well as inter-protein residue contacts at the complex level. We demonstrate PAIRpred's performance on Docking Benchmark 4.0 and recent CAPRI targets. We present a detailed performance analysis outlining the contribution of different sequence and structure features, together with a comparison to a variety of existing interface prediction techniques. We have also studied the impact of binding-associated conformational change on prediction accuracy and found PAIRpred to be more robust to such structural changes than existing schemes. As an illustration of the potential applications of PAIRpred, we provide a case study in which PAIRpred is used to analyze the nature and specificity of the interface in the interaction of human ISG15 protein with NS1 protein from influenza A virus. Python code for PAIRpred is available at http://combi.cs.colostate.edu/supplements/pairpred/. © 2013 Wiley Periodicals, Inc.

  2. Protein secondary structure imaging with ultrabroadband multiplex coherent anti-Stokes Raman scattering (CARS) microspectroscopy.

    Science.gov (United States)

    Bito, Kotatsu; Okuno, Masanari; Kano, Hideaki; Tokuhara, Shihomi; Naito, Satoru; Masukawa, Yoshinori; Leproux, Philippe; Couderc, Vincent; Hamaguchi, Hiro-o

    2012-02-02

    Protein secondary structures in human hair have been studied with ultrabroadband multiplex coherent anti-Stokes Raman scattering (CARS) microspectroscopy. The CARS peak-shift mapping method has been developed and applied to hair samples with and without treatments by chemical reduction and mechanical extension. It clearly visualizes the treatment induced changes in protein secondary structures and their spatial distributions. Using the new imaging technique, we found a multilayered structure in the human hair cortex.

  3. Effects of lysine residues on structural characteristics and stability of tau proteins

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Myeongsang; Baek, Inchul; Choi, Hyunsung; Kim, Jae In; Na, Sungsoo, E-mail: nass@korea.ac.kr

    2015-10-23

    Pathological amyloid proteins have been implicated in neuro-degenerative diseases, specifically Alzheimer's, Parkinson's, Lewy-body diseases and prion related diseases. In prion related diseases, functional tau proteins can be transformed into pathological agents by environmental factors, including oxidative stress, inflammation, Aβ-mediated toxicity and covalent modification. These pathological agents are stable under physiological conditions and are not easily degraded. This un-degradable characteristic of tau proteins enables their utilization as functional materials to capturing the carbon dioxides. For the proper utilization of amyloid proteins as functional materials efficiently, a basic study regarding their structural characteristic is necessary. Here, we investigated the basic tau protein structure of wild-type (WT) and tau proteins with lysine residues mutation at glutamic residue (Q2K) on tau protein at atomistic scale. We also reported the size effect of both the WT and Q2K structures, which allowed us to identify the stability of those amyloid structures. - Highlights: • Lysine mutation effect alters the structure conformation and characteristic of tau. • Over the 15 layers both WT and Q2K models, both tau proteins undergo fractions. • Lysine mutation causes the increment of non-bonded energy and solvent accessible surface area. • Structural instability of Q2K model was proved by the number of hydrogen bonds analysis.

  4. The role of proline residues in the structure and function of human MT2 melatonin receptor.

    Science.gov (United States)

    Mazna, Petr; Grycova, Lenka; Balik, Ales; Zemkova, Hana; Friedlova, Eliska; Obsilova, Veronika; Obsil, Tomas; Teisinger, Jan

    2008-11-01

    Melatonin functions as an essential regulator of various physiological processes in all vertebrate species. In mammals, two G protein-coupled melatonin receptors (GPCR) mediate some melatonin's actions: MT1 and MT2. Transmembrane domains (TM) of most GPCRs contain a set of highly conserved proline residues that presumably play important structural and functional roles. As TM segments of MT2 receptor display several interesting differences in expression of specific proline residues compared to other rhodopsin-like receptors (rGPCRs), we investigated the role of proline residues in the structure and function of this receptor. All prolines in TM segments of MT2 receptor were individually replaced with alanine and/or glycine. In addition, the unusual NAxxY motif located in TM7 was mutated to generate highly conserved NPxxY motif found in the majority of rGPCR proteins. Following transient expression in CHO-K1 cells, binding properties of the mutant receptors and their ability to transduce signals were analyzed using (125)I-mel- and [(35)S]GTPgammaS-binding assays, respectively. The impact of the performed mutations on the receptor structure was assessed by molecular dynamic simulations of MT2 receptors embedded in the fully hydrated phospholipid bilayer. Our results indicate that residues P174, P212 and P266 are important for the ligand binding and/or signaling of the human MT2 receptor. We also show that changes within the unusual NAxxY sequence in the TM7 (mutations A305P and A305V) produce defective MT2 receptors indicating an important role of this motif in the function of melatonin receptors.

  5. Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information.

    Science.gov (United States)

    Kandoi, Gaurav; Leelananda, Sumudu P; Jernigan, Robert L; Sen, Taner Z

    2017-01-01

    Predicting the secondary structure of a protein from its sequence still remains a challenging problem. The prediction accuracies remain around 80 %, and for very diverse methods. Using evolutionary information and machine learning algorithms in particular has had the most impact. In this chapter, we will first define secondary structures, then we will review the Consensus Data Mining (CDM) technique based on the robust GOR algorithm and Fragment Database Mining (FDM) approach. GOR V is an empirical method utilizing a sliding window approach to model the secondary structural elements of a protein by making use of generalized evolutionary information. FDM uses data mining from experimental structure fragments, and is able to successfully predict the secondary structure of a protein by combining experimentally determined structural fragments based on sequence similarities of the fragments. The CDM method combines predictions from GOR V and FDM in a hierarchical manner to produce consensus predictions for secondary structure. In other words, if sequence fragment are not available, then it uses GOR V to make the secondary structure prediction. The online server of CDM is available at http://gor.bb.iastate.edu/cdm/ .

  6. Testing Mediation Using Multiple Regression and Structural Equation Modeling Analyses in Secondary Data

    Science.gov (United States)

    Li, Spencer D.

    2011-01-01

    Mediation analysis in child and adolescent development research is possible using large secondary data sets. This article provides an overview of two statistical methods commonly used to test mediated effects in secondary analysis: multiple regression and structural equation modeling (SEM). Two empirical studies are presented to illustrate the…

  7. A review of inducing compressive residual stress - shot peening; on structural metal and welded connection

    Science.gov (United States)

    Kanchidurai, S.; Krishanan, P. A.; Baskar, K.; Saravana Raja Mohan, K.

    2017-07-01

    Shot peening treatment (SPT) is a significant mechanical method to enhance the surface of the material by inducing compressive residual stress on the layer. This study provides a review of prominent improvement in fatigue life on high strength aluminium alloy, steel and welded connection by SPT. Compressive residual stress measurement and its factors data are extracted from assorted literature, optimized peening process commented in this paper, also different types of mechanical peening methods and its effectiveness are mentioned. Fatigue life improvement is focused commented to welded structural connections. The extracted results shows significant changes in the surface layer of metals, aluminium alloy 15 - 250% of fatigue life improvement, steel plain members 6-200% of fatigue life improvement, welded connections 50-75% of fatigue life improvement and significant improvement in mechanical properties like roughness reduction, wear, hardness, tensile strength, corrosion and scuffing.

  8. Effect of residual sericin on the structural characteristics and properties of regenerated silk films.

    Science.gov (United States)

    Lee, Ji Hye; Song, Dae Woong; Park, Young Hwan; Um, In Chul

    2016-08-01

    Regenerated silk film has been increasingly attracting the research community's attention for biomedical applications due to its good biocompatibility and excellent cyto-compatibility. However, some limitations regarding its mechanical properties, such as brittleness, have restricted the use of silk films for industrial biomedical applications. In this study, regenerated silk films with different residual sericin content were prepared applying controlled degumming conditions to evaluate the effect of sericin content on the structure and properties of the films generated. When the residual sericin content increased to 0.6%, crystallinity index and breaking strength of silk films were increased. Above this value, these parameters then decreased. A 1.5 fold increase of silk film elongation properties was obtained when incorporating 16% sericin. Regardless of sericin content, all regenerated silk films showed excellent cyto-compatibility, comparable to the one obtained with tissue culture plates. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Secondary systems modeled as fuzzy sub-structures

    DEFF Research Database (Denmark)

    Tarp-Johansen, Niels Jacob; Ditlevsen, Ove Dalager; Lin, Y.K.

    1998-01-01

    in the simplest case be modeled by attaching random single degree of freedom oscillators, called fuzzies, to the master structure at randomly distributed points of the structure. Each of these fuzzies are characterized by a random triplet of mass, eigenfrequency, and damping ratio. This characterization can...... be combined with a model of the random distribution of the fuzzies over the structure by letting the entire system of fuzzies be characterized as a triplet of random fields over the structure. Two specific examples, a Poisson point pulse field and a Poisson square wave field, of such a triplet field...... the probabilistic properties of the impulse response function, say, or of the nonergodic steady state response to stationary excitation, say. The study prepares for a finite element model of a flexible master structure with a fuzzy subsystem attached to it....

  10. Large deviations for random trees and the branching of RNA secondary structures.

    Science.gov (United States)

    Bakhtin, Yuri; Heitsch, Christine E

    2009-01-01

    We give a Large Deviation Principle (LDP) with explicit rate function for the distribution of vertex degrees in plane trees, a combinatorial model of RNA secondary structures. We calculate the typical degree distributions based on nearest neighbor free energies, and compare our results with the branching configurations found in two sets of large RNA secondary structures. We find substantial agreement overall, with some interesting deviations which merit further study.

  11. Inflatable Habitat with Integrated Primary and Secondary Structure, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Paragon Space Development Corp (Paragon) and Thin Red Line Aerospace (TRLA) proposes to explore the utilization of inflatable structures by designing a habitation...

  12. Covalent bond symmetry breaking and protein secondary structure

    OpenAIRE

    Lundgren, Martin; Niemi, Antti J.

    2011-01-01

    Both symmetry and organized breaking of symmetry have a pivotal r\\^ole in our understanding of structure and pattern formation in physical systems, including the origin of mass in the Universe and the chiral structure of biological macromolecules. Here we report on a new symmetry breaking phenomenon that takes place in all biologically active proteins, thus this symmetry breaking relates to the inception of life. The unbroken symmetry determines the covalent bond geometry of a sp3 hybridized ...

  13. 4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing.

    Science.gov (United States)

    Seibel, Philipp N; Müller, Tobias; Dandekar, Thomas; Schultz, Jörg; Wolf, Matthias

    2006-11-13

    In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong predictions. Hand-crafted and hand-improved alignments are necessary and meanwhile good common practice. For RNA sequences often the primary sequence as well as a secondary structure consensus is well known, e.g., the cloverleaf structure of the t-RNA. Recently, some alignment editors are proposed that are able to include and model both kinds of information. However, with the advent of a large amount of reliable RNA sequences together with their solved secondary structures (available from e.g. the ITS2 Database), we are faced with the problem to handle sequences and their associated secondary structures synchronously. 4SALE fills this gap. The application allows a fast sequence and synchronous secondary structure alignment for large data sets and for the first time synchronous manual editing of aligned sequences and their secondary structures. This study describes an algorithm for the synchronous alignment of sequences and their associated secondary structures as well as the main features of 4SALE used for further analyses and editing. 4SALE builds an optimal and unique starting point for every RNA sequence and structure analysis. 4SALE, which provides an user-friendly and intuitive interface, is a comprehensive toolbox for RNA analysis based on sequence and secondary structure information. The program connects sequence and structure databases like the ITS2 Database to phylogeny programs as for example the CBCAnalyzer. 4SALE is written in JAVA and therefore platform independent. The software is freely available and distributed from the website at http://4sale.bioapps.biozentrum.uni-wuerzburg.de.

  14. 4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing

    Directory of Open Access Journals (Sweden)

    Schultz Jörg

    2006-11-01

    Full Text Available Abstract Background In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong predictions. Hand-crafted and hand-improved alignments are necessary and meanwhile good common practice. For RNA sequences often the primary sequence as well as a secondary structure consensus is well known, e.g., the cloverleaf structure of the t-RNA. Recently, some alignment editors are proposed that are able to include and model both kinds of information. However, with the advent of a large amount of reliable RNA sequences together with their solved secondary structures (available from e.g. the ITS2 Database, we are faced with the problem to handle sequences and their associated secondary structures synchronously. Results 4SALE fills this gap. The application allows a fast sequence and synchronous secondary structure alignment for large data sets and for the first time synchronous manual editing of aligned sequences and their secondary structures. This study describes an algorithm for the synchronous alignment of sequences and their associated secondary structures as well as the main features of 4SALE used for further analyses and editing. 4SALE builds an optimal and unique starting point for every RNA sequence and structure analysis. Conclusion 4SALE, which provides an user-friendly and intuitive interface, is a comprehensive toolbox for RNA analysis based on sequence and secondary structure information. The program connects sequence and structure databases like the ITS2 Database to phylogeny programs as for example the CBCAnalyzer. 4SALE is written in JAVA and therefore platform independent. The software is freely available and distributed from the website at http://4sale.bioapps.biozentrum.uni-wuerzburg.de

  15. Lectin obtained from the red seaweed Bryothamnion triquetrum: Secondary structure and anti-inflammatory activity in mice.

    Science.gov (United States)

    Fontenelle, Thais Pontes Carvalho; Lima, Glauber Cruz; Mesquita, Jacilane Ximenes; de Souza Lopes, José Luiz; de Brito, Tarcísio Vieira; das Chagas Vieira Júnior, Francisco; Sales, Adriano Bezerra; Aragão, Karoline Saboia; Souza, Marcellus Henrique Loiola Ponte; Dos Reis Barbosa, André Luiz; Freitas, Ana Lúcia Ponte

    2018-02-13

    Seaweeds are sources of biomolecules with biological activities and pharmacological potential - for example, lectins, a group of proteins that can bind reversibly to carbohydrates or compounds containing them. The aim of this study was to elucidate the structural properties of a lectin extracted from the red seaweed Bryothamnion triquetrum (BtL) and to investigate its anti-inflammatory activity in mice. The lectin was purified by precipitation with ammonium sulfate and ion-exchange chromatography. Its secondary structure and tryptophan (Trp) microenvironment were analyzed by circular dichroism spectroscopy and steady-state fluorescence spectroscopy, respectively. The anti-inflammatory effect was evaluated by means of paw edema induced by carrageenan or dextran, myeloperoxidase activity in paw tissue, and by measurement of leukocyte and neutrophil migration and cytokine quantification in a peritonitis model. The secondary structure of BtL is mostly composed of β-strands and unordered conformation, and it is quite resistant to extremes of pH and temperature, preserving the exposure of Trp residues under these conditions. In an assessment of biological activities, groups of mice were subjected to pretreatment with BtL before the inflammatory stimulus. BtL had anti-inflammatory effects in the models tested, and hence may be considered a molecule with potential to be used in the pharmaceutical industry. Copyright © 2017. Published by Elsevier B.V.

  16. RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model.

    Science.gov (United States)

    Jabbari, Hosna; Wark, Ian; Montemagno, Carlo

    2018-01-01

    RNA is a biopolymer with various applications inside the cell and in biotechnology. Structure of an RNA molecule mainly determines its function and is essential to guide nanostructure design. Since experimental structure determination is time-consuming and expensive, accurate computational prediction of RNA structure is of great importance. Prediction of RNA secondary structure is relatively simpler than its tertiary structure and provides information about its tertiary structure, therefore, RNA secondary structure prediction has received attention in the past decades. Numerous methods with different folding approaches have been developed for RNA secondary structure prediction. While methods for prediction of RNA pseudoknot-free structure (structures with no crossing base pairs) have greatly improved in terms of their accuracy, methods for prediction of RNA pseudoknotted secondary structure (structures with crossing base pairs) still have room for improvement. A long-standing question for improving the prediction accuracy of RNA pseudoknotted secondary structure is whether to focus on the prediction algorithm or the underlying energy model, as there is a trade-off on computational cost of the prediction algorithm versus the generality of the method. The aim of this work is to argue when comparing different methods for RNA pseudoknotted structure prediction, the combination of algorithm and energy model should be considered and a method should not be considered superior or inferior to others if they do not use the same scoring model. We demonstrate that while the folding approach is important in structure prediction, it is not the only important factor in prediction accuracy of a given method as the underlying energy model is also as of great value. Therefore we encourage researchers to pay particular attention in comparing methods with different energy models.

  17. GC content around splice sites affects splicing through pre-mRNA secondary structures

    Directory of Open Access Journals (Sweden)

    Chen Liang

    2011-01-01

    Full Text Available Abstract Background Alternative splicing increases protein diversity by generating multiple transcript isoforms from a single gene through different combinations of exons or through different selections of splice sites. It has been reported that RNA secondary structures are involved in alternative splicing. Here we perform a genomic study of RNA secondary structures around splice sites in humans (Homo sapiens, mice (Mus musculus, fruit flies (Drosophila melanogaster, and nematodes (Caenorhabditis elegans to further investigate this phenomenon. Results We observe that GC content around splice sites is closely associated with the splice site usage in multiple species. RNA secondary structure is the possible explanation, because the structural stability difference among alternative splice sites, constitutive splice sites, and skipped splice sites can be explained by the GC content difference. Alternative splice sites tend to be GC-enriched and exhibit more stable RNA secondary structures in all of the considered species. In humans and mice, splice sites of first exons and long exons tend to be GC-enriched and hence form more stable structures, indicating the special role of RNA secondary structures in promoter proximal splicing events and the splicing of long exons. In addition, GC-enriched exon-intron junctions tend to be overrepresented in tissue-specific alternative splice sites, indicating the functional consequence of the GC effect. Compared with regions far from splice sites and decoy splice sites, real splice sites are GC-enriched. We also found that the GC-content effect is much stronger than the nucleotide-order effect to form stable secondary structures. Conclusion All of these results indicate that GC content is related to splice site usage and it may mediate the splicing process through RNA secondary structures.

  18. Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy.

    Science.gov (United States)

    Garmann, Rees F; Gopal, Ajaykumar; Athavale, Shreyas S; Knobler, Charles M; Gelbart, William M; Harvey, Stephen C

    2015-05-01

    The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures. © 2015 Garmann et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  19. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

    Directory of Open Access Journals (Sweden)

    Dandekar Thomas

    2010-01-01

    Full Text Available Abstract Background In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. Results This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Conclusions Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. Reviewers This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber and Eugene V. Koonin. Open peer review Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.

  20. Probing the glycosidic linkage: secondary structures in the gas phase

    International Nuclear Information System (INIS)

    Simons, John P; Cristina Stanca-Kaposta, E; Cocinero, Emilio J; Liu, B; Davis, Benjamin G; Gamblin, David P; Kroemer, Romano T

    2008-01-01

    The functional importance of carbohydrates in biological processes, particularly those involving specific molecular recognition, is immense. Characterizing the three-dimensional (3D) structures of carbohydrates and glycoproteins, and their interactions with other molecules, not least the ubiquitous solvent, water, is a key starting point for understanding these processes. The combination of laser-based electronic and vibrational spectroscopy of mass-selected carbohydrate molecules and their hydrated complexes, conducted under molecular beam conditions, with ab initio computation is providing a uniquely powerful means of characterizing 3D carbohydrate conformations; the structures of their hydrated complexes, the hydrogen-bonded networks they support (or which support them); and the factors that determine their conformational and structural preferences.

  1. Probing the glycosidic linkage: secondary structures in the gas phase

    Energy Technology Data Exchange (ETDEWEB)

    Simons, John P; Cristina Stanca-Kaposta, E; Cocinero, Emilio J; Liu, B [Chemistry Department, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (United Kingdom); Davis, Benjamin G; Gamblin, David P [Chemistry Department, Chemical Research Laboratory, 12 Mansfield Road, Oxford OX1 4TA (United Kingdom); Kroemer, Romano T [Sanofi-Aventis, CRVA, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine (France)], E-mail: John.Simons@chem.ox.ac.uk

    2008-10-15

    The functional importance of carbohydrates in biological processes, particularly those involving specific molecular recognition, is immense. Characterizing the three-dimensional (3D) structures of carbohydrates and glycoproteins, and their interactions with other molecules, not least the ubiquitous solvent, water, is a key starting point for understanding these processes. The combination of laser-based electronic and vibrational spectroscopy of mass-selected carbohydrate molecules and their hydrated complexes, conducted under molecular beam conditions, with ab initio computation is providing a uniquely powerful means of characterizing 3D carbohydrate conformations; the structures of their hydrated complexes, the hydrogen-bonded networks they support (or which support them); and the factors that determine their conformational and structural preferences.

  2. Porous carbonaceous electrode structure and method for secondary electrochemical cell

    Science.gov (United States)

    Kaun, Thomas D.

    1977-03-08

    Positive and negative electrodes are provided as rigid, porous carbonaceous matrices with particulate active material fixedly embedded. Active material such as metal chalcogenides, solid alloys of alkali metal or alkaline earth metals along with other metals and their oxides in particulate form are blended with a thermosetting resin and a solid volatile to form a paste mixture. Various electrically conductive powders or current collector structures can be blended or embedded into the paste mixture which can be molded to the desired electrode shape. The molded paste is heated to a temperature at which the volatile transforms into vapor to impart porosity as the resin begins to cure into a rigid solid structure.

  3. An image processing approach to computing distances between RNA secondary structures dot plots

    Directory of Open Access Journals (Sweden)

    Sapiro Guillermo

    2009-02-01

    Full Text Available Abstract Background Computing the distance between two RNA secondary structures can contribute in understanding the functional relationship between them. When used repeatedly, such a procedure may lead to finding a query RNA structure of interest in a database of structures. Several methods are available for computing distances between RNAs represented as strings or graphs, but none utilize the RNA representation with dot plots. Since dot plots are essentially digital images, there is a clear motivation to devise an algorithm for computing the distance between dot plots based on image processing methods. Results We have developed a new metric dubbed 'DoPloCompare', which compares two RNA structures. The method is based on comparing dot plot diagrams that represent the secondary structures. When analyzing two diagrams and motivated by image processing, the distance is based on a combination of histogram correlations and a geometrical distance measure. We introduce, describe, and illustrate the procedure by two applications that utilize this metric on RNA sequences. The first application is the RNA design problem, where the goal is to find the nucleotide sequence for a given secondary structure. Examples where our proposed distance measure outperforms others are given. The second application locates peculiar point mutations that induce significant structural alternations relative to the wild type predicted secondary structure. The approach reported in the past to solve this problem was tested on several RNA sequences with known secondary structures to affirm their prediction, as well as on a data set of ribosomal pieces. These pieces were computationally cut from a ribosome for which an experimentally derived secondary structure is available, and on each piece the prediction conveys similarity to the experimental result. Our newly proposed distance measure shows benefit in this problem as well when compared to standard methods used for assessing

  4. Argumentation in Secondary School Students' Structured and Unstructured Chat Discussions

    Science.gov (United States)

    Salminen, Timo; Marttunen, Miika; Laurinen, Leena

    2012-01-01

    Joint construction of new knowledge demands that persons can express their statements in a convincing way and explore other people's arguments constructively. For this reason, more knowledge on different means to support collaborative argumentation is needed. This study clarifies whether structured interaction supports students' critical and…

  5. Synonymous codon usage in different protein secondary structural ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    2007-06-21

    Jun 21, 2007 ... usage of Lactobacillus species; Nucleic Acids Res. 22. 929–936. Siemion I Z and Siemion P J 1994 The informational context of the third base in amino acid codons; Biosystems 33. 139–148. Tao X and Dafu D 1998 The relationship between synonymous codon usage and protein Structure; FEBS Lett.

  6. Hemin and bile pigments are the secondary structure regulators of intrinsically disordered antimicrobial peptides.

    Science.gov (United States)

    Zsila, Ferenc; Juhász, Tünde; Bősze, Szilvia; Horváti, Kata; Beke-Somfai, Tamás

    2018-02-01

    The interaction of protoporphyrin compounds of human origin with the major bee venom component melittin (26 a.a., Z +6) and its hybrid derivative (CM15, 15 a.a., Z +6) were studied by a combination of various spectroscopic methods. Throughout a two-state, concentration-dependent process, hemin and its metabolites (biliverdin, bilirubin, bilirubin ditaurate) increase the parallel β-sheet content of the natively unfolded melittin, suggesting the oligomerization of the peptide chains. In contrast, α-helix promoting effect was observed with the also disordered but more cationic CM15. According to fluorescence quenching experiments, the sole Trp residue of melittin is the key player during the binding, in the vicinity of which the first pigment molecule is accommodated presumably making indole-porphyrin π-π stacking interaction. As circular dichroism titration data suggest, cooperative association of additional ligands subsequently occurs, resulting in multimeric complexes with an apparent dissociation constant ranged from 20 to 65 μM. Spectroscopic measurements conducted with the bilirubin catabolite urobilin and stercobilin refer to the requirement of intact dipyrrinone moieties for inducing secondary structure transformations. The binding topography of porphyrin rings on a model parallel β-sheet motif was evaluated by absorption spectroscopy and computational modeling showing a slipped-cofacial binding mode responsible for the red shift and hypochromism of the Soret band. Our results may aid to recognize porphyrin-responsive binding motifs of biologically relevant, intrinsically disordered peptides and proteins, where transient conformations play a vital role in their functions. © 2017 Wiley Periodicals, Inc.

  7. Secondary Structure Adopted by the Gly-Gly-X Repetitive Regions of Dragline Spider Silk

    Directory of Open Access Journals (Sweden)

    Geoffrey M. Gray

    2016-12-01

    Full Text Available Solid-state NMR and molecular dynamics (MD simulations are presented to help elucidate the molecular secondary structure of poly(Gly-Gly-X, which is one of the most common structural repetitive motifs found in orb-weaving dragline spider silk proteins. The combination of NMR and computational experiments provides insight into the molecular secondary structure of poly(Gly-Gly-X segments and provides further support that these regions are disordered and primarily non-β-sheet. Furthermore, the combination of NMR and MD simulations illustrate the possibility for several secondary structural elements in the poly(Gly-Gly-X regions of dragline silks, including β-turns, 310-helicies, and coil structures with a negligible population of α-helix observed.

  8. A Comparative Taxonomy of Parallel Algorithms for RNA Secondary Structure Prediction

    Science.gov (United States)

    Al-Khatib, Ra’ed M.; Abdullah, Rosni; Rashid, Nur’Aini Abdul

    2010-01-01

    RNA molecules have been discovered playing crucial roles in numerous biological and medical procedures and processes. RNA structures determination have become a major problem in the biology context. Recently, computer scientists have empowered the biologists with RNA secondary structures that ease an understanding of the RNA functions and roles. Detecting RNA secondary structure is an NP-hard problem, especially in pseudoknotted RNA structures. The detection process is also time-consuming; as a result, an alternative approach such as using parallel architectures is a desirable option. The main goal in this paper is to do an intensive investigation of parallel methods used in the literature to solve the demanding issues, related to the RNA secondary structure prediction methods. Then, we introduce a new taxonomy for the parallel RNA folding methods. Based on this proposed taxonomy, a systematic and scientific comparison is performed among these existing methods. PMID:20458364

  9. Backbone chemical shifts assignments, secondary structure, and ligand binding of a family GH-19 chitinase from moss, Bryum coronatum.

    Science.gov (United States)

    Shinya, Shoko; Nagata, Takuya; Ohnuma, Takayuki; Taira, Toki; Nishimura, Shigenori; Fukamizo, Tamo

    2012-10-01

    Family GH19 chitinases have been recognized as important in the plant defense against fungal pathogens. However, their substrate-recognition mechanism is still unknown. We report here the first resonance assignment of NMR spectrum of a GH19 chitinase from moss, Bryum coronatum (BcChi-A). The backbone signals were nearly completely assigned, and the secondary structure was estimated based on the chemical shift values. The addition of the chitin dimer to the enzyme solution perturbed the chemical shifts of HSQC resonances of the amino acid residues forming the putative substrate-binding cleft. Further NMR analysis of the ligand binding to BcChi-A will improve understanding of the substrate-recognition mechanism of GH-19 enzymes.

  10. A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer).

    Science.gov (United States)

    Berkowitz, Nathan D; Silverman, Ian M; Childress, Daniel M; Kazan, Hilal; Wang, Li-San; Gregory, Brian D

    2016-05-17

    RNA molecules fold into complex three-dimensional shapes, guided by the pattern of hydrogen bonding between nucleotides. This pattern of base pairing, known as RNA secondary structure, is critical to their cellular function. Recently several diverse methods have been developed to assay RNA secondary structure on a transcriptome-wide scale using high-throughput sequencing. Each approach has its own strengths and caveats, however there is no widely available tool for visualizing and comparing the results from these varied methods. To address this, we have developed Structure Surfer, a database and visualization tool for inspecting RNA secondary structure in six transcriptome-wide data sets from human and mouse ( http://tesla.pcbi.upenn.edu/strucuturesurfer/ ). The data sets were generated using four different high-throughput sequencing based methods. Each one was analyzed with a scoring pipeline specific to its experimental design. Users of Structure Surfer have the ability to query individual loci as well as detect trends across multiple sites. Here, we describe the included data sets and their differences. We illustrate the database's function by examining known structural elements and we explore example use cases in which combined data is used to detect structural trends. In total, Structure Surfer provides an easy-to-use database and visualization interface for allowing users to interrogate the currently available transcriptome-wide RNA secondary structure information for mammals.

  11. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

    Science.gov (United States)

    Hafsa, Noor E; Arndt, David; Wishart, David S

    2015-07-01

    The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Texture, residual stress and structural analysis of thin films using a combined X-ray analysis

    International Nuclear Information System (INIS)

    Lutterotti, L.; Chateigner, D.; Ferrari, S.; Ricote, J.

    2004-01-01

    Advanced thin films for today's industrial and research needs require highly specialized methodologies for a successful quantitative characterization. In particular, in the case of multilayer and/or unknown phases a global approach is necessary to obtain some or all the required information. A full approach has been developed integrating novel texture and residual stress methodologies with the Rietveld method (Acta Cryst. 22 (1967) 151) (for crystal structure analysis) and it has been coupled with the reflectivity analysis. The complete analysis can be done at once and offers several benefits: the thicknesses obtained from reflectivity can be used to correct the diffraction spectra, the phase analysis help to identify the layers and to determine the electron density profile for reflectivity; quantitative texture is needed for quantitative phase and residual stress analyses; crystal structure determination benefits of the previous. To achieve this result, it was necessary to develop some new methods, especially for texture and residual stresses. So it was possible to integrate them in the Rietveld, full profile fitting of the patterns. The measurement of these spectra required a special reflectometer/diffractometer that combines a thin parallel beam (for reflectivity) and a texture/stress goniometer with a curved large position sensitive detector. This new diffraction/reflectivity X-ray machine has been used to test the combined approach. Several spectra and the reflectivity patterns have been collected at different tilting angles and processed at once by the special software incorporating the aforementioned methodologies. Some analysis examples will be given to show the possibilities offered by the method

  13. Does high pressure have any effect on the structure of alpha amylase and its ability to binding to the oligosaccharides having 3-7 residues? Molecular dynamics study.

    Science.gov (United States)

    Vahidi, S Hooman; Bozorgmehr, Mohammad Reza; Morsali, Ali; Beyramabadi, S Ali

    2018-03-01

    Studies have shown that deletion of amino acids from the C-terminus of amylase do not alter its amylolytic activity. Although high pressure is used to modify the structure and function of this enzyme, the effects of high pressures on the structures of the wild-type and truncated amylases have not yet been understood at the molecular level. Using molecular dynamic simulations and docking, we studied the structures of wild-type and truncated Taka-amylases at high pressures (1000-4000 bar). To construct the truncated Taka-amylase, 50 and 100 C-terminal residues were removed in two separate steps. Results of simulation showed that, although the overall shape partly agglomerates with rise in pressure, high pressure fails to modify the structure of the barrel-like region of the β-sheet in the wild-type and truncated enzymes. A comparison of contact graphs revealed that the changes at the N-terminus were less extensive than those at the C-terminus. Further analysis showed that 10 regions of the secondary structures changed due to pressure change in wild-type amylase, of which 6 regions were associated with the loops and 4 with helix, while the structure of β-sheets remained unchanged. The docking of maltotriose, maltotetraose, maltopentaose, maltohexaose, and maltoheptaose with the averaged structures obtained from different simulations was conducted to characterize the influence of pressure on the activities of the wild-type and truncated enzymes. The results showed that maltoheptaose made hydrophobic contacts with residues Tyr238-Asp117-Tyr82-Leu166-Leu232-Tyr155 and hydrogen contacts with residues Asp233-Gly234-Asp206-Arg204-His296-Glu230. Similar results were obtained for other malto-oligosaccharides. Copyright © 2018 Elsevier Inc. All rights reserved.

  14. Analysis of a systematic search-based algorithm for determining protein backbone structure from a minimum number of residual dipolar couplings.

    Science.gov (United States)

    Wang, Lincong; Donald, Bruce Randall

    2004-01-01

    We have developed an ab initio algorithm for determining a protein backbone structure using global orientational restraints on internuclear vectors derived from residual dipolar couplings (RDCs) measured in one or two different aligning media by solution nuclear magnetic resonance (NMR) spectroscopy [14, 15]. Specifically, the conformation and global orientations of individual secondary structure elements are computed, independently, by an exact solution, systematic search-based minimization algorithm using only 2 RDCs per residue. The systematic search is built upon a quartic equation for computing, exactly and in constant time, the directions of an internuclear vector from RDCs, and linear or quadratic equations for computing the sines and cosines of backbone dihedral (phi, psi) angles from two vectors in consecutive peptide planes. In contrast to heuristic search such as simulated annealing (SA) or Monte-Carlo (MC) used by other NMR structure determination algorithms, our minimization algorithm can be analyzed rigorously in terms of expected algorithmic complexity and the coordinate precision of the protein structure as a function of error in the input data. The algorithm has been successfully applied to compute the backbone structures of three proteins using real NMR data.

  15. Single molecule studies of surface-induced secondary structure in a model peptide

    Science.gov (United States)

    English, Douglas S.; Cunningham, Joy A.; Wehri, Sarah C.; Petrik, Amy F.; Okamoto, Kenji

    2004-10-01

    We have proposed using single molecule fluorescence resonant energy transfer (SM-FRET) to investigate the induction of secondary structure in model, surface-active peptides upon binding at an interface. The ability for SM-FRET to distinguish structural heterogeneity will offer a distinct advantage over traditional biophysical methods in these types of studies. Ensemble methods mask heterogeneity and only provide an average measure of secondary structural features. Because secondary structure contributes greatly to the energetics of dehydrating the amide backbone, detailed information of conformational distributions is crucial to the understanding of the thermodynamic cycle involved. Here we present results from our first efforts at using SM-FRET to study an amphipathic α-helix forming peptide immobilized at the solid-liquid interface between an aqueous solution and an octadecylsilane modified glass surface. This system serves as a model for future studies of peptide partitioning to lipid bilayers and other relevant interfaces.

  16. Secondary Structure Analysis of Native Cellulose by Molecular Dynamics Simulations with Coarse Grained Model

    Science.gov (United States)

    Wu, Shuai; Zhan, Hai-yi; Wang, Hong-ming; Ju, Yan

    2012-04-01

    The secondary structure of different Iβ cellulose was analyzed by a molecular dynamics simulation with MARTINI coarse-grained force field, where each chain of the cellulose includes 40 D-glucoses units. Calculation gives a satisfied description about the secondary structure of the cellulose. As the chain number increasing, the cellulose becomes the form of a helix, with the diameter of screw growing and spiral rising. Interestingly, the celluloses with chain number N 4 of 6, 24 and 36 do show right-hand twisting. On the contrast, the celluloses with N 8 of 12, 16 chains are left-hand twisting. These simulations indicate that the cellulose with chain number larger than 36 will break down to two parts. Besides, the result indicates that 36-chains cellulose model is the most stable among all models. Furthermore, the Lennard-Jones potential determines the secondary structure. In addition, an equation was set up to analyze the twisting structure.

  17. DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families

    DEFF Research Database (Denmark)

    Sander, Adam F.; Lavstsen, Thomas; Rask, Thomas Salhøj

    2014-01-01

    -erythrocyte membrane protein 1 structural domains. The recombinogenic potential of these 50-mers is not parasite-specific because these sequences also induce recombination when transferred to the yeast Saccharomyces cerevisiae. Genetic cross data suggest that DNA secondary structures (DSS) act as inducers...

  18. Structural class prediction of protein using novel feature extraction method from chaos game representation of predicted secondary structure.

    Science.gov (United States)

    Zhang, Lichao; Kong, Liang; Han, Xiaodong; Lv, Jinfeng

    2016-07-07

    Protein structural class prediction plays an important role in protein structure and function analysis, drug design and many other biological applications. Extracting good representation from protein sequence is fundamental for this prediction task. In recent years, although several secondary structure based feature extraction strategies have been specially proposed for low-similarity protein sequences, the prediction accuracy still remains limited. To explore the potential of secondary structure information, this study proposed a novel feature extraction method from the chaos game representation of predicted secondary structure to mainly capture sequence order information and secondary structure segments distribution information in a given protein sequence. Several kinds of prediction accuracies obtained by the jackknife test are reported on three widely used low-similarity benchmark datasets (25PDB, 1189 and 640). Compared with the state-of-the-art prediction methods, the proposed method achieves the highest overall accuracies on all the three datasets. The experimental results confirm that the proposed feature extraction method is effective for accurate prediction of protein structural class. Moreover, it is anticipated that the proposed method could be extended to other graphical representations of protein sequence and be helpful in future research. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. SucStruct: Prediction of succinylated lysine residues by using structural properties of amino acids.

    Science.gov (United States)

    López, Yosvany; Dehzangi, Abdollah; Lal, Sunil Pranit; Taherzadeh, Ghazaleh; Michaelson, Jacob; Sattar, Abdul; Tsunoda, Tatsuhiko; Sharma, Alok

    2017-06-15

    Post-Translational Modification (PTM) is a biological reaction which contributes to diversify the proteome. Despite many modifications with important roles in cellular activity, lysine succinylation has recently emerged as an important PTM mark. It alters the chemical structure of lysines, leading to remarkable changes in the structure and function of proteins. In contrast to the huge amount of proteins being sequenced in the post-genome era, the experimental detection of succinylated residues remains expensive, inefficient and time-consuming. Therefore, the development of computational tools for accurately predicting succinylated lysines is an urgent necessity. To date, several approaches have been proposed but their sensitivity has been reportedly poor. In this paper, we propose an approach that utilizes structural features of amino acids to improve lysine succinylation prediction. Succinylated and non-succinylated lysines were first retrieved from 670 proteins and characteristics such as accessible surface area, backbone torsion angles and local structure conformations were incorporated. We used the k-nearest neighbors cleaning treatment for dealing with class imbalance and designed a pruned decision tree for classification. Our predictor, referred to as SucStruct (Succinylation using Structural features), proved to significantly improve performance when compared to previous predictors, with sensitivity, accuracy and Mathew's correlation coefficient equal to 0.7334-0.7946, 0.7444-0.7608 and 0.4884-0.5240, respectively. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. A pairwise residue contact area-based mean force potential for discrimination of native protein structure

    Directory of Open Access Journals (Sweden)

    Pezeshk Hamid

    2010-01-01

    Full Text Available Abstract Background Considering energy function to detect a correct protein fold from incorrect ones is very important for protein structure prediction and protein folding. Knowledge-based mean force potentials are certainly the most popular type of interaction function for protein threading. They are derived from statistical analyses of interacting groups in experimentally determined protein structures. These potentials are developed at the atom or the amino acid level. Based on orientation dependent contact area, a new type of knowledge-based mean force potential has been developed. Results We developed a new approach to calculate a knowledge-based potential of mean-force, using pairwise residue contact area. To test the performance of our approach, we performed it on several decoy sets to measure its ability to discriminate native structure from decoys. This potential has been able to distinguish native structures from the decoys in the most cases. Further, the calculated Z-scores were quite high for all protein datasets. Conclusions This knowledge-based potential of mean force can be used in protein structure prediction, fold recognition, comparative modelling and molecular recognition. The program is available at http://www.bioinf.cs.ipm.ac.ir/softwares/surfield

  1. Remote homology detection using a kernel method that combines sequence and secondary-structure similarity scores.

    Science.gov (United States)

    Wieser, Daniela; Niranjan, Mahesan

    2009-01-01

    Distant evolutionary relationships between proteins with low sequence similarity are difficult to recognise by computational methods. Consequently, many sequences obtained from large-scale sequencing projects cannot be assigned to any known proteins or families despite being evolutionarily related. To boost sensitivity, various sequence-based methods have been modified to make use of the better conserved secondary structure. Most of these methods are instance-based or generative. Here, we introduce a kernel-based remote homology detection method that allows for a combination of sequence and secondary-structure similarity scores in a discriminative approach. We studied the ability of the method to predict superfamily membership as defined by the SCOP database. We show that a kernel method that combined sequence similarity scores with predicted secondary-structure similarity scores performed similar to a classifier that used scores calculated from sequences and true secondary structures, but performed better than a sequence-only based classifier and achieved a better mean than recently published results on the same data-set. It can be concluded that SVM classifiers trained to predict homology between distantly related proteins, become more accurate, if a joint sequence/secondary-structure similarity score approach is used.

  2. RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

    Science.gov (United States)

    Ellington, Roni; Wachira, James

    2010-01-01

    The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems. PMID:20810968

  3. Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria.

    Science.gov (United States)

    Negassa, Wakene C; Guber, Andrey K; Kravchenko, Alexandra N; Marsh, Terence L; Hildebrandt, Britton; Rivers, Mark L

    2015-01-01

    Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S-18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75-80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g(-1) soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g(-1) soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C

  4. Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria.

    Directory of Open Access Journals (Sweden)

    Wakene C Negassa

    Full Text Available Physical protection of soil carbon (C is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i decomposition of added plant residue, (ii CO2 emission from soil, and (iii structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S-18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm pores, 75-80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g(-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g(-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of

  5. Properties of Soil Pore Space Regulate Pathways of Plant Residue Decomposition and Community Structure of Associated Bacteria

    Science.gov (United States)

    Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; Marsh, Terence L.; Hildebrandt, Britton; Rivers, Mark L.

    2015-01-01

    Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C

  6. PreSSAPro: a software for the prediction of secondary structure by amino acid properties.

    Science.gov (United States)

    Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

    2007-10-01

    PreSSAPro is a software, available to the scientific community as a free web service designed to provide predictions of secondary structures starting from the amino acid sequence of a given protein. Predictions are based on our recently published work on the amino acid propensities for secondary structures in either large but not homogeneous protein data sets, as well as in smaller but homogeneous data sets corresponding to protein structural classes, i.e. all-alpha, all-beta, or alpha-beta proteins. Predictions result improved by the use of propensities evaluated for the right protein class. PreSSAPro predicts the secondary structure according to the right protein class, if known, or gives a multiple prediction with reference to the different structural classes. The comparison of these predictions represents a novel tool to evaluate what sequence regions can assume different secondary structures depending on the structural class assignment, in the perspective of identifying proteins able to fold in different conformations. The service is available at the URL http://bioinformatica.isa.cnr.it/PRESSAPRO/.

  7. Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data.

    Science.gov (United States)

    Tan, Zhen; Sharma, Gaurav; Mathews, David H

    2017-07-25

    Secondary structure prediction is an important problem in RNA bioinformatics because knowledge of structure is critical to understanding the functions of RNA sequences. Significant improvements in prediction accuracy have recently been demonstrated though the incorporation of experimentally obtained structural information, for instance using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) mapping. However, such mapping data is currently available only for a limited number of RNA sequences. In this article, we present a method for extending the benefit of experimental mapping data in secondary structure prediction to homologous sequences. Specifically, we propose a method for integrating experimental mapping data into a comparative sequence analysis algorithm for secondary structure prediction of multiple homologs, whereby the mapping data benefits not only the prediction for the specific sequence that was mapped but also other homologs. The proposed method is realized by modifying the TurboFold II algorithm for prediction of RNA secondary structures to utilize basepairing probabilities guided by SHAPE experimental data when such data are available. The SHAPE-mapping-guided basepairing probabilities are obtained using the RSample method. Results demonstrate that the SHAPE mapping data for a sequence improves structure prediction accuracy of other homologous sequences beyond the accuracy obtained by sequence comparison alone (TurboFold II). The updated version of TurboFold II is freely available as part of the RNAstructure software package. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  8. Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory.

    Science.gov (United States)

    Lin, Luan; McKerrow, Wilson H; Richards, Bryce; Phonsom, Chukiat; Lawrence, Charles E

    2018-03-05

    The nearest neighbor model and associated dynamic programming algorithms allow for the efficient estimation of the RNA secondary structure Boltzmann ensemble. However because a given RNA secondary structure only contains a fraction of the possible helices that could form from a given sequence, the Boltzmann ensemble is multimodal. Several methods exist for clustering structures and finding those modes. However less focus is given to exploring the underlying reasons for this multimodality: the presence of conflicting basepairs. Information theory, or more specifically mutual information, provides a method to identify those basepairs that are key to the secondary structure. To this end we find most informative basepairs and visualize the effect of these basepairs on the secondary structure. Knowing whether a most informative basepair is present tells us not only the status of the particular pair but also provides a large amount of information about which other pairs are present or not present. We find that a few basepairs account for a large amount of the structural uncertainty. The identification of these pairs indicates small changes to sequence or stability that will have a large effect on structure. We provide a novel algorithm that uses mutual information to identify the key basepairs that lead to a multimodal Boltzmann distribution. We then visualize the effect of these pairs on the overall Boltzmann ensemble.

  9. A Reference Database for Circular Dichroism Spectroscopy Covering Fold and Secondary Structure Space

    International Nuclear Information System (INIS)

    Lees, J.; Miles, A.; Wien, F.; Wallace, B.

    2006-01-01

    Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined. This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology

  10. IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming.

    Science.gov (United States)

    Sato, Kengo; Kato, Yuki; Hamada, Michiaki; Akutsu, Tatsuya; Asai, Kiyoshi

    2011-07-01

    Pseudoknots found in secondary structures of a number of functional RNAs play various roles in biological processes. Recent methods for predicting RNA secondary structures cover certain classes of pseudoknotted structures, but only a few of them achieve satisfying predictions in terms of both speed and accuracy. We propose IPknot, a novel computational method for predicting RNA secondary structures with pseudoknots based on maximizing expected accuracy of a predicted structure. IPknot decomposes a pseudoknotted structure into a set of pseudoknot-free substructures and approximates a base-pairing probability distribution that considers pseudoknots, leading to the capability of modeling a wide class of pseudoknots and running quite fast. In addition, we propose a heuristic algorithm for refining base-paring probabilities to improve the prediction accuracy of IPknot. The problem of maximizing expected accuracy is solved by using integer programming with threshold cut. We also extend IPknot so that it can predict the consensus secondary structure with pseudoknots when a multiple sequence alignment is given. IPknot is validated through extensive experiments on various datasets, showing that IPknot achieves better prediction accuracy and faster running time as compared with several competitive prediction methods. The program of IPknot is available at http://www.ncrna.org/software/ipknot/. IPknot is also available as a web server at http://rna.naist.jp/ipknot/. satoken@k.u-tokyo.ac.jp; ykato@is.naist.jp Supplementary data are available at Bioinformatics online.

  11. Structure-sweetness relationship in egg white lysozyme: role of lysine and arginine residues on the elicitation of lysozyme sweetness.

    Science.gov (United States)

    Masuda, Tetsuya; Ide, Nobuyuki; Kitabatake, Naofumi

    2005-10-01

    Lysozyme is one of the sweet-tasting proteins. To clarify the structure-sweetness relationship and the basicity-sweetness relationship in lysozyme, we have generated lysozyme mutants with Pichia systems. Alanine substitution of lysine residues demonstrated that two out of six lysine residues, Lys13 and Lys96, are required for lysozyme sweetness, while the remaining four lysine residues do not play a significant role in the perception of sweetness. Arginine substitution of lysine residues revealed that the basicity, but not the shape, of the side chain plays a significant role in sweetness. Single alanine substitutions of arginine residues showed that three arginine residues, Arg14, Arg21, and Arg73, play significant roles in lysozyme sweetness, whereas Arg45, Arg68, Arg125 and chemical modification by 1,2-cyclohexanedione did not affect sweetness. From investigation of the charge-specific mutations, we found that the basicity of a broad surface region formed by five positively charged residues, Lys13, Lys96, Arg14, Arg21, and Arg73, is required for lysozyme sweetness. Differences in the threshold values among sweet-tasting proteins might be caused by the broadness and/or the density of charged residues on the protein surface.

  12. Residuation theory

    CERN Document Server

    Blyth, T S; Sneddon, I N; Stark, M

    1972-01-01

    Residuation Theory aims to contribute to literature in the field of ordered algebraic structures, especially on the subject of residual mappings. The book is divided into three chapters. Chapter 1 focuses on ordered sets; directed sets; semilattices; lattices; and complete lattices. Chapter 2 tackles Baer rings; Baer semigroups; Foulis semigroups; residual mappings; the notion of involution; and Boolean algebras. Chapter 3 covers residuated groupoids and semigroups; group homomorphic and isotone homomorphic Boolean images of ordered semigroups; Dubreil-Jacotin and Brouwer semigroups; and loli

  13. Knowledge-based computational intelligence development for predicting protein secondary structures from sequences.

    Science.gov (United States)

    Shen, Hong-Bin; Yi, Dong-Liang; Yao, Li-Xiu; Yang, Jie; Chou, Kuo-Chen

    2008-10-01

    In the postgenomic age, with the avalanche of protein sequences generated and relatively slow progress in determining their structures by experiments, it is important to develop automated methods to predict the structure of a protein from its sequence. The membrane proteins are a special group in the protein family that accounts for approximately 30% of all proteins; however, solved membrane protein structures only represent less than 1% of known protein structures to date. Although a great success has been achieved for developing computational intelligence techniques to predict secondary structures in both globular and membrane proteins, there is still much challenging work in this regard. In this review article, we firstly summarize the recent progress of automation methodology development in predicting protein secondary structures, especially in membrane proteins; we will then give some future directions in this research field.

  14. RNA secondary structure prediction based on SHAPE data in helix regions.

    Science.gov (United States)

    Lotfi, Mohadeseh; Zare-Mirakabad, Fatemeh; Montaseri, Soheila

    2015-09-07

    RNA molecules play important and fundamental roles in biological processes. Frequently, the functional form of single-stranded RNA molecules requires a specific tertiary structure. Classically, RNA structure determination has mostly been accomplished by X-Ray crystallography or Nuclear Magnetic Resonance approaches. These experimental methods are time consuming and expensive. In the past two decades, some computational methods and algorithms have been developed for RNA secondary structure prediction. In these algorithms, minimum free energy is known as the best criterion. However, the results of algorithms show that minimum free energy is not a sufficient criterion to predict RNA secondary structure. These algorithms need some additional knowledge about the structure, which has to be added in the methods. Recently, the information obtained from some experimental data, called SHAPE, can greatly improve the consistency between the native and predicted RNA secondary structure. In this paper, we investigate the influence of SHAPE data on four types of RNA substructures, helices, loops, base pairs from the start and end of helices and two base pairs from the start and end of helices. The results show that SHAPE data in helix regions can improve the prediction. We represent a new method to apply SHAPE data in helix regions for finding RNA secondary structure. Finally, we compare the results of the method on a set of RNAs to predict minimum free energy structure based on considering all SHAPE data and only SHAPE data in helix regions as pseudo free energy and without SHAPE data (without any pseudo free energy). The results show that RNA secondary structure prediction based on considering only SHAPE data in helix regions is more successful than not considering SHAPE data and it provides competitive results in comparison with considering all SHAPE data. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Structure of bradavidin-C-terminal residues act as intrinsic ligands.

    Directory of Open Access Journals (Sweden)

    Jenni Leppiniemi

    Full Text Available Bradavidin is a homotetrameric biotin-binding protein from Bradyrhizobium japonicum, a nitrogen fixing and root nodule-forming symbiotic bacterium of the soybean. Wild-type (wt bradavidin has 138 amino acid residues, whereas the C-terminally truncated core-bradavidin has only 118 residues. We have solved the X-ray structure of wt bradavidin and found that the C-terminal amino acids of each subunit were uniquely bound to the biotin-binding pocket of an adjacent subunit. The biotin-binding pocket occupying peptide (SEKLSNTK was named "Brad-tag" and it serves as an intrinsic stabilizing ligand in wt bradavidin. The binding of Brad-tag to core-bradavidin was analysed by isothermal titration calorimetry and a binding affinity of ∼25 µM was measured. In order to study the potential of Brad-tag, a green fluorescent protein tagged with Brad-tag was prepared and successfully concentrated from a bacterial cell lysate using core-bradavidin-functionalized Sepharose resin.

  16. Bayesian Inference using Neural Net Likelihood Models for Protein Secondary Structure Prediction

    Directory of Open Access Journals (Sweden)

    Seong-Gon Kim

    2011-06-01

    Full Text Available Several techniques such as Neural Networks, Genetic Algorithms, Decision Trees and other statistical or heuristic methods have been used to approach the complex non-linear task of predicting Alpha-helicies, Beta-sheets and Turns of a proteins secondary structure in the past. This project introduces a new machine learning method by using an offline trained Multilayered Perceptrons (MLP as the likelihood models within a Bayesian Inference framework to predict secondary structures proteins. Varying window sizes are used to extract neighboring amino acid information and passed back and forth between the Neural Net models and the Bayesian Inference process until there is a convergence of the posterior secondary structure probability.

  17. Mineral Association Changes the Secondary Structure and Dynamics of Murine Amelogenin

    Energy Technology Data Exchange (ETDEWEB)

    Lu, J. X.; Xu, Y. S.; Buchko, G. W.; Shaw, W. J.

    2013-10-15

    Biomineralization proteins, present during the formation of hard tissues including bones, teeth, egg shells and nacre, result in the exquisite structures and properties of the resulting materials.[1] The structure of these proteins is often implicated in the control of the mineral properties, however very little structural data is available for the bulk of these proteins due to the difficulty in determining structures of immobilized proteins. Solid-state NMR is uniquely suited to the study of the structure of proteins bound to surfaces, demonstrated with the structural and orientation insights provided for the hydroxyapatite mineralization proteins statherin and the amelogenin, LRAP.[2] While these data are some of the only structural data available for this important class of protein, the experiments are often expensive and time consuming, due to the need to prepare and measure samples with isolated spin pairs, and are limited to a size of ~60 residues. In this work, we utilized a combination of 1D and recent 2D[3] solid-state NMR techniques along with a sparsely labelled sample to characterize the structure and dynamics of potential HAP binding residues of the 180 residue enamel protein, amelogenin. Amelogenin nanospheres and mineral bound amelogenin were investigated and a shift from unstructured to β-sheet structure was observed, along with a decrease in protein flexibility. This work provides the first molecular level structure and dynamic information of full-length amelogenin on the surface of hydroxyapatite (HAP) and within nanospheres, and demonstrates the ability to evaluate structural characteristics of large biomineralization proteins bound to their physiologically relevant surface. The research was performed at the Pacific Northwest National Laboratory (PNNL), a facility operated by Battelle for the U.S. Department of Energy, with a portion of it performed at the W.R. Wiley Environmental Molecular Sciences Laboratory (EMSL), a national scientific user

  18. FragKB: structural and literature annotation resource of conserved peptide fragments and residues.

    Directory of Open Access Journals (Sweden)

    Ashish V Tendulkar

    Full Text Available BACKGROUND: FragKB (Fragment Knowledgebase is a repository of clusters of structurally similar fragments from proteins. Fragments are annotated with information at the level of sequence, structure and function, integrating biological descriptions derived from multiple existing resources and text mining. METHODOLOGY: FragKB contains approximately 400,000 conserved fragments from 4,800 representative proteins from PDB. Literature annotations are extracted from more than 1,700 articles and are available for over 12,000 fragments. The underlying systematic annotation workflow of FragKB ensures efficient update and maintenance of this database. The information in FragKB can be accessed through a web interface that facilitates sequence and structural visualization of fragments together with known literature information on the consequences of specific residue mutations and functional annotations of proteins and fragment clusters. FragKB is accessible online at http://ubio.bioinfo.cnio.es/biotools/fragkb/. SIGNIFICANCE: The information presented in FragKB can be used for modeling protein structures, for designing novel proteins and for functional characterization of related fragments. The current release is focused on functional characterization of proteins through inspection of conservation of the fragments.

  19. FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information.

    Science.gov (United States)

    Bose, Tungadri; Dutta, Anirban; Mh, Mohammed; Gandhi, Hemang; Mande, Sharmila S

    2015-09-01

    Given the importance of RNA secondary structures in defining their biological role, it would be convenient for researchers seeking RNA data if both sequence and structural information pertaining to RNA molecules are made available together. Current nucleotide data repositories archive only RNA sequence data. Furthermore, storage formats which can frugally represent RNA sequence as well as structure data in a single file, are currently unavailable. This article proposes a novel storage format, 'FASTR', for concomitant representation of RNA sequence and structure. The storage efficiency of the proposed FASTR format has been evaluated using RNA data from various microorganisms. Results indicate that the size of FASTR formatted files (containing both RNA sequence as well as structure information) are equivalent to that of FASTA-format files, which contain only RNA sequence information. RNA secondary structure is typically represented using a combination of a string of nucleotide characters along with the corresponding dot-bracket notation indicating structural attributes. 'FASTR' - the novel storage format proposed in the present study enables a frugal representation of both RNA sequence and structural information in the form of a single string. In spite of having a relatively smaller storage footprint, the resultant 'fastr' string(s) retain all sequence as well as secondary structural information that could be stored using a dot-bracket notation. An implementation of the 'FASTR' methodology is available for download at http://metagenomics.atc.tcs.com/compression/fastr.

  20. Web-Beagle: a web server for the alignment of RNA secondary structures.

    Science.gov (United States)

    Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2015-07-01

    Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Comparison of Welding Residual Stresses of Hybrid Laser-Arc Welding and Submerged Arc Welding in Offshore Steel Structures

    DEFF Research Database (Denmark)

    Andreassen, Michael Joachim; Yu, Zhenzhen; Liu, Stephen

    2016-01-01

    In the offshore industry, welding-induced distortion and tensile residual stresses have become a major concern in relation to the structural integrity of a welded structure. Particularly, the continuous increase in size of welded plates and joints needs special attention concerning welding induced...... are hybrid laser-arc welding (HLAW) and submerged arc welding (SAW). Both welding methods are applied for a full penetration butt-weld of 10 mm thick plates made of thermomechanically hot-rolled, low-carbon, fine-grain S355ML grade steel used in offshore steel structures. The welding residual stress state...

  2. "Parallel factor analysis of multi-excitation ultraviolet resonance Raman spectra for protein secondary structure determination".

    Science.gov (United States)

    Oshokoya, Olayinka O; JiJi, Renee D

    2015-09-10

    Protein secondary structural analysis is important for understanding the relationship between protein structure and function, or more importantly how changes in structure relate to loss of function. The structurally sensitive protein vibrational modes (amide I, II, III and S) in deep-ultraviolet resonance Raman (DUVRR) spectra resulting from the backbone C-O and N-H vibrations make DUVRR a potentially powerful tool for studying secondary structure changes. Experimental studies reveal that the position and intensity of the four amide modes in DUVRR spectra of proteins are largely correlated with the varying fractions of α-helix, β-sheet and disordered structural content of proteins. Employing multivariate calibration methods and DUVRR spectra of globular proteins with varying structural compositions, the secondary structure of a protein with unknown structure can be predicted. A disadvantage of multivariate calibration methods is the requirement of known concentration or spectral profiles. Second-order curve resolution methods, such as parallel factor analysis (PARAFAC), do not have such a requirement due to the "second-order advantage." An exceptional feature of DUVRR spectroscopy is that DUVRR spectra are linearly dependent on both excitation wavelength and secondary structure composition. Thus, higher order data can be created by combining protein DUVRR spectra of several proteins collected at multiple excitation wavelengths to give multi-excitation ultraviolet resonance Raman data (ME-UVRR). PARAFAC has been used to analyze ME-UVRR data of nine proteins to resolve the pure spectral, excitation and compositional profiles. A three factor model with non-negativity constraints produced three unique factors that were correlated with the relative abundance of helical, β-sheet and poly-proline II dihedral angles. This is the first empirical evidence that the typically resolved "disordered" spectrum represents the better defined poly-proline II type structure

  3. Artificial Intelligence in Prediction of Secondary Protein Structure Using CB513 Database

    Science.gov (United States)

    Avdagic, Zikrija; Purisevic, Elvir; Omanovic, Samir; Coralic, Zlatan

    2009-01-01

    In this paper we describe CB513 a non-redundant dataset, suitable for development of algorithms for prediction of secondary protein structure. A program was made in Borland Delphi for transforming data from our dataset to make it suitable for learning of neural network for prediction of secondary protein structure implemented in MATLAB Neural-Network Toolbox. Learning (training and testing) of neural network is researched with different sizes of windows, different number of neurons in the hidden layer and different number of training epochs, while using dataset CB513. PMID:21347158

  4. A 9-state hidden Markov model using protein secondary structure information for protein fold recognition.

    Science.gov (United States)

    Lee, Sun Young; Lee, Jong Yun; Jung, Kwang Su; Ryu, Keun Ho

    2009-06-01

    In protein fold recognition, the main disadvantage of hidden Markov models (HMMs) is the employment of large-scale model architectures which require large data sets and high computational resources for training. Also, HMMs must consider sequential information about secondary structures of proteins, to improve prediction performance and reduce model parameters. Therefore, we propose a novel method for protein fold recognition based on a hidden Markov model, called a 9-state HMM. The method can (i) reduce the number of states using secondary structure information about proteins for each fold and (ii) recognize protein folds more accurately than other HMMs.

  5. Protein Secondary Structure Prediction Using AutoEncoder Network and Bayes Classifier

    Science.gov (United States)

    Wang, Leilei; Cheng, Jinyong

    2018-03-01

    Protein secondary structure prediction is belong to bioinformatics,and it's important in research area. In this paper, we propose a new prediction way of protein using bayes classifier and autoEncoder network. Our experiments show some algorithms including the construction of the model, the classification of parameters and so on. The data set is a typical CB513 data set for protein. In terms of accuracy, the method is the cross validation based on the 3-fold. Then we can get the Q3 accuracy. Paper results illustrate that the autoencoder network improved the prediction accuracy of protein secondary structure.

  6. Artificial Intelligence in Prediction of Secondary Protein Structure Using CB513 Database.

    Science.gov (United States)

    Avdagic, Zikrija; Purisevic, Elvir; Omanovic, Samir; Coralic, Zlatan

    2009-03-01

    In this paper we describe CB513 a non-redundant dataset, suitable for development of algorithms for prediction of secondary protein structure. A program was made in Borland Delphi for transforming data from our dataset to make it suitable for learning of neural network for prediction of secondary protein structure implemented in MATLAB Neural-Network Toolbox. Learning (training and testing) of neural network is researched with different sizes of windows, different number of neurons in the hidden layer and different number of training epochs, while using dataset CB513.

  7. Structural brain differences in school-age children with residual speech sound errors.

    Science.gov (United States)

    Preston, Jonathan L; Molfese, Peter J; Mencl, W Einar; Frost, Stephen J; Hoeft, Fumiko; Fulbright, Robert K; Landi, Nicole; Grigorenko, Elena L; Seki, Ayumi; Felsenfeld, Susan; Pugh, Kenneth R

    2014-01-01

    The purpose of the study was to identify structural brain differences in school-age children with residual speech sound errors. Voxel based morphometry was used to compare gray and white matter volumes for 23 children with speech sound errors, ages 8;6-11;11, and 54 typically speaking children matched on age, oral language, and IQ. We hypothesized that regions associated with production and perception of speech sounds would differ between groups. Results indicated greater gray matter volumes for the speech sound error group relative to typically speaking controls in bilateral superior temporal gyrus. There was greater white matter volume in the corpus callosum for the speech sound error group, but less white matter volume in right lateral occipital gyrus. Results may indicate delays in neuronal pruning in critical speech regions or differences in the development of networks for speech perception and production. Copyright © 2013 Elsevier Inc. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Chen Chun

    2008-03-01

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

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

    Science.gov (United States)

    Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi

    2008-03-31

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

  10. Recycling organic residues in agriculture impacts soil-borne microbial community structure, function and N2O emissions.

    NARCIS (Netherlands)

    Suleiman, A.K.A.; Lourenço, Késia S.; Pitombo, L.; Mendes, Lukas W.; Roesch, L.F.W.; Pijl, A.S.; do Carmo, J.B.; Cantarella, Heitor; Kuramae, E.E.

    2018-01-01

    Recycling residues is a sustainable alternative to improve soil structure and increase the stock of nutrients. However, information about the magnitude and duration of disturbances caused by crop and industrial wastes on soil microbial community structure and function is still scarce. The objective

  11. Ectomycorrhizal community structure and function in relation to forest residue harvesting and wood ash applications

    International Nuclear Information System (INIS)

    Mahmood, Shahid

    2000-05-01

    Ectomycorrhizal fungi form symbiotic associations with tree roots and assist in nutrient-uptake and -cycling in forest ecosystems, thereby constituting a most significant part of the microbial community. The aims of the studies described in this thesis were to evaluate the potential of DNA-based molecular methods in below-ground ectomycorrhizal community studies and to investigate changes in ectomycorrhizal communities on spruce roots in sites with different N deposition, and in sites subjected to harvesting of forest residues or application of wood ash. The ability of selected ectomycorrhizal fungi to mobilise nutrients from wood ash and to colonise root systems in the presence and absence of ash was also studied. In total 39 ectomycorrhizal species were detected in the experimental forests located in southern Sweden. At each site five to six species colonised around 60% of the root tips. The dominant species, common to the sites, were Tylospora fibrillosa, Thelephora terrestris and Cenococcum geophilum. Differences between two sites with differing levels of N deposition suggested that community structure may be influenced by N deposition, although site history, location and degree of isolation may also influence species composition. Repeated harvesting of forest residues reduced numbers of mycorrhizal roots in the humus layer to approximately 50% of that in control plots but no shift in the ectomycorrhizal community could be detected. At another site, application of granulated wood ash induced a shift in ectomycorrhizal community structure and three ectomycorrhizal fungi ('ash fungi') were found to colonise ash granules. Two 'ash fungi' showed a superior ability to solubilise stabilised wood ash in laboratory experiments compared to other ectomycorrhizal isolates from the same site. In laboratory microcosms containing intact mycorrhizal mycelia, colonisation of wood ash patches by one 'ash fungus' was good whereas colonisation by Piloderma croceum was poor. In a

  12. Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

    Science.gov (United States)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

    NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

  13. FTIR study of secondary structure of bovine serum albumin and ovalbumin

    International Nuclear Information System (INIS)

    Abrosimova, K V; Shulenina, O V; Paston, S V

    2016-01-01

    Proteins structure is the critical factor for their functioning. Fourier transform infrared spectroscopy provides a possibility to obtain information about secondary structure of proteins in different states and also in a whole biological samples. Infrared spectra of egg white from the untreated and hard-boiled hen's egg, and also of chicken ovalbumin and bovine serum albumin in lyophilic form and in aqueous solution were studied. Lyophilization of investigated globular proteins is accompanied by the decrease of a-helix structures and the increase in amount of intermolecular β-sheets. Analysis of infrared spectrum of egg white allowed to make an estimation of OVA secondary structure and to observe α-to-β structural transformation as a result of the heat denaturation. (paper)

  14. Structural elucidation of the nonclassical secondary cell wall polysaccharide from Bacillus cereus ATCC 10987. Comparison with the polysaccharides from Bacillus anthracis and B. cereus type strain ATCC 14579 reveals both unique and common structural features.

    Science.gov (United States)

    Leoff, Christine; Choudhury, Biswa; Saile, Elke; Quinn, Conrad P; Carlson, Russell W; Kannenberg, Elmar L

    2008-10-31

    Nonclassical secondary cell wall polysaccharides constitute a major cell wall structure in the Bacillus cereus group of bacteria. The structure of the secondary cell wall polysaccharide from Bacillus cereus ATCC 10987, a strain that is closely related to Bacillus anthracis, was determined. This polysaccharide was released from the cell wall with aqueous hydrogen fluoride (HF) and purified by gel filtration chromatography. The purified polysaccharide, HF-PS, was characterized by glycosyl composition and linkage analyses, mass spectrometry, and one- and two-dimensional NMR analysis. The results showed that the B. cereus ATCC 10987 HF-PS has a repeating oligosaccharide consisting of a -->6)-alpha-GalNAc-(1-->4)-beta-ManNAc-(1-->4)-beta-GlcNAc-(1--> trisaccharide that is substituted with beta-Gal at O3 of the alpha-GalNAc residue and nonstoichiometrically acetylated at O3 of the N-acetylmannosamine (ManNAc) residue. Comparison of this structure with that of the B. anthracis HF-PS and with structural data obtained for the HF-PS from B. cereus type strain ATCC 14579 revealed that each HF-PS had the same general structural theme consisting of three HexNAc and one Hex residues. A common structural feature in the HF-PSs from B. cereus ATCC 10987 and B. anthracis was the presence of a repeating unit consisting of a HexNAc(3) trisaccharide backbone in which two of the three HexNAc residues are GlcNAc and ManNAc and the third can be either GlcNAc or GalNAc. The implications of these results with regard to the possible functions of the HF-PSs are discussed.

  15. [Establishment of industry promotion technology system in Chinese medicine secondary exploitation based on "component structure theory"].

    Science.gov (United States)

    Cheng, Xu-Dong; Feng, Liang; Zhang, Ming-Hua; Gu, Jun-Fei; Jia, Xiao-Bin

    2014-10-01

    The purpose of the secondary exploitation of Chinese medicine is to improve the quality of Chinese medicine products, enhance core competitiveness, for better use in clinical practice, and more effectively solve the patient suffering. Herbs, extraction, separation, refreshing, preparation and quality control are all involved in the industry promotion of Chinese medicine secondary exploitation of industrial production. The Chinese medicine quality improvement and industry promotion could be realized with the whole process of process optimization, quality control, overall processes improvement. Based on the "component structure theory", "multi-dimensional structure & process dynamic quality control system" and systematic and holistic character of Chinese medicine, impacts of whole process were discussed. Technology systems of Chinese medicine industry promotion was built to provide theoretical basis for improving the quality and efficacy of the secondary development of traditional Chinese medicine products.

  16. Bioinformatics approaches for structural and functional analysis of proteins in secondary metabolism in Withania somnifera.

    Science.gov (United States)

    Sanchita; Singh, Swati; Sharma, Ashok

    2014-11-01

    Withania somnifera (Ashwagandha) is an affluent storehouse of large number of pharmacologically active secondary metabolites known as withanolides. These secondary metabolites are produced by withanolide biosynthetic pathway. Very less information is available on structural and functional aspects of enzymes involved in withanolides biosynthetic pathways of Withiana somnifera. We therefore performed a bioinformatics analysis to look at functional and structural properties of these important enzymes. The pathway enzymes taken for this study were 3-Hydroxy-3-methylglutaryl coenzyme A reductase, 1-Deoxy-D-xylulose-5-phosphate synthase, 1-Deoxy-D-xylulose-5-phosphate reductase, farnesyl pyrophosphate synthase, squalene synthase, squalene epoxidase, and cycloartenol synthase. The prediction of secondary structure was performed for basic structural information. Three-dimensional structures for these enzymes were predicted. The physico-chemical properties such as pI, AI, GRAVY and instability index were also studied. The current information will provide a platform to know the structural attributes responsible for the function of these protein until experimental structures become available.

  17. Analysis of the secondary structure of ITS transcripts in peritrich ciliates (Ciliophora, Oligohymenophorea): implications for structural evolution and phylogenetic reconstruction.

    Science.gov (United States)

    Sun, Ping; Clamp, John C; Xu, Dapeng

    2010-07-01

    Despite extensive previous morphological work, little agreement has been reached about phylogenetic relationships among peritrich ciliates, making it difficult to study the evolution of the group in a phylogenetic framework. In this study, the nucleotide characteristics and secondary structures of internal transcribed spacers 1 and 2 (ITS1 and ITS2) of 26 peritrich ciliates in 12 genera were analyzed. Information from secondary structures of ITS1 and ITS2 then was used to perform the first systematic study of ITS regions in peritrich ciliates, including one species of Rhabdostyla for which no sequence has been reported previously. Lengths of ITS1 and ITS2 sequences varied relatively little among taxa studied, but their G+C content was highly variable. General secondary structure models of ITS1 and ITS2 were proposed for peritrich ciliates and their reliability was assessed by compensatory base changes. The secondary structure of ITS1 contains three major helices in peritrich ciliates and deviations from this basic structure were found in all taxa examined. The core structure of peritrich ITS2 includes four helices, with helix III as the longest and containing a motif 5'-MAC versus GUK-3' at its apex as well as a YU-UY mismatch in helix II. In addition, the structural motifs of both ITS secondary structures were identified. Phylogenetic analyses using ITS data were performed by means of Bayesian inference, maximum likelihood and neighbor joining methods. Trees had a consistent branching pattern that included the following features: (1) Rhabdostyla always clustered with members of the family Vorticellidae, instead of members of the family Epistylididae, in which it is now classified on the basis of morphology. (2) The systematically questionable genus Ophrydium closely associated with Carchesium, forming a clearly defined, monophyletic group within the Vorticellidae. This supported the hypothesis derived from previous study based on small subunit rRNA gene sequences

  18. Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes

    DEFF Research Database (Denmark)

    Weile, Christian; Gardner, Paul P; Hedegaard, Mads M

    2007-01-01

    BACKGROUND: Within the last decade a large number of noncoding RNA genes have been identified, but this may only be the tip of the iceberg. Using comparative genomics a large number of sequences that have signals concordant with conserved RNA secondary structures have been discovered in the human...

  19. The Turn of the Screw: An Exercise in Protein Secondary Structure

    Science.gov (United States)

    Pikaart, Michael

    2011-01-01

    An exercise using simple paper strips to illustrate protein helical and sheet secondary structures is presented. Drawing on the rich historical context of the use of physical models in protein biochemistry by early practitioners, in particular Linus Pauling, the purpose of this activity is to cultivate in students a hands-on, intuitive sense of…

  20. Molecular systematics of Barbatosphaeria (Sordariomycetes): multigene phylogeny and secondary ITS structure

    Czech Academy of Sciences Publication Activity Database

    Réblová, Martina; Réblová, K.; Štěpánek, Václav

    2015-01-01

    Roč. 35, December 2015 (2015), s. 21-38 ISSN 0031-5850 R&D Projects: GA ČR GAP506/12/0038 Institutional support: RVO:67985939 ; RVO:61388971 Keywords : Barbatosphaeria * molecular systematic * ITS secondary structures Subject RIV: EF - Botanics; EE - Microbiology, Virology (MBU-M) Impact factor: 5.725, year: 2015

  1. Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands

    NARCIS (Netherlands)

    Kowalchuk, G.A.; Stienstra, A.W.; Heilig, G.H.J.; Stephen, J.R.; Woldendorp, J.W.

    2000-01-01

    The community structure of beta-subclass Proteobacteria ammonia-oxidizing bacteria was determined in semi-natural chalk grassland soils at different stages of secondary succession. Both culture-mediated (most probable number; MPN) and direct nucleic acid-based approaches targeting genes encoding 16S

  2. Secondary structure of prokaryotic 5S ribosomal ribonucleic acids: a study with ribonucleases

    DEFF Research Database (Denmark)

    Douthwaite, S; Garrett, R A

    1981-01-01

    , we were able to distinguish between primary and secondary cutting positions and also to establish the relative degree of cutting. The data reveal the predicted similarities of the higher order structure in the two RNAs but also demonstrate a few significant differences. The data also provide direct...

  3. Instruction in text-structure as a determinant of senior secondary ...

    African Journals Online (AJOL)

    The study determined the effectiveness of instruction in text-structure on achievement of students in English narrative text. The pretest-posttest control group quasi experimental design was adopted for the study. The participants were 120 students in intact classes from four purposively selected senior secondary schools in ...

  4. Tropical rain-forest matrix quality affects bat assemblage structure in secondary forest patches

    NARCIS (Netherlands)

    Vleut, I.; Levy-Tacher, I.; Galindo-Gonzalez, J.; Boer, de W.F.; Ramirez-Marcial, N.

    2012-01-01

    We studied Phyllostomidae bat assemblage structure in patches of secondary forest dominated by the pioneer tree Ochroma pyramidale, largely (.85%) or partially (,35%) surrounded by a matrix of tropical rain forest, to test 3 hypotheses: the highest bat diversity and richness is observed in the

  5. [Conserved motifs in the primary and secondary ITS1 structures in bryophytes].

    Science.gov (United States)

    Milyutina, I A; Ignatov, M S

    2015-01-01

    A study of the ITS1 nucleotide sequences of 1000 moss species of 62 families, 11 liverwort species from five orders, and one hornwort Anthoceros agrestis identified five highly conserved motifs (CM1-CM5), which are presumably involved in pre-rRNA processing. Although the ITS1 sequences substantially differ in length and the extent of divergence, the conserved motifs are found in all of them. ITS1 secondary structures were constructed for 76 mosses, and main regularities at conserved motif positioning were observed. The positions of processing sites in the ITS1 secondary structure of the yeast Saccharomyces cerevisiae were found to be similar to the positions of the conserved motifs in the ITS1 secondary structures of mosses and liverworts. In addition, a potential hairpin formation in the putative secondary structure of a pre-rRNA fragment was considered for the region between ITS1 CM4-CM5 and a highly conserved region between hairpins 49 and 50 (H49 and H50) of the 18S rRNA.

  6. Glassy transition in a disordered model for the RNA secondary structure

    International Nuclear Information System (INIS)

    Pagnani, A.; Parisi, G.; Ricci-Tersenghi, F.

    2000-04-01

    We numerically study a disordered model for the RNA secondary structure and we find that it undergoes a phase transition, with a breaking of the replica symmetry in the low temperature region (like in spin glasses). Our results are based on the exact evaluation of the partition function. (author)

  7. Influences of model structure and calibration data size on predicting chlorine residuals in water storage tanks.

    Science.gov (United States)

    Hua, Pei; de Oliveira, Keila Roberta Ferreira; Cheung, Peter; Gonçalves, Fábio Veríssimo; Zhang, Jin

    2018-04-09

    This study evaluated the influences of model structure and calibration data size on the modelling performance for the prediction of chlorine residuals in household drinking water storage tanks. The tank models, which consisted of two modules, i.e., hydraulic mixing and water quality modelling processes, were evaluated under identical calibration conditions. The hydraulic mixing modelling processes investigated included the continuously stirred tank reactor (CSTR) and multi-compartment (MC) methods, and the water quality modelling processes included first order (FO), single-reactant second order (SRSO), and variable reaction rate coefficients (VRRC) second order chlorine decay kinetics. Different combinations of these hydraulic mixing and water quality methods formed six tank models. Results show that by applying the same calibration datasets, the tank models that included the MC method for modelling the hydraulic mixing provided better predictions compared to the CSTR method. In terms of water quality modelling, VRRC kinetics showed better predictive abilities compared to FO and SRSO kinetics. It was also found that the overall tank model performance could be substantially improved when a proper method was chosen for the simulation of hydraulic mixing, i.e., the accuracy of the hydraulic mixing modelling plays a critical role in the accuracy of the tank model. Advances in water quality modelling improve the calibration process, i.e., the size of the datasets used for calibration could be reduced when a suitable kinetics method was applied. Although the accuracies of all six models increased with increasing calibration dataset size, the tank model that consisted of the MC and VRRC methods was the most suitable of the tank models as it could satisfactorily predict chlorine residuals in household tanks by using invariant parameters calibrated against the minimum dataset size. Copyright © 2018 Elsevier B.V. All rights reserved.

  8. Characterization of the residual structure in the unfolded state of the Delta 131 Delta fragment of staphylococcal nuclease

    DEFF Research Database (Denmark)

    Francis, C. J.; Lindorff-Larsen, Kresten; Best, R. B.

    2006-01-01

    The determination of the conformational preferences in unfolded states of proteins constitutes an important challenge in structural biology. We use inter-residue distances estimated from site-directed spin-labeling NMR experimental measurements as ensemble-averaged restraints in all-atom molecular...... dynamics simulations to characterise the residual structure of the 131 fragment of staphylococcal nuclease under physiological conditions. Our findings indicate that 131 under these conditions shows a tendency to form transiently hydrophobic clusters similar to those present in the native state of wild...

  9. Bi-objective integer programming for RNA secondary structure prediction with pseudoknots.

    Science.gov (United States)

    Legendre, Audrey; Angel, Eric; Tahi, Fariza

    2018-01-15

    RNA structure prediction is an important field in bioinformatics, and numerous methods and tools have been proposed. Pseudoknots are specific motifs of RNA secondary structures that are difficult to predict. Almost all existing methods are based on a single model and return one solution, often missing the real structure. An alternative approach would be to combine different models and return a (small) set of solutions, maximizing its quality and diversity in order to increase the probability that it contains the real structure. We propose here an original method for predicting RNA secondary structures with pseudoknots, based on integer programming. We developed a generic bi-objective integer programming algorithm allowing to return optimal and sub-optimal solutions optimizing simultaneously two models. This algorithm was then applied to the combination of two known models of RNA secondary structure prediction, namely MEA and MFE. The resulting tool, called BiokoP, is compared with the other methods in the literature. The results show that the best solution (structure with the highest F 1 -score) is, in most cases, given by BiokoP. Moreover, the results of BiokoP are homogeneous, regardless of the pseudoknot type or the presence or not of pseudoknots. Indeed, the F 1 -scores are always higher than 70% for any number of solutions returned. The results obtained by BiokoP show that combining the MEA and the MFE models, as well as returning several optimal and several sub-optimal solutions, allow to improve the prediction of secondary structures. One perspective of our work is to combine better mono-criterion models, in particular to combine a model based on the comparative approach with the MEA and the MFE models. This leads to develop in the future a new multi-objective algorithm to combine more than two models. BiokoP is available on the EvryRNA platform: https://EvryRNA.ibisc.univ-evry.fr .

  10. Residual mode correction in calibrating nonlinear damper for vibration control of flexible structures

    Science.gov (United States)

    Sun, Limin; Chen, Lin

    2017-10-01

    Residual mode correction is found crucial in calibrating linear resonant absorbers for flexible structures. The classic modal representation augmented with stiffness and inertia correction terms accounting for non-resonant modes improves the calibration accuracy and meanwhile avoids complex modal analysis of the full system. This paper explores the augmented modal representation in calibrating control devices with nonlinearity, by studying a taut cable attached with a general viscous damper and its Equivalent Dynamic Systems (EDSs), i.e. the augmented modal representations connected to the same damper. As nonlinearity is concerned, Frequency Response Functions (FRFs) of the EDSs are investigated in detail for parameter calibration, using the harmonic balance method in combination with numerical continuation. The FRFs of the EDSs and corresponding calibration results are then compared with those of the full system documented in the literature for varied structural modes, damper locations and nonlinearity. General agreement is found and in particular the EDS with both stiffness and inertia corrections (quasi-dynamic correction) performs best among available approximate methods. This indicates that the augmented modal representation although derived from linear cases is applicable to a relatively wide range of damper nonlinearity. Calibration of nonlinear devices by this means still requires numerical analysis while the efficiency is largely improved owing to the system order reduction.

  11. Secondary flow structure in a model curved artery: 3D morphology and circulation budget analysis

    Science.gov (United States)

    Bulusu, Kartik V.; Plesniak, Michael W.

    2015-11-01

    In this study, we examined the rate of change of circulation within control regions encompassing the large-scale vortical structures associated with secondary flows, i.e. deformed Dean-, Lyne- and Wall-type (D-L-W) vortices at planar cross-sections in a 180° curved artery model (curvature ratio, 1/7). Magnetic resonance velocimetry (MRV) and particle image velocimetry (PIV) experiments were performed independently, under the same physiological inflow conditions (Womersley number, 4.2) and using Newtonian blood-analog fluids. The MRV-technique performed at Stanford University produced phase-averaged, three-dimensional velocity fields. Secondary flow field comparisons of MRV-data to PIV-data at various cross-sectional planes and inflow phases were made. A wavelet-decomposition-based approach was implemented to characterize various secondary flow morphologies. We hypothesize that the persistence and decay of arterial secondary flow vortices is intrinsically related to the influence of the out-of-plane flow, tilting, in-plane convection and diffusion-related factors within the control regions. Evaluation of these factors will elucidate secondary flow structures in arterial hemodynamics. Supported by the National Science Foundation under Grant Number CBET-0828903, and GW Center for Biomimetics and Bioinspired Engineering (COBRE). The MRV data were acquired at Stanford University in collaboration with Christopher Elkins and John Eaton.

  12. The Relationship between Secondary Structure and Biodegradation Behavior of Silk Fibroin Scaffolds

    Directory of Open Access Journals (Sweden)

    Yongpei Hu

    2012-01-01

    Full Text Available Silk fibroin has a unique and useful combination of properties, including good biocompatibility and excellent mechanical performance. These features provided early clues to the utility of regenerated silk fibroin as a scaffold/matrix for tissue engineering. The silk fibroin scaffolds used for tissue engineering should degrade at a rate that matches the tissue growth rate. The relationship between secondary structure and biodegradation behavior of silk fibroin scaffolds was investigated in this study. Scaffolds with different secondary structure were prepared by controlling the freezing temperature and by treatment with carbodiimide or ethanol. The quantitative proportions of each secondary structure were obtained by Fourier transform infrared spectroscopy (FTIR, and each sample was then degraded in vitro with collagenase IA for 18 days. The results show that a high content of β-sheet structure leads to a low degradation rate. The random coil region in the silk fibroin material is degraded, whereas the crystal region remains stable and the amount of β-sheet structure increases during incubation. The results demonstrate that it is possible to control the degradation rate of a silk fibroin scaffold by controlling the content of β-sheet structure.

  13. Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach.

    Science.gov (United States)

    Rashid, Shamima; Saraswathi, Saras; Kloczkowski, Andrzej; Sundaram, Suresh; Kolinski, Andrzej

    2016-09-13

    Protein secondary structure prediction (SSP) has been an area of intense research interest. Despite advances in recent methods conducted on large datasets, the estimated upper limit accuracy is yet to be reached. Since the predictions of SSP methods are applied as input to higher-level structure prediction pipelines, even small errors may have large perturbations in final models. Previous works relied on cross validation as an estimate of classifier accuracy. However, training on large numbers of protein chains compromises the classifier ability to generalize to new sequences. This prompts a novel approach to training and an investigation into the possible structural factors that lead to poor predictions. Here, a small group of 55 proteins termed the compact model is selected from the CB513 dataset using a heuristics-based approach. In a prior work, all sequences were represented as probability matrices of residues adopting each of Helix, Sheet and Coil states, based on energy calculations using the C-Alpha, C-Beta, Side-chain (CABS) algorithm. The functional relationship between the conformational energies computed with CABS force-field and residue states is approximated using a classifier termed the Fully Complex-valued Relaxation Network (FCRN). The FCRN is trained with the compact model proteins. The performance of the compact model is compared with traditional cross-validated accuracies and blind-tested on a dataset of G Switch proteins, obtaining accuracies of ∼81 %. The model demonstrates better results when compared to several techniques in the literature. A comparative case study of the worst performing chain identifies hydrogen bond contacts that lead to Coil ⇔ Sheet misclassifications. Overall, mispredicted Coil residues have a higher propensity to participate in backbone hydrogen bonding than correctly predicted Coils. The implications of these findings are: (i) the choice of training proteins is important in preserving the generalization of a

  14. Secondary structure-based analysis of mouse brain small RNA sequences obtained by using next-generation sequencing.

    Science.gov (United States)

    Kiyosawa, Hidenori; Okumura, Akio; Okui, Saya; Ushida, Chisato; Kawai, Gota

    2015-08-01

    In order to find novel structured small RNAs, next-generation sequencing was applied to small RNA fractions with lengths ranging from 40 to 140 nt and secondary structure-based clustering was performed. Sequences of structured RNAs were effectively clustered and analyzed by secondary structure. Although more than 99% of the obtained sequences were known RNAs, 16 candidate mouse structured small non-coding RNAs (MsncRs) were isolated. Based on these results, the merits of secondary structure-based analysis are discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Ectomycorrhizal community structure and function in relation to forest residue harvesting and wood ash applications

    Energy Technology Data Exchange (ETDEWEB)

    Mahmood, Shahid

    2000-05-01

    Ectomycorrhizal fungi form symbiotic associations with tree roots and assist in nutrient-uptake and -cycling in forest ecosystems, thereby constituting a most significant part of the microbial community. The aims of the studies described in this thesis were to evaluate the potential of DNA-based molecular methods in below-ground ectomycorrhizal community studies and to investigate changes in ectomycorrhizal communities on spruce roots in sites with different N deposition, and in sites subjected to harvesting of forest residues or application of wood ash. The ability of selected ectomycorrhizal fungi to mobilise nutrients from wood ash and to colonise root systems in the presence and absence of ash was also studied. In total 39 ectomycorrhizal species were detected in the experimental forests located in southern Sweden. At each site five to six species colonised around 60% of the root tips. The dominant species, common to the sites, were Tylospora fibrillosa, Thelephora terrestris and Cenococcum geophilum. Differences between two sites with differing levels of N deposition suggested that community structure may be influenced by N deposition, although site history, location and degree of isolation may also influence species composition. Repeated harvesting of forest residues reduced numbers of mycorrhizal roots in the humus layer to approximately 50% of that in control plots but no shift in the ectomycorrhizal community could be detected. At another site, application of granulated wood ash induced a shift in ectomycorrhizal community structure and three ectomycorrhizal fungi ('ash fungi') were found to colonise ash granules. Two 'ash fungi' showed a superior ability to solubilise stabilised wood ash in laboratory experiments compared to other ectomycorrhizal isolates from the same site. In laboratory microcosms containing intact mycorrhizal mycelia, colonisation of wood ash patches by one 'ash fungus' was good whereas colonisation by

  16. A study of some asphaltenes solutions structure and of a Safaniya vacuum residue

    Energy Technology Data Exchange (ETDEWEB)

    Guille, V.

    1996-05-20

    A lot of problems in the petroleum industry are due to the presence of asphaltenes compounds in petroleum products. A good knowledge of the chemical composition and the different properties of asphaltenes in solution are necessary to cope with these difficulties. We have then examined a Safaniya Vacuum Residue (VR) and its fractions (asphaltenes, resins, aromatics and saturates). In order to describe the macro-structure of these complex colloidal systems, we used different characterisation techniques: small angle X-ray and neutron scattering (SAXS and SANS), rheology and electron microscopy. Scattering techniques allows us to precise the model for asphaltenes and resins in solution. These macromolecules are poly-dispersed disk-like particles with thickness and diameter which are respectively close to 1 to 10 nm. The average molecular weight is equal to 106 000 for asphaltenes and 3 300 for resins. We have shown that SAXS is more sensitive to the scattering of the aromatic part of the molecule. Adding n-heptane induces first a de-solvation of the molecules and then an aggregation up to flocculation. These solutions present large heterogeneities due to concentration fluctuations. A huge difference in the chemical composition of the different asphaltenes molecules can explain these fluctuations. These heterogeneities are stable as a function of temperature; this means that exist strong molecular interactions. Ultracentrifugation gives two different fractions which contain different chemical structures, more or less aromatic. Solutions, in good solvent, of these two fractions are homogeneous but a mixture of these two fractions exhibits, heterogeneities. SAXS gives information about the structure of VR. We have observed the presence of large density fluctuations up to 300 deg. C. Rheological measurements confirm three-dimensional organisation. (author). 11 refs., 11 figs., 49 tabs.

  17. Rigidity of poly-L-glutamic acid scaffolds: Influence of secondary and supramolecular structure

    Energy Technology Data Exchange (ETDEWEB)

    Perticaroli, Stefania [ORNL; Ehlers, Georg [ORNL; Feygenson, Mikhail [ORNL; Sokolov, Alexei P [ORNL

    2015-01-01

    Poly-L-glutamic acid (PGA) is a widely used biomaterial, with applications ranging from drug delivery and biological glues to food products and as a tissue engineering scaffold. A biodegradable material with flexible conjugation functional groups, tunable secondary structure, and mechanical properties, PGA has potential as a tunable matrix material in mechanobiology. Some recent studies in proteins connecting dynamics, nanometer length scale rigidity, and secondary structure suggest a new point of view from which to analyze and develop this promising material. Our paper characterizes the structure, topology, and rigidity properties of PGA prepared with different molecular weights and secondary structures through various techniques including scanning electron microscopy, FTIR, light, and neutron scattering spectroscopy. On the length scale of a few nanometers, rigidity is determined by hydrogen bonding interactions in the presence of neutral species and by electrostatic interactions when the polypeptide is negatively charged. Finally, when probed over hundreds of nanometers, the rigidity of these materials is modified by long range intermolecular interactions that are introduced by the supramolecular structure.

  18. SecStAnT: secondary structure analysis tool for data selection, statistics and models building.

    Science.gov (United States)

    Maccari, Giuseppe; Spampinato, Giulia L B; Tozzini, Valentina

    2014-03-01

    Atomistic or coarse grained (CG) potentials derived from statistical distributions of internal variables have recently become popular due to the need of simplified interactions for reaching larger scales in simulations or more efficient conformational space sampling. However, the process of parameterization of accurate and predictive statistics-based force fields requires a huge amount of work and is prone to the introduction of bias and errors. This article introduces SecStAnT, a software for the creation and analysis of protein structural datasets with user-defined primary/secondary structure composition, with a particular focus on the CG representation. In addition, the possibility of managing different resolutions and the primary/secondary structure selectivity allow addressing the mapping-backmapping of atomistic to CG representation and study the secondary to primary structure relations. Sample datasets and distributions are reported, including interpretation of structural features. SecStAnT is available free of charge at secstant.sourceforge.net/. Source code is freely available on request, implemented in Java and supported on Linux, MS Windows and OSX.

  19. Two-dimensional NMR studies of squash family inhibitors. Sequence-specific proton assignments and secondary structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III

    Energy Technology Data Exchange (ETDEWEB)

    Krisnamoorthi, R.; Yuxi Gong; Chanlan Sun Lin (Kansas State Univ., Manhattan (United States)); VanderVelde, D. (Univ. of Kansas, Lawrence (United States))

    1992-01-28

    The solution structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III*) was investigated by two-dimensional proton nuclear magnetic resonance (2D NMR) spectroscopy. CMTI-III*, prepared by reacting CMTI-III with trypsin which cleaved the Arg5-Ile6 peptide bond, had the two fragments held together by a disulfide linkage. Sequence-specific {sup 1}H NMR resonance assignments were made for all the 29 amino acid residues of the protein. The secondary structure of CMTI-III*, as deduced from NOESY cross peaks and identification of slowly exchanging hydrogens, contains two turns, a 3{sub 10}-helix, and a triple-stranded {beta}-sheet. Sequential proton assignments were also made for the virgin inhibitor, CMTI-III, at pH 4.71, 30C. Comparison of backbone hydrogen chemical shifts of CMTI-III and CMTI-III* revealed significant changes for residues located far away from the reactive-site region as well as for those located near it, indicating tertiary structural changes that are transmitted through most of the 29 residues of the inhibitor protein. These chemical shift changes were relatively small compared to changes that occurred upon hydrolysis of the reactive-site peptide bond between Arg 5 and Ile6 in CMTI-III.

  20. Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots

    DEFF Research Database (Denmark)

    Kato, Yuki; Gorodkin, Jan; Havgaard, Jakob Hull

    2017-01-01

    . Methods: Here we present a fast and efficient method, DotcodeR, for detecting structurally similar RNAs in genomic sequences by comparing their corresponding coarse-grained secondary structure dot plots at string level. This allows us to perform an all-against-all scan of all window pairs from two genomes...... without alignment. Results: Our computational experiments with simulated data and real chromosomes demonstrate that the presented method has good sensitivity. Conclusions: DotcodeR can be useful as a pre-filter in a genomic comparative scan for structured RNAs....

  1. Improving succinylation prediction accuracy by incorporating the secondary structure via helix, strand and coil, and evolutionary information from profile bigrams

    Science.gov (United States)

    Lal, Sunil Pranit; Taherzadeh, Ghazaleh; Sattar, Abdul; Tsunoda, Tatsuhiko; Sharma, Alok

    2018-01-01

    Post-translational modification refers to the biological mechanism involved in the enzymatic modification of proteins after being translated in the ribosome. This mechanism comprises a wide range of structural modifications, which bring dramatic variations to the biological function of proteins. One of the recently discovered modifications is succinylation. Although succinylation can be detected through mass spectrometry, its current experimental detection turns out to be a timely process unable to meet the exponential growth of sequenced proteins. Therefore, the implementation of fast and accurate computational methods has emerged as a feasible solution. This paper proposes a novel classification approach, which effectively incorporates the secondary structure and evolutionary information of proteins through profile bigrams for succinylation prediction. The proposed predictor, abbreviated as SSEvol-Suc, made use of the above features for training an AdaBoost classifier and consequently predicting succinylated lysine residues. When SSEvol-Suc was compared with four benchmark predictors, it outperformed them in metrics such as sensitivity (0.909), accuracy (0.875) and Matthews correlation coefficient (0.75). PMID:29432431

  2. Secondary structure estimation and properties analysis of stretched Asian and Caucasian hair.

    Science.gov (United States)

    Zhou, A J; Liu, H L; Du, Z Q

    2015-02-01

    In this previous work, we investigated the secondary structure changes of stretched yak hairs by deconvolution, secondary derivation, and curve fitting and determined the number of bands and their positions in order to resolve the protein spectrum of Raman spectroscopy. The secondary structure estimation and properties analysis of stretched Asian and Caucasian hair were investigated by Fourier transform infrared spectroscopy, tensile curves, and measurement of density. The hairs were stretched, dried, and baked at ratios 20%, 40%, 60%, 80% and 100%. The analysis of the amide I band indicated that the transformation from α-helix to β-pleated structure occurred during the stretching process, which could be verified from the tensile analysis. The cysteine oxide in S-O vibration area exhibited that stretching led to the breakage of the disulfide bonds. When the stretching ratio of Caucasian hair was more than a certain ratio, the fiber macromolecular structure was destroyed because Caucasian hair had finer diameter and less medulla than Asian hair. The β turn was easier to retract compared with other conformations, resulted in the content increase. The density measurements revealed that the structure of Caucasian hair was indeed more destroyed than that of Asian hair. The cuticles characterization indicated the length of scales was stretched longer and the thickness became thinner. Caucasian hair tended to collapse to form small fragments at the early stage of stretching. With the increase in stretching ratio, the scales of Caucasian hair lifted up, then flaked off and the scale interval increased accordingly. Asian hair was more easily peeled off than Caucasian hair cuticles with the increase in stretching ratio. The secondary structure of Caucasian hair was destroyed more easily than that of Asian hair. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. Peptide secondary structures in the gas phase: consensus motif of N-linked glycoproteins.

    Science.gov (United States)

    Cocinero, Emilio J; Stanca-Kaposta, E Cristina; Gamblin, David P; Davis, Benjamin G; Simons, John P

    2009-01-28

    The possibility of secondary structure acting as a primary determinant in nature's choice of the consensus sequon, NXS/T in all N-linked glycoproteins, has been addressed by determining the intrinsic secondary structures of the capped oligopeptide, Ac-NGS-NHBn, and two "mutants", Ac-QGS-NHBn and Ac-NPS-NHBn, by use of infrared laser ion dip spectroscopy in the gas phase coupled with ab initio and density functional theory calculation. Their global minimum energy conformations, exclusively or preferentially populated in all three peptides, display marked differences. NGS adopts an open, S-shaped backbone conformation rather than the C(10) "Asx" turn structure that all previous measurements have identified in solution; the difference can be related to the high dipole moment of the "Asx" conformation and structural selection in a polar environment. QGS adopts a similar but more rigid backbone structure, supported by markedly stronger hydrogen bonds. NPS adopts an Asx turn coupled with a C(10) beta-turn backbone conformation, a structure also adopted in a crystal environment. These and other more subtle structural differences, particularly those involving interactions with the carboxamide side chain, provide strong evidence for the operation of structural constraints, and a potential insight into the unique reactivity of the asparagine side chain toward enzymatic glycosylation.

  4. Reflection of the energy structure of a tungsten monocrystal nearsurface area in the secondary electron spectrum

    International Nuclear Information System (INIS)

    Artamonov, O.M.; Smirnov, O.M.; Terekhov, A.N.

    1982-01-01

    Formation of secondary electron energy spectrum during emission from the crystal layer near the surface has been considered, at that layer energy structure can be different from volumetric energy structure. Its thickness depends on the predominant mechanism of electron scattering and is determined by corresponding phenomenological parameters. It is shown that the structure in the secondary electron spectrum appears in the case when energy structure of emitting monocrystal layer can not be described in the approximation of almost free electron gas and, as experimental investigations show, approaches energy zone structure of its volume. It is also show that in the case when the energy structure of the emitting layer is satisfactorily described with the model of almost free electron gas, the SE spectrum is characterized with traditional cascade minimum. Experimental investigation of SE energy distribution was carried out for the W monocrystalline face (110). It was established that distinct structure in the SE spectrum appears only after electrochemical polishing of the specimen surface. It is related to the appearance of ''far'' order in the monocrystal emission layer on initially disturbed tungsten surface during such treatment. Disturbance of tungsten monocrystal surface structure on its oxidation in O 2 atmosphere results in the appearance of the cascade maximum and disappearance of distinct peculiarities in the SE spectrum

  5. Effects of LSP on micro-structures and residual stresses in a 4 mm CLAM steel weld joints

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Xizhang, E-mail: chenxizhang@wzu.edu.cn [School of Mechanical and Electrical Engineering, Wenzhou University., Wenzhou 325035 (China); School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu (China); Fang, Yuanyuan [School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu (China); Zhang, Shuyan; Kelleher, Joe F. [ISIS, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX (United Kingdom); Zhou, Jianzhong [School of Mechanical Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu (China)

    2015-05-15

    The effects of laser shock processing (LSP) on the distribution of residual stress and micro-structure of China Low Activation Martensitic (CLAM) steel weldment were investigated via neutron diffraction and optical microscope (OM). A pair of 4 mm CLAM steel plates joined by GTA welding. Special attention is paid to the generation of high level compressive residual stresses introduced by LSP. Residual stress in longitudinal, normal and transversal direction at weldment surface and longitudinal stress through thickness are evaluated via neutron diffraction. Compressive residual stress after LSP occurred at more than 90% areas within the weld joint, it is almost double the areas of compressive stress compare to weldment surface before LSP. The maximum compressive normal residual stress becomes to −183 MPa after LSP from −63 MPa before LSP. The Modification of surface micro-structures including weld zone (WZ), heat affected zone (HAZ) and base metal (BM) are also discussed. Results to date demonstrate that laser shock processing has been a great potential method for the improvement of mechanical performance of components.

  6. Effects of LSP on micro-structures and residual stresses in a 4 mm CLAM steel weld joints

    International Nuclear Information System (INIS)

    Chen, Xizhang; Fang, Yuanyuan; Zhang, Shuyan; Kelleher, Joe F.; Zhou, Jianzhong

    2015-01-01

    The effects of laser shock processing (LSP) on the distribution of residual stress and micro-structure of China Low Activation Martensitic (CLAM) steel weldment were investigated via neutron diffraction and optical microscope (OM). A pair of 4 mm CLAM steel plates joined by GTA welding. Special attention is paid to the generation of high level compressive residual stresses introduced by LSP. Residual stress in longitudinal, normal and transversal direction at weldment surface and longitudinal stress through thickness are evaluated via neutron diffraction. Compressive residual stress after LSP occurred at more than 90% areas within the weld joint, it is almost double the areas of compressive stress compare to weldment surface before LSP. The maximum compressive normal residual stress becomes to −183 MPa after LSP from −63 MPa before LSP. The Modification of surface micro-structures including weld zone (WZ), heat affected zone (HAZ) and base metal (BM) are also discussed. Results to date demonstrate that laser shock processing has been a great potential method for the improvement of mechanical performance of components

  7. A Dynamic Programming Algorithm for Finding the Optimal Placement of a Secondary Structure Topology in Cryo-EM Data.

    Science.gov (United States)

    Biswas, Abhishek; Ranjan, Desh; Zubair, Mohammad; He, Jing

    2015-09-01

    The determination of secondary structure topology is a critical step in deriving the atomic structures from the protein density maps obtained from electron cryomicroscopy technique. This step often relies on matching the secondary structure traces detected from the protein density map to the secondary structure sequence segments predicted from the amino acid sequence. Due to inaccuracies in both sources of information, a pool of possible secondary structure positions needs to be sampled. One way to approach the problem is to first derive a small number of possible topologies using existing matching algorithms, and then find the optimal placement for each possible topology. We present a dynamic programming method of Θ(Nq(2)h) to find the optimal placement for a secondary structure topology. We show that our algorithm requires significantly less computational time than the brute force method that is in the order of Θ(q(N) h).

  8. A contribution to understanding the structure of amphivasal secondary bundles in monocotyledons

    Directory of Open Access Journals (Sweden)

    Joanna Jura-Morawiec

    2014-04-01

    Full Text Available Secondary growth of monocotyledonous plants is connected with the activity of the monocot cambium that accumulates most of the derivatives inner to the cambial cylinder. These derivatives differentiate into (a secondary bundles with the amphivasal arrangement, i.e. xylem composed of tracheids surrounds the phloem cells and (b the parenchymatous secondary conjunctive tissue in which the bundles are embedded. The amphivasal secondary bundles differ in the arrangement of xylem cells as visible on single cross sections through the secondary body of the monocots. Apart from the bundles with typical ring of tracheids also the bundles where tracheids do not quite surround the phloem are present. We aimed to elucidate the cross sectional anatomy of the amphivasal secondary bundles with the use of the serial sectioning method which allowed us to follow very precisely the bundle structure along its length. The studies were carried out with the samples of secondary tissues collected from the stem of Dracaena draco L. growing in the greenhouses of the Polish Academy of Sciences Botanical Garden – CBDC in Powsin and the Adam Mickiewicz University Botanical Garden. The material was fixed in a mixture of glycerol and ethanol (1:1; v/v, dehydrated stepwise with graded ethanol series and finally embedded in epon resin. Afterwards, the material was sectioned with microtome into continuous series of thin (3 μm sections, stained with PAS/toluidine blue and examined under the light microscope. The results, described in details in Jura‑Morawiec & Wiland-Szymańska (2014, revealed novel facts about tracheids arrangement. Each amphivasal bundle is composed of sectors where tracheids form a ring as well as of such where tracheids are separated by vascular parenchyma cells. We hypothesize that strands of vascular parenchyma cells locally separating the tracheids enable radial transport of assimilates from sieve elements of the bundle towards the sink tissues, e

  9. Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases.

    Directory of Open Access Journals (Sweden)

    Takuji Oyama

    Full Text Available CpMan5B is a glycoside hydrolase (GH family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196 in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.

  10. Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases.

    Science.gov (United States)

    Oyama, Takuji; Schmitz, George E; Dodd, Dylan; Han, Yejun; Burnett, Alanna; Nagasawa, Naoko; Mackie, Roderick I; Nakamura, Haruki; Morikawa, Kosuke; Cann, Isaac

    2013-01-01

    CpMan5B is a glycoside hydrolase (GH) family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196) in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.

  11. A molecular thermodynamic approach to predict the secondary structure of homopolypeptides in aqueous systems.

    Science.gov (United States)

    Chen, C C; Zhu, Y; King, J A; Evans, L B

    1992-10-01

    Under physiological conditions, many polypeptide chains spontaneously fold into discrete and tightly packed three-dimensional structures. The folded polypeptide chain conformation is believed to represent a minimum Gibbs energy of the system, governed by the weak interactions that operate between the amino acid residues and between the residues and the solvent. A semiempirical molecular thermodynamic model is proposed to represent the Gibbs energy of folding of aqueous homopolypeptide systems. The model takes into consideration both the entropy contribution and the enthalpy contribution of folding homopolypeptide chains in aqueous solutions. The entropy contribution is derived from the Flory-Huggins expression for the entropy of mixing. It accounts for the entropy loss in folding a random-coiled polypeptide chain into a specific polypeptide conformation. The enthalpy contribution is derived from a molecular segment-based Non-Random Two Liquid (NRTL) local composition model [H. Renon and J. M. Prausnitz (1968) AIChE J., Vol. 14, pp. 135-142; C.-C. Chen and L. B. Evans (1986) AIChE J., Vol. 32, pp. 444-454], which takes into consideration of the residue-residue, residue-solvent, and solvent-solvent binary physical interactions along with the local compositions of amino acid residues in aqueous homopolypeptides. The UNIFAC group contribution method [A. Fredenslund, R. L. Jones, and J. M. Prausnitz (1975) AIChE J., 21, 1086-1099; A. Fredenslund, J. Gmehling, and P. Rasmussen (1977) Vapor-Liquid Equilibrium Using UNIFAC, Elsevier Scientific Publishing Company, Amsterdam], developed originally to estimate the excess Gibbs energy of solutions of small molecules, was used to estimate the NRTL binary interaction parameters. The model yields a hydrophobicity scale for the 20 amino acid side chains, which compares favorably with established scales [Y. Nozaki and C. Tanford (1971) Journal of Biological Chemistry, Vol. 46, pp. 2211-2217; E. B. Leodidis and T. A. Hatton (1990

  12. HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information

    Directory of Open Access Journals (Sweden)

    Hu Jianjun

    2011-05-01

    Full Text Available Abstract Background Accurate prediction of binding residues involved in the interactions between proteins and small ligands is one of the major challenges in structural bioinformatics. Heme is an essential and commonly used ligand that plays critical roles in electron transfer, catalysis, signal transduction and gene expression. Although much effort has been devoted to the development of various generic algorithms for ligand binding site prediction over the last decade, no algorithm has been specifically designed to complement experimental techniques for identification of heme binding residues. Consequently, an urgent need is to develop a computational method for recognizing these important residues. Results Here we introduced an efficient algorithm HemeBIND for predicting heme binding residues by integrating structural and sequence information. We systematically investigated the characteristics of binding interfaces based on a non-redundant dataset of heme-protein complexes. It was found that several sequence and structural attributes such as evolutionary conservation, solvent accessibility, depth and protrusion clearly illustrate the differences between heme binding and non-binding residues. These features can then be separately used or combined to build the structure-based classifiers using support vector machine (SVM. The results showed that the information contained in these features is largely complementary and their combination achieved the best performance. To further improve the performance, an attempt has been made to develop a post-processing procedure to reduce the number of false positives. In addition, we built a sequence-based classifier based on SVM and sequence profile as an alternative when only sequence information can be used. Finally, we employed a voting method to combine the outputs of structure-based and sequence-based classifiers, which demonstrated remarkably better performance than the individual classifier alone

  13. Substrate specificity determinants of the methanogen homoaconitase enzyme: structure and function of small subunit residues

    Energy Technology Data Exchange (ETDEWEB)

    Jeyakanthan, Jeyaraman [National Synchrotron Radiation Research Center; Drevland, Randy [University of Texas, Austin; Gayathri, Dasara [University of Madras; Velmurugan, Devadasan [University of Madras; Shinkai, Akeo [SPring8/JASRI, Mikazuki, Hyogo and RIKEN, Japan; Kuramitsu, Seiki [SPring8/JASRI, Mikazuki, Hyogo and RIKEN, Japan; Yokoyama, Shigeyuki [University of Tokyo, Tokyo, Japan; Graham, David E [ORNL

    2010-01-01

    The aconitase family of hydro-lyase enzymes includes three classes of proteins that catalyze the isomerization of -hydroxyacids to -hydroxyacids. Besides aconitase, isopropylmalate isomerase (IPMI) proteins specifically catalyze the isomerization of , -dicarboxylates with hydrophobic -chain groups, and homoaconitase (HACN) proteins catalyze the isomerization of tricarboxylates with variable chain length -carboxylate groups. These enzymes stereospecific hydro-lyase activities make them attractive catalysts to produce diastereomers from unsaturated precursors. However, sequence similarity and convergent evolution among these proteins leads to widespread misannotation and uncertainty about gene function. To find the substrate specificity determinants of homologous IPMI and HACN proteins from Methanocaldococcus jannaschii, the small-subunit HACN protein (MJ1271) was crystallized for X-ray diffraction. The structural model showed characteristic residues in a flexible loop region between 2 and 3 that distinguish HACN from IPMI and aconitase proteins. Site-directed mutagenesis of MJ1271 produced loop-region variant proteins that were reconstituted with wild-type MJ1003 large-subunit protein. The heteromers formed promiscuous hydro-lyases with reduced activity but broader substrate specificity. Both R26K and R26V variants formed relatively efficient IPMI enzymes, while the T27A variant had uniformly lower specificity constants for both IPMI and HACN substrates. The R26V T27Y variant resembles the MJ1277 IPMI small subunit in its flexible loop sequence, but demonstrated the broad substrate specificity of the R26V variant. These mutations may reverse the evolution of HACN activity from an ancestral IPMI gene, demonstrating the evolutionary potential for promiscuity in hydro-lyase enzymes. Understanding these specificity determinants enables the functional reannotation of paralogous HACN and IPMI genes in numerous genome sequences. These structural and kinetic results will

  14. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.

    Science.gov (United States)

    Mathews, D H; Sabina, J; Zuker, M; Turner, D H

    1999-05-21

    An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization. Thermodynamic parameters for the stabilities of secondary structure motifs are revised to include expanded sequence dependence as revealed by recent experiments. Additional algorithmic improvements include reduced search time and storage for multibranch loop free energies and improved imposition of folding constraints. An extended database of 151,503 nt in 955 structures? determined by comparative sequence analysis was assembled to allow optimization of parameters not based on experiments and to test the accuracy of the algorithm. On average, the predicted lowest free energy structure contains 73 % of known base-pairs when domains of fewer than 700 nt are folded; this compares with 64 % accuracy for previous versions of the algorithm and parameters. For a given sequence, a set of 750 generated structures contains one structure that, on average, has 86 % of known base-pairs. Experimental constraints, derived from enzymatic and flavin mononucleotide cleavage, improve the accuracy of structure predictions. Copyright 1999 Academic Press.

  15. TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

    Directory of Open Access Journals (Sweden)

    Sharma Gaurav

    2011-04-01

    Full Text Available Abstract Background The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence. The most accurate computational methods predict conserved structures for a set of homologous RNA sequences. These methods usually suffer from high computational complexity. In this paper, TurboFold, a novel and efficient method for secondary structure prediction for multiple RNA sequences, is presented. Results TurboFold takes, as input, a set of homologous RNA sequences and outputs estimates of the base pairing probabilities for each sequence. The base pairing probabilities for a sequence are estimated by combining intrinsic information, derived from the sequence itself via the nearest neighbor thermodynamic model, with extrinsic information, derived from the other sequences in the input set. For a given sequence, the extrinsic information is computed by using pairwise-sequence-alignment-based probabilities for co-incidence with each of the other sequences, along with estimated base pairing probabilities, from the previous iteration, for the other sequences. The extrinsic information is introduced as free energy modifications for base pairing in a partition function computation based on the nearest neighbor thermodynamic model. This process yields updated estimates of base pairing probability. The updated base pairing probabilities in turn are used to recompute extrinsic information, resulting in the overall iterative estimation procedure that defines TurboFold. TurboFold is benchmarked on a number of ncRNA datasets and compared against alternative secondary structure prediction methods. The iterative procedure in TurboFold is shown to improve estimates of base pairing probability with each iteration, though only small gains are obtained beyond three iterations. Secondary structures composed of base pairs with estimated probabilities higher than a

  16. Residual stresses and structural integrity in nuclear structural materials: recent developments and results from neutron and synchrotron x-ray diffraction experiments

    International Nuclear Information System (INIS)

    Steuwer, A.; Daniels, JE

    2008-01-01

    Over the last few years, significant progress has been made in the investigation of residual stresses over a variety of length scales in nuclear structural materials, ranging from stainless steels to hydrided zirconium alloys. In this manuscript we review some of these developments, such as, in-situ characterization of stresses at crack tips in steels and zirconium alloys, residual stresses around welds, and the characterization of hydrided zirconium alloys. Neutron and synchrotron X-ray diffraction are essential and complementary tools in this approach, and their applicability to structural integrity issues is discussed in view of existing and future large-scale research facilities. (au)

  17. Morphogenic and structural traits of Brachiaria brizantha cv. Marandu under different nitrogen levels and residues heights

    Directory of Open Access Journals (Sweden)

    Eleuza Clarete Junqueira de Sales

    2014-10-01

    Full Text Available The objective of this study was to evaluate the rate of leaf appearance, leaf elongation rate, number of green leaves, length of blade and stem of Brachiaria brizantha cv. Marandu under different nitrogen levels and two residue heights. A randomized block design was used in a 4 x 2 factorial scheme, four doses of nitrogen (100, 200, 300 and 400 kg N ha-1 year-1 and two residue heights (5 and 15 cm. There was significant interaction between residue height and nitrogen levels for leaf appearance rate (P> 0.05 of signal grass, which was influenced negatively and linearly (P 0.05 between the levels of nitrogen x residue height on the number of green leaves. The dosage that provided the highest stalk in the residue height of 5 cm was of 271.5 kg N ha -1. An increase of 0.0745 cm tiller -1 day-1 for 1 kg of N ha -1 applied to height of 15 cm of residue was observed. Nitrogen fertilization contributes positively to growth and development of rates of appearance and leaf extension. The management of pasture of Brachiaria brizantha cv. Marandu with 5 cm of residue and fertilization with 100 kg N ha -1 provided better answer morphogenic traits.

  18. Molecular characterization of pouched amphistome parasites (Trematoda: Gastrothylacidae) using ribosomal ITS2 sequence and secondary structures.

    Science.gov (United States)

    Ghatani, S; Shylla, J A; Tandon, V; Chatterjee, A; Roy, B

    2012-03-01

    Members of the family Gastrothylacidae (Trematoda: Digenea: Paramphistomata) are parasitic in ruminants throughout Africa and Asia. In north-east India, five species of pouched amphistomes, namely Fischoederius cobboldi, F. elongatus, Gastrothylax crumenifer, Carmyerius spatiosus and Velasquezotrema tripurensis, belonging to this family have been reported so far. In the present study, the molecular phylogeny of these five gastrothylacid species is derived using the second internal transcribed spacer (ITS2) sequence and secondary structure analyses. ITS2 sequence analysis was carried out to see the occurrence of interspecific variations among the species. Phylogenetic analyses were performed for primary sequence data alone as well as the combined sequence-structure information using neighbour-joining and Bayesian approaches. The sequence analysis revealed that there exist considerable interspecific variations among the various gastrothylacid fluke species. In contrast, the inferred secondary structures for the five species using minimum free energy modelling showed structural identities, in conformity with the core four-helix domain structure that has been recently identified as common to almost all eukaryotic taxa. The phylogenetic tree reconstructed using combined sequence-structure data showed a better resolution, as compared to the one using sequence data alone, with the gastrothylacid species forming a monophyletic group that is well separated from members of the other family, Paramphistomidae, of the amphistomid flukes group. The study provides the molecular characterization based on primary sequence data of the rDNA ITS2 region of the gastrothylacid amphistome flukes. Results also demonstrate the phylogenetic utility of the ITS2 sequence-secondary structure data for inferences at higher taxonomic levels.

  19. RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.

    Science.gov (United States)

    Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

    2012-01-01

    RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. http://www.cemb.edu.pk/sw.html RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.

  20. Correlation between protein secondary structure, backbone bond angles, and side-chain orientations

    Science.gov (United States)

    Lundgren, Martin; Niemi, Antti J.

    2012-08-01

    We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central Cα carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the Cβ carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the Cα-Cβ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.

  1. An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences

    Czech Academy of Sciences Publication Activity Database

    Pánek, Josef; Modrák, Martin; Schwarz, Marek

    2017-01-01

    Roč. 8, OCT 10 (2017), s. 1-11, č. článku 147. ISSN 1664-8021 R&D Projects: GA ČR GA15-00885S; GA MŠk(CZ) LM2015047 Institutional support: RVO:61388971 Keywords : RNA * secondary structure * homology Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 3.789, year: 2016

  2. CentroidFold: a web server for RNA secondary structure prediction

    OpenAIRE

    Sato, Kengo; Hamada, Michiaki; Asai, Kiyoshi; Mituyama, Toutai

    2009-01-01

    The CentroidFold web server (http://www.ncrna.org/centroidfold/) is a web application for RNA secondary structure prediction powered by one of the most accurate prediction engine. The server accepts two kinds of sequence data: a single RNA sequence and a multiple alignment of RNA sequences. It responses with a prediction result shown as a popular base-pair notation and a graph representation. PDF version of the graph representation is also available. For a multiple alignment sequence, the ser...

  3. A generalized threading model using integer programming that allows for secondary structure element deletion.

    Science.gov (United States)

    Ellrott, Kyle; Guo, Jun-tao; Olman, Victor; Xu, Ying

    2006-01-01

    Integer programming is a combinatorial optimization method that has been successfully applied to the protein threading problem. We seek to expand the model optimized by this technique to allow for a more accurate description of protein threading. We have developed and implemented an expanded model of integer programming that has the capability to model secondary structure element deletion, which was not possible in previous version of integer programming based optimization.

  4. SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

    Science.gov (United States)

    Tong, Jing; Pei, Jimin; Grishin, Nick V

    2015-09-03

    Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

  5. Model based fault detection and diagnosis using structured residual approach in a multi-input multi-output system

    Directory of Open Access Journals (Sweden)

    Asokan A.

    2007-01-01

    Full Text Available Fault detection and isolation (FDI is a task to deduce from observed variable of the system if any component is faulty, to locate the faulty components and also to estimate the fault magnitude present in the system. This paper provides a systematic method of fault diagnosis to detect leak in the three-tank process. The proposed scheme makes use of structured residual approach for detection, isolation and estimation of faults acting on the process [1]. This technique includes residual generation and residual evaluation. A literature review showed that the conventional fault diagnosis methods like the ordinary Chisquare (ψ2 test method, generalized likelihood ratio test have limitations such as the "false alarm" problem. From the results it is inferred that the proposed FDI scheme diagnoses better when compared to other conventional methods.

  6. Analysis of residual stress in the resin of metal-resin adhesion structures by scanning acoustic microscopy.

    Science.gov (United States)

    Ohno, Hiroki; Endo, Kazuhiko; Nagano-Takebe, Futami; Ida, Yusuke; Kakino, Ken; Narita, Toshio

    2013-01-01

    The residual stress caused by polymerization shrinkage and thermal contraction of a heat-curing resin containing 4-META on a metal-resin structure was measured by a scanning acoustic microscope. The tensile residual stress in the resin occurred within 70 µm of the adhesion interface with a flat plate specimen. The maximum tensile stress was about 58 MPa at the interface. On a metal plate specimen with retention holes, ring-like cracks in the resin occurred around the retention holes with the adhesive specimen and many linear cracks occurred in the resin vertical to the longitudinal direction of the metal frame with the non-adhesive specimens. There was tensile residual stress on the resin surface at the center of the retention holes of the adhesion specimen, indicating that the stress in the specimen with surface treatment for adhesion was higher than in that without surface treatment.

  7. Two distinct 18S rRNA secondary structures in Dipodascus (Hemiascomycetes).

    Science.gov (United States)

    Ueda-Nishimura, K; Mikata, K

    2000-05-01

    The nucleotide sequences of the 18S rRNA gene from ascomycetous yeast-like fungi in the genera Dipodascus, Galactomyces and Geotrichum were determined and the tested strains were separated into two groups by sequence length. In group 1, the length and secondary structure of 18S rRNA corresponded to those of typical eukaryotes. In group 2, the 18S rRNA gene sequences were about 150 nt shorter than those of most other eukaryotes and the predicted secondary structure lacked helices 10 and E21-5. Many substitutions and some deletions in group 2 18S rRNA gene were not only found in variable regions, but also in regions that are highly conserved among ascomycetes. Despite the considerable differences in 18S rRNA gene sequence and secondary structure between group 2 and other fungi, including group 1, phylogenetic analysis revealed that groups 1 and 2 are closely related. These findings suggest that a number of deletions occurred in the 18S rRNA of the common ancestor of group 2 strains.

  8. CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction applications.

    Science.gov (United States)

    Lei, Guoqing; Dou, Yong; Wan, Wen; Xia, Fei; Li, Rongchun; Ma, Meng; Zou, Dan

    2012-01-01

    Prediction of ribonucleic acid (RNA) secondary structure remains one of the most important research areas in bioinformatics. The Zuker algorithm is one of the most popular methods of free energy minimization for RNA secondary structure prediction. Thus far, few studies have been reported on the acceleration of the Zuker algorithm on general-purpose processors or on extra accelerators such as Field Programmable Gate-Array (FPGA) and Graphics Processing Units (GPU). To the best of our knowledge, no implementation combines both CPU and extra accelerators, such as GPUs, to accelerate the Zuker algorithm applications. In this paper, a CPU-GPU hybrid computing system that accelerates Zuker algorithm applications for RNA secondary structure prediction is proposed. The computing tasks are allocated between CPU and GPU for parallel cooperate execution. Performance differences between the CPU and the GPU in the task-allocation scheme are considered to obtain workload balance. To improve the hybrid system performance, the Zuker algorithm is optimally implemented with special methods for CPU and GPU architecture. Speedup of 15.93× over optimized multi-core SIMD CPU implementation and performance advantage of 16% over optimized GPU implementation are shown in the experimental results. More than 14% of the sequences are executed on CPU in the hybrid system. The system combining CPU and GPU to accelerate the Zuker algorithm is proven to be promising and can be applied to other bioinformatics applications.

  9. CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction applications

    Science.gov (United States)

    2012-01-01

    Background Prediction of ribonucleic acid (RNA) secondary structure remains one of the most important research areas in bioinformatics. The Zuker algorithm is one of the most popular methods of free energy minimization for RNA secondary structure prediction. Thus far, few studies have been reported on the acceleration of the Zuker algorithm on general-purpose processors or on extra accelerators such as Field Programmable Gate-Array (FPGA) and Graphics Processing Units (GPU). To the best of our knowledge, no implementation combines both CPU and extra accelerators, such as GPUs, to accelerate the Zuker algorithm applications. Results In this paper, a CPU-GPU hybrid computing system that accelerates Zuker algorithm applications for RNA secondary structure prediction is proposed. The computing tasks are allocated between CPU and GPU for parallel cooperate execution. Performance differences between the CPU and the GPU in the task-allocation scheme are considered to obtain workload balance. To improve the hybrid system performance, the Zuker algorithm is optimally implemented with special methods for CPU and GPU architecture. Conclusions Speedup of 15.93× over optimized multi-core SIMD CPU implementation and performance advantage of 16% over optimized GPU implementation are shown in the experimental results. More than 14% of the sequences are executed on CPU in the hybrid system. The system combining CPU and GPU to accelerate the Zuker algorithm is proven to be promising and can be applied to other bioinformatics applications. PMID:22369626

  10. Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade

    Science.gov (United States)

    Samanta, Sudipta; Mukherjee, Sanchita

    2018-01-01

    The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.

  11. Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade.

    Science.gov (United States)

    Samanta, Sudipta; Mukherjee, Sanchita

    2018-01-28

    The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.

  12. Topology-dependent swichability of peptide secondary structures in bioconjugates with complex architectures.

    Science.gov (United States)

    Börner, Hans G; Sütterlin, Romina I; Theato, Patrick; Wiss, Kerstin T

    2014-01-01

    Peptide sequences, which exhibit a reversible pH-responsive coil to α-helix secondary structure transition, are conjugated to polymer precursors to yield linear AB and graft ABA peptide-poly(ethylene oxide) conjugates. While the PEO B-block is comparable, the conjugates differ in topologies of the peptide bearing A-blocks. The influences of topology on the structure transitions in the peptide segments are investigated, comparing linear AB-bioconjugates with graft ABA-bioconjugates having multiple peptide segments combined in star or pom-pom topologies. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Exploiting the Past and the Future in Protein Secondary Structure Prediction

    DEFF Research Database (Denmark)

    Baldi, Pierre; Brunak, Søren; Frasconi, P

    1999-01-01

    predictions based on variable ranges of dependencies. These architectures extend recurrent neural networks, introducing non-causal bidirectional dynamics to capture both upstream and downstream information. The prediction algorithm is completed by the use of mixtures of estimators that leverage evolutionary......Motivation: Predicting the secondary structure of a protein (alpha-helix, beta-sheet, coil) is an important step towards elucidating its three-dimensional structure, as well as its function. Presently, the best predictors are based on machine learning approaches, in particular neural network...

  14. Secondary structure and domain architecture of the 23S and 5S rRNAs.

    Science.gov (United States)

    Petrov, Anton S; Bernier, Chad R; Hershkovits, Eli; Xue, Yuzhen; Waterbury, Chris C; Hsiao, Chiaolong; Stepanov, Victor G; Gaucher, Eric A; Grover, Martha A; Harvey, Stephen C; Hud, Nicholas V; Wartell, Roger M; Fox, George E; Williams, Loren Dean

    2013-08-01

    We present a de novo re-determination of the secondary (2°) structure and domain architecture of the 23S and 5S rRNAs, using 3D structures, determined by X-ray diffraction, as input. In the traditional 2° structure, the center of the 23S rRNA is an extended single strand, which in 3D is seen to be compact and double helical. Accurately assigning nucleotides to helices compels a revision of the 23S rRNA 2° structure. Unlike the traditional 2° structure, the revised 2° structure of the 23S rRNA shows architectural similarity with the 16S rRNA. The revised 2° structure also reveals a clear relationship with the 3D structure and is generalizable to rRNAs of other species from all three domains of life. The 2° structure revision required us to reconsider the domain architecture. We partitioned the 23S rRNA into domains through analysis of molecular interactions, calculations of 2D folding propensities and compactness. The best domain model for the 23S rRNA contains seven domains, not six as previously ascribed. Domain 0 forms the core of the 23S rRNA, to which the other six domains are rooted. Editable 2° structures mapped with various data are provided (http://apollo.chemistry.gatech.edu/RibosomeGallery).

  15. Secondary structure and domain architecture of the 23S and 5S rRNAs

    Science.gov (United States)

    Petrov, Anton S.; Bernier, Chad R.; Hershkovits, Eli; Xue, Yuzhen; Waterbury, Chris C.; Hsiao, Chiaolong; Stepanov, Victor G.; Gaucher, Eric A.; Grover, Martha A.; Harvey, Stephen C.; Hud, Nicholas V.; Wartell, Roger M.; Fox, George E.; Williams, Loren Dean

    2013-01-01

    We present a de novo re-determination of the secondary (2°) structure and domain architecture of the 23S and 5S rRNAs, using 3D structures, determined by X-ray diffraction, as input. In the traditional 2° structure, the center of the 23S rRNA is an extended single strand, which in 3D is seen to be compact and double helical. Accurately assigning nucleotides to helices compels a revision of the 23S rRNA 2° structure. Unlike the traditional 2° structure, the revised 2° structure of the 23S rRNA shows architectural similarity with the 16S rRNA. The revised 2° structure also reveals a clear relationship with the 3D structure and is generalizable to rRNAs of other species from all three domains of life. The 2° structure revision required us to reconsider the domain architecture. We partitioned the 23S rRNA into domains through analysis of molecular interactions, calculations of 2D folding propensities and compactness. The best domain model for the 23S rRNA contains seven domains, not six as previously ascribed. Domain 0 forms the core of the 23S rRNA, to which the other six domains are rooted. Editable 2° structures mapped with various data are provided (http://apollo.chemistry.gatech.edu/RibosomeGallery). PMID:23771137

  16. Influence of Finite Element Size in Residual Strength Prediction of Composite Structures

    Science.gov (United States)

    Satyanarayana, Arunkumar; Bogert, Philip B.; Karayev, Kazbek Z.; Nordman, Paul S.; Razi, Hamid

    2012-01-01

    The sensitivity of failure load to the element size used in a progressive failure analysis (PFA) of carbon composite center notched laminates is evaluated. The sensitivity study employs a PFA methodology previously developed by the authors consisting of Hashin-Rotem intra-laminar fiber and matrix failure criteria and a complete stress degradation scheme for damage simulation. The approach is implemented with a user defined subroutine in the ABAQUS/Explicit finite element package. The effect of element size near the notch tips on residual strength predictions was assessed for a brittle failure mode with a parametric study that included three laminates of varying material system, thickness and stacking sequence. The study resulted in the selection of an element size of 0.09 in. X 0.09 in., which was later used for predicting crack paths and failure loads in sandwich panels and monolithic laminated panels. Comparison of predicted crack paths and failure loads for these panels agreed well with experimental observations. Additionally, the element size vs. normalized failure load relationship, determined in the parametric study, was used to evaluate strength-scaling factors for three different element sizes. The failure loads predicted with all three element sizes provided converged failure loads with respect to that corresponding with the 0.09 in. X 0.09 in. element size. Though preliminary in nature, the strength-scaling concept has the potential to greatly reduce the computational time required for PFA and can enable the analysis of large scale structural components where failure is dominated by fiber failure in tension.

  17. Analysis of the in vitro secondary structure of cucumber mosaic virus satellite RNA.

    Science.gov (United States)

    Bernal, J J; García-Arenal, F

    1997-01-01

    The solution conformation of two variants of cucumber mosaic virus satellite RNA (CMV satRNA) was analyzed using several enzymatic and chemical probes. Ribonuclease T1 and nuclease S1 were used to map unpaired nucleotides, and nuclease V1 was used to detect double-stranded, or stacked, bases. Chemical probing with dimethylsulphate and diethylpyrocarbonate also identified unpaired and unstacked nucleotides, respectively. Modified or cleaved positions were identified by direct gel electrophoresis of radioactively labeled RNA, or by analysis of DNA sequence patterns generated by primer-extension with reverse transcriptase. Additional information was obtained by a gel-fractionation method under nondenaturing conditions for the identification of base paired fragments. On these data, a model for the in vitro secondary structure of CMV satRNA is proposed. Results support the existence of a complex structure with 51% of nucleotides involved in base pairs (40 G:C, 28 G:U, and 18 A:U pairs). Several structural elements, numbered I-VI, were defined, and interactions between separate domains are suggested. Comparisons of experimental data and a formerly reported secondary structure model for CMV satRNA support the validity of the structure we propose. PMID:9292503

  18. Preferential melting of secondary structures during protein unfolding in different solvents: Competition between hydrophobic solvation and hydrogen bonding

    Science.gov (United States)

    Bagchi, Biman; Roy, Susmita; Ghosh, Rikhia

    2014-03-01

    Aqueous binary mixtures such as water-DMSO, water-urea, and water-ethanol are known to serve as denaturants of a host of proteins, although the detailed mechanism is often not known. Here we combine studies on several proteins in multiple binary mixtures to obtain a unified understanding of the phenomenon. We compare with experiments to support the simulation findings. The proteins considered include (i) chicken villin head piece (HP-36), (ii) immunoglobulin binding protein G (GB1), (iii) myoglobin and (iv) lysozyme. We find that for amphiphilic solvents like DMSO, the hydrophobic groups and the strong hydrogen bonding ability of the >S =O oxygen atom act together to facilitate the unfolding. However, the hydrophilic solvents like urea, due to the presence of more hydrophilic ends (C =O and two NH2) has a high propensity of forming hydrogen bonds with the side-chain residues and backbone of beta-sheet than the same of alpha helix. Such diversity among the unfolding pathways of a given protein in different chemical environments is especially characterized by the preferential solvation of a particular secondary structure.

  19. Cadmium and Secondary Structure-dependent Function of a Degron in the Pca1p Cadmium Exporter*

    Science.gov (United States)

    Smith, Nathan; Wei, Wenzhong; Zhao, Miaoyun; Qin, Xiaojuan; Seravalli, Javier; Kim, Heejeong; Lee, Jaekwon

    2016-01-01

    Protein turnover is a critical cellular process regulating biochemical pathways and destroying terminally misfolded or damaged proteins. Pca1p, a cadmium exporter in the yeast Saccharomyces cerevisiae, is rapidly degraded by the endoplasmic reticulum-associated degradation (ERAD) system via a cis-acting degron that exists at the 250–350 amino acid region of Pca1p and is transferable to other proteins to serve as a degradation signal. Cadmium stabilizes Pca1p in a manner dependent on the degron. This suggested that cadmium-mediated masking of the degron impedes its interaction with the molecular factors involved in the ERAD. The characteristics and mechanisms of action of the degron in Pca1p and most of those in other proteins however remain to be determined. The results presented here indicate that specific cysteine residues in a degron of Pca1p sense cadmium. An unbiased approach selecting non-functional degrons indicated a critical role of hydrophobic amino acids in the degron for its function. A secondary structure modeling predicted the formation of an amphipathic helix. Site-directed mutagenesis confirmed the functional significance of the hydrophobic patch. Last, hydrophobic amino acids in the degron- and cadmium-binding region affected the interaction of Pca1p with the Ssa1p molecular chaperone, which is involved in ERAD. These results reveal the mechanism of action of the degron, which might be useful for the identification and characterization of other degrons. PMID:27059957

  20. 1H, 13C and 15N resonance assignments and secondary structure analysis of CmPI-II, a serine protease inhibitor isolated from marine snail Cenchritis muricatus.

    Science.gov (United States)

    Cabrera-Muñoz, Aymara; Rojas, Laritza; Alonso-del-Rivero Antigua, Maday; Pires, José Ricardo

    2016-04-01

    A protease inhibitor (CmPI-II) (UNIPROT: IPK2_CENMR) from the marine mollusc Cenchritis muricatus, has been isolated and characterized. It is the first member of a new group (group 3) of non-classical Kazal-type inhibitors. CmPI-II is a tight-binding inhibitor of serine proteases: trypsin, human neutrophil elastase (HNE), subtilisin A and pancreatic elastase. This specificity is exceptional in the members of Kazal-type inhibitor family. Several models of three-dimensional structure of CmPI-II have been constructed by homology with other inhibitors of the family but its structure has not yet been solved experimentally. Here we report the (1)H, (15)N and (13)C chemical shift assignments of CmPI-II as basis for NMR structure determination and interaction studies. Secondary structure analyses deduced from the NMR chemical shift data have identified three β-strands β1: residues 14-19, β2: 23-35 and β3: 43-45 and one helix α1: 28-37 arranged in the sequential order β1-β2-α1-β3. These secondary structure elements suggest that CmPI-II adopts the typical scaffold of a Kazal-type inhibitor.

  1. Secbase: database module to retrieve secondary structure elements with ligand binding motifs.

    Science.gov (United States)

    Koch, Oliver; Cole, Jason; Block, Peter; Klebe, Gerhard

    2009-10-01

    Secbase is presented as a novel extension module of Relibase. It integrates the information about secondary structure elements into the retrieval facilities of Relibase. The data are accessible via the extended Relibase user interface, and integrated retrieval queries can be addressed using an extended version of Reliscript. The primary information about alpha-helices and beta-sheets is used as provided by the PDB. Furthermore, a uniform classification of all turn families, based on recent clustering methods, and a new helix assignment that is based on this turn classification has been included. Algorithms to analyze the geometric features of helices and beta-strands were also implemented. To demonstrate the performance of the Secbase implementation, some application examples are given. They provide new insights into the involvement of secondary structure elements in ligand binding. A survey of water molecules detected next to the N-terminus of helices is analyzed to show their involvement in ligand binding. Additionally, the parallel oriented NH groups at the alpha-helix N-termini provide special binding motifs to bind particular ligand functional groups with two adjacent oxygen atoms, e.g., as found in negatively charged carboxylate or phosphate groups, respectively. The present study also shows that the specific structure of the first turn of alpha-helices provides a suitable explanation for stabilizing charged structures. The magnitude of the overall helix macrodipole seems to have no or only a minor influence on binding. Furthermore, an overview of the involvement of secondary structure elements with the recognition of some important endogenous ligands such as cofactors shows some distinct preference for particular binding motifs and amino acids.

  2. Teaching the foundations of quantum mechanics in secondary school: a proposed conceptual structure

    Directory of Open Access Journals (Sweden)

    Maria de los Angeles Fanaro

    2009-03-01

    Full Text Available This paper is part of a doctoral thesis that investigates Basic Quantum Mechanics (QM teaching in high school. A Conceptual Structure of Reference (CSR based on the Path Integral Method of Feynman (1965 was rebuilt and a Proposed Conceptual Structure for Teaching (PCST (Otero, 2006, 2007 the basics of Quantum Mechanics at secondary school was designed, analysed and carried out. This PCST does not follow the historical route and it is complementary to the canonical formalism. The concepts: probability distribution, quantum system, x(t alternative, amplitude of probability, sum of probability amplitude, action, Planck's constant, and classic-quantum transition were rebuilt with the students. Mathematical formalism was avoided by using simulation software assistance. The Proposed Conceptual Structure for Teaching (PCST is described and some results from the test carried out by the class group are discussed. This information allows the analysis of the Conceptual Structure Effectively Reconstructed (CSER to be initiated with the students.

  3. Application of data mining tools for classification of protein structural class from residue based averaged NMR chemical shifts.

    Science.gov (United States)

    Kumar, Arun V; Ali, Rehana F M; Cao, Yu; Krishnan, V V

    2015-10-01

    The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is necessary to develop new computational methods and tools for protein structural information that is directly related to function. Nuclear magnetic resonance (NMR) provides powerful means to determine three-dimensional structures of proteins in the solution state. However, translation of the NMR spectral parameters to even low-resolution structural information such as protein class requires multiple time consuming steps. In this paper, we present an unorthodox method to predict the protein structural class directly by using the residue's averaged chemical shifts (ACS) based on machine learning algorithms. Experimental chemical shift information from 1491 proteins obtained from Biological Magnetic Resonance Bank (BMRB) and their respective protein structural classes derived from structural classification of proteins (SCOP) were used to construct a data set with 119 attributes and 5 different classes. Twenty four different classification schemes were evaluated using several performance measures. Overall the residue based ACS values can predict the protein structural classes with 80% accuracy measured by Matthew correlation coefficient. Specifically protein classes defined by mixed αβ or small proteins are classified with >90% correlation. Our results indicate that this NMR-based method can be utilized as a low-resolution tool for protein structural class identification without any prior chemical shift assignments. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Resonance assignment and secondary structure determination and stability of the recombinant human uteroglobin with heteronuclear multidimensional NMR

    Energy Technology Data Exchange (ETDEWEB)

    Carlomagno, Teresa [University of Naples ' Federico II' , Department of Chemistry (Italy); Mantile, Giuditta [Section on Developmental Genetics, Heritable Disorders Branch (United States); Bazzo, Renzo [IRBM P. Angeletti, Spa. (Italy); Miele, Lucio [Section on Developmental Genetics, Heritable Disorders Branch (United States); Paolillo, Livio [University of Naples ' Federico II' , Department of Chemistry (Italy); Mukherjee, Anil B. [Section on Developmental Genetics, Heritable Disorders Branch (United States); Barbato, Gaetano [IRBM P. Angeletti, Spa. (Italy)

    1997-01-15

    Human uteroglobin (h-UG) or Clara cell 10kDa (cc10kDa) is a steroid-dependent, 17 kDahomodimeric, secretory protein with potent anti-inflammatory/immunomodulatory properties. However, the exact physiological role still remains to be determined. It has been hypothesised that its activity is exerted through the binding of a specific target represented by a small molecule (still unknown), and that the binding is regulated by the formation/disruption of two cysteine bonds. The binding properties of the reduced UG have been proved in vitro for several different molecules, but no in vivo data are available to date. However, binding has been observed between reduced rabbit UG and a protein of an apparent molecular mass of 90 kDa and, more recently, we found an h-UG-binding protein (putative receptor), of an apparent molecular mass of 190 kDa, on the surface of several cell types. The recognition involves oxidised h-UG. These findings pose the problem of the relevance of the oxidation state in the recognition process. To determine the solution structure of the oxidised h-UG, we produced wild-type as well as uniformly 15N- and 15N/13C-labelled samples of the recombinant protein. The assignments of the 1H, 15N and 13C resonances are presented,based on a series of homonuclear 2D and 3D and heteronuclear 2D and 3D double and triple resonance NMR experiments. Our results indicate that h-UG is an extremely stable protein under a wide range of temperatures and pH conditions. The secondary structure in solution is in general agreement with previously reported crystal structures of rabbit UG, suggesting that cc10kDa and h-UG are indeed the same protein. Small local differences found in the N-and C-terminal helices seem to support the hypothesis that flexibility involves these residues;moreover, it possibly accounts for the residual binding properties observed when the protein is in the oxidised state.

  5. [Characterization of 5S rRNA gene sequence and secondary structure in gymnosperms].

    Science.gov (United States)

    Liu, Zhan-Lin; Zhang, Da-Ming; Wang, Xiao-Ru

    2003-01-01

    In higher plants the primary and the secondary structures of 5S ribosomal RNA gene are considered highly conservative. Little is known about the 5S rRNA gene structure, organization and variation in gyimnosperms. In this study we analyzed sequence and structure variation of 5S rRNA gene in Pinus through cloning and sequencing multiple copies of 5S rDNA repeats from individual trees of five pines, P. bungeana, P. tabulaeformis, P. yunnanensis, P. massoniana and P. densata. Pinus bungeana is from the subgenus Strobus while the other four are from the subgenus Pinus (diploxylon pines). Our results revealed variations in both primary and secondary structure among copies of 5S rDNA within individual genomes and between species. 5S rRNA gene in Pinus is 120 bp long in most of the 122 clones we sequenced except for one or two deletions in three clones. Among these clones 50 unique sequences were identified and they were shared by different pine species. Our sequences were compared to 13 sequences each representing a different gymnosperm species, and to six sequences representing both angiosperm monocots and dicots. Average sequence similarity was 97.1% among Pinus species and 94.3% between Pinus and other gymnosperms. Between gymnosperms and angiosperms the sequence similarity decreased to 88.1%. Similar to other molecular data, significant sequence divergence was found between the two Pinus subgenera. The 5S gene tree (neighbor-joining tree) grouped the four diploxylon pines together and separated them distinctly from P. bungeana. Comparison of sequence divergence within individuals and between species suggested that concerted evolution has been very weak especially after the divergence of the four diploxylon pines. The phylogenetic information contained in the 5S rRNA gene is limited due to its shorter length and the difficulties in identifying orthologous and paralogous copies of rDNA multigene family further complicate its phylogenetic application. Pinus densata is a

  6. Crumple: a method for complete enumeration of all possible pseudoknot-free RNA secondary structures.

    Directory of Open Access Journals (Sweden)

    Samuel Bleckley

    Full Text Available The diverse landscape of RNA conformational space includes many canyons and crevices that are distant from the lowest minimum free energy valley and remain unexplored by traditional RNA structure prediction methods. A complete description of the entire RNA folding landscape can facilitate identification of biologically important conformations. The Crumple algorithm rapidly enumerates all possible non-pseudoknotted structures for an RNA sequence without consideration of thermodynamics while filtering the output with experimental data. The Crumple algorithm provides an alternative approach to traditional free energy minimization programs for RNA secondary structure prediction. A complete computation of all non-pseudoknotted secondary structures can reveal structures that would not be predicted by methods that sample the RNA folding landscape based on thermodynamic predictions. The free energy minimization approach is often successful but is limited by not considering RNA tertiary and protein interactions and the possibility that kinetics rather than thermodynamics determines the functional RNA fold. Efficient parallel computing and filters based on experimental data make practical the complete enumeration of all non-pseudoknotted structures. Efficient parallel computing for Crumple is implemented in a ring graph approach. Filters for experimental data include constraints from chemical probing of solvent accessibility, enzymatic cleavage of paired or unpaired nucleotides, phylogenetic covariation, and the minimum number and lengths of helices determined from crystallography or cryo-electron microscopy. The minimum number and length of helices has a significant effect on reducing conformational space. Pairing constraints reduce conformational space more than single nucleotide constraints. Examples with Alfalfa Mosaic Virus RNA and Trypanosome brucei guide RNA demonstrate the importance of evaluating all possible structures when pseduoknots, RNA

  7. Perturbation-induced secondary flow structures due to fractured stents in arterial curvatures

    Science.gov (United States)

    Bulusu, Kartik V.; Popma, Christopher; Penna, Leanne; Plesniak, Michael W.

    2012-11-01

    An in vitro experimental investigation of secondary flow structures was performed downstream of a model stent that embodied a ``Type-IV'' stent fracture, i.e. complete transverse fracture of elements and element displacement (of 3 diameters). One part of the fractured stent was located in the curved region of a test section comprised of a 180-degree bent tube, and the velocity field measured with PIV. Secondary flow morphologies downstream of the stent were identified with a continuous wavelet transform (CWT) algorithm (PIVlet 1.2) using a 2D Ricker wavelet. A comparison of wavelet transformed vorticity fields of fractured and unfractured model stents is presented under physiological inflow conditions. During systolic deceleration, a breakdown in symmetry of vortical structures occurred with the unfractured stent, but not with the fractured model stent. Potential mechanisms to explain the differences in secondary flow morphologies include redirection of vorticity from the meridional plane of the bend to the normal plane and diffusion of vorticity. Supported by the National Science Foundation, Grant No. CBET-0828903 and GW Center for Biomimetics and Bioinspired Engineering (COBRE).

  8. Prediction of RNA secondary structures: from theory to models and real molecules

    International Nuclear Information System (INIS)

    Schuster, Peter

    2006-01-01

    RNA secondary structures are derived from RNA sequences, which are strings built form the natural four letter nucleotide alphabet, {AUGC}. These coarse-grained structures, in turn, are tantamount to constrained strings over a three letter alphabet. Hence, the secondary structures are discrete objects and the number of sequences always exceeds the number of structures. The sequences built from two letter alphabets form perfect structures when the nucleotides can form a base pair, as is the case with {GC} or {AU}, but the relation between the sequences and structures differs strongly from the four letter alphabet. A comprehensive theory of RNA structure is presented, which is based on the concepts of sequence space and shape space, being a space of structures. It sets the stage for modelling processes in ensembles of RNA molecules like evolutionary optimization or kinetic folding as dynamical phenomena guided by mappings between the two spaces. The number of minimum free energy (mfe) structures is always smaller than the number of sequences, even for two letter alphabets. Folding of RNA molecules into mfe energy structures constitutes a non-invertible mapping from sequence space onto shape space. The preimage of a structure in sequence space is defined as its neutral network. Similarly the set of suboptimal structures is the preimage of a sequence in shape space. This set represents the conformation space of a given sequence. The evolutionary optimization of structures in populations is a process taking place in sequence space, whereas kinetic folding occurs in molecular ensembles that optimize free energy in conformation space. Efficient folding algorithms based on dynamic programming are available for the prediction of secondary structures for given sequences. The inverse problem, the computation of sequences for predefined structures, is an important tool for the design of RNA molecules with tailored properties. Simultaneous folding or cofolding of two or more RNA

  9. 3x2 Classroom Goal Structures, Motivational Regulations, Self-Concept, and Affectivity in Secondary School.

    Science.gov (United States)

    Méndez-Giménez, Antonio; Cecchini-Estrada, José-Antonio; Fernández-Río, Javier; Prieto Saborit, José Antonio; Méndez-Alonso, David

    2017-09-20

    The main objective was to analyze relationships and predictive patterns between 3x2 classroom goal structures (CGS), and motivational regulations, dimensions of self-concept, and affectivity in the context of secondary education. A sample of 1,347 secondary school students (56.6% young men, 43.4% young women) from 10 different provinces of Spain agreed to participate (M age = 13.43, SD = 1.05). Hierarchical regression analyses indicated the self-approach CGS was the most adaptive within the spectrum of self-determination, followed by the task-approach CGS. The other-approach CGS had an ambivalent influence on motivation. Task-approach and self-approach CGS predicted academic self-concept (p self-concept (p self-concept was predicted by the task-approach and other-approach CGS's (p self-approach (negatively) CGS (p self- and task-based goals for students in their classes.

  10. Infrared spectroscopic study of photoreceptor membrane and purple membrane. Protein secondary structure and hydrogen deuterium exchange

    International Nuclear Information System (INIS)

    Downer, N.W.; Bruchman, T.J.; Hazzard, J.H.

    1986-01-01

    Infrared spectroscopy in the interval from 1800 to 1300 cm-1 has been used to investigate the secondary structure and the hydrogen/deuterium exchange behavior of bacteriorhodopsin and bovine rhodopsin in their respective native membranes. The amide I' and amide II' regions from spectra of membrane suspensions in D2O were decomposed into constituent bands by use of a curve-fitting procedure. The amide I' bands could be fit with a minimum of three theoretical components having peak positions at 1664, 1638, and 1625 cm-1 for bacteriorhodopsin and 1657, 1639, and 1625 cm-1 for rhodopsin. For both of these membrane proteins, the amide I' spectrum suggests that alpha-helix is the predominant form of peptide chain secondary structure, but that a substantial amount of beta-sheet conformation is present as well. The shape of the amide I' band was pH-sensitive for photoreceptor membranes, but not for purple membrane, indicating that membrane-bound rhodopsin undergoes a conformation change at acidic pH. Peptide hydrogen exchange of bacteriorhodopsin and rhodopsin was monitored by observing the change in the ratio of integrated absorbance (Aamide II'/Aamide I') during the interval from 1.5 to 25 h after membranes were introduced into buffered D2O. The fraction of peptide groups in a very slowly exchanging secondary structure was estimated to be 0.71 for bacteriorhodopsin at pD 7. The corresponding fraction in vertebrate rhodopsin was estimated to be less than or equal to 0.60. These findings are discussed in relationship to previous studies of hydrogen exchange behavior and to structural models for both proteins

  11. STUDY OF THE EFFECT OF MIXED ALKOXIDES OXYPROPYLATED AROMATIC SECONDARY AMINES ON THE STRUCTURE OF DIENE POLYMERS

    Directory of Open Access Journals (Sweden)

    A. V. Firsova

    2014-01-01

    Full Text Available Summary. This article discusses the relationship structure of the diene and styrene-butadiene copolymers (SBR, the structure of the part of the initiating system of n-butyl lithium + modifier, which is a mixed alkoxide of an alkali and alkaline earth metals, which allows to control the microstructure of the diene polymer and its molecular weight characteristics. Alcohol derivatives selected high-boiling alcohols tetra (hydroxypropyl ethylenediamine (lapromol - 294 and tetrahydrofurfuryl alcohol (TGFS. The scheme of obtaining styrene-butadiene random copolymers (SBR with a high content (64 ± 4 % of vinyl units was developed. The process of copolymerization with sodium-calcium-lithium complex Са(С4Н9 2 • С4Н9Na • LiOR was carried out. After water decontamination residues deactivated complex remain in the polymer as a filler. Studied the copolymerization of butadiene with styrene in the presence of lithium amide, which is obtained on the basis of the alcohols containing the group - NH -. With the increasing solubility of the branching alkoxides increases in hydrocarbon solvents. Found that sodium alkoxide hydroxypropyl aniline decane insoluble, the sodium alcoholate hydroxypropyl toluidine soluble in decane. The results of studies of the effect of mixed alkoxides oxypropylated aromatic secondary amines on the structure of diene polymers. The Providing the necessary initiation systems for preparing functionalized polymers. It was revealed that secondary amines from which the lithium amides are inactive, so the polymerization of monomers was carried out in the presence of electron as that used glycol ethers - diglyme, THF, 2,2 - ditetragidrofurfuril propane, which increase polymer-filler interaction. The results of research of the microstructure of the diene part of SBR obtained in the mixed alkali metal alkoxide with a mixture of lapromol alcohols, toluidine and TGFS showed that increasing toluidine consisting of mixed modifier reduces

  12. RESIDUAL STRESS MEASUREMENTS AND STRUCTURAL INTEGRITY IMPLICATIONS FOR SELECTIVE LASER MELTED TI-6AL-4V

    Directory of Open Access Journals (Sweden)

    Knowles, C. R.

    2012-11-01

    Full Text Available Selective laser melting (SLM of Ti-6Al-4V has significant potential in the aerospace and biotechnology industries. SLM employs a focused laser beam to melt successive layers of metallic powder into complex components. This process can result in the generation of high thermally-induced residual stresses. These residual stresses, together with micro-flaws/ pores from the inherent fabrication process, may lead to premature fatigue crack initiation and propagation at relatively low cyclic stresses. The hole-drilling strain gauge method was used to evaluate residual stresses within SLM Ti-6Al-4V specimens, with the intention of understanding the associated mechanisms for the successful application of SLM Ti-6Al-4V in industry.

  13. Optimized set of two-dimensional experiments for fast sequential assignment, secondary structure determination, and backbone fold validation of 13C/15N-labelled proteins

    International Nuclear Information System (INIS)

    Bersch, Beate; Rossy, Emmanuel; Coves, Jacques; Brutscher, Bernhard

    2003-01-01

    NMR experiments are presented which allow backbone resonance assignment, secondary structure identification, and in favorable cases also molecular fold topology determination from a series of two-dimensional 1 H- 15 N HSQC-like spectra. The 1 H- 15 N correlation peaks are frequency shifted by an amount ± ω X along the 15 N dimension, where ω X is the C α , C β , or H α frequency of the same or the preceding residue. Because of the low dimensionality (2D) of the experiments, high-resolution spectra are obtained in a short overall experimental time. The whole series of seven experiments can be performed in typically less than one day. This approach significantly reduces experimental time when compared to the standard 3D-based methods. The here presented methodology is thus especially appealing in the context of high-throughput NMR studies of protein structure, dynamics or molecular interfaces

  14. Solution NMR structure and inhibitory effect against amyloid-β fibrillation of Humanin containing a d-isomerized serine residue.

    Science.gov (United States)

    Alsanousi, Nesreen; Sugiki, Toshihiko; Furuita, Kyoko; So, Masatomo; Lee, Young-Ho; Fujiwara, Toshimichi; Kojima, Chojiro

    2016-09-02

    Humanin comprising 24 amino acid residues is a bioactive peptide that has been isolated from the brain tissue of patients with Alzheimer's disease. Humanin reportedly suppressed aging-related death of various cells due to amyloid fibrils and oxidative stress. There are reports that the cytoprotective activity of Humanin was remarkably enhanced by optical isomerization of the Ser14 residue from l to d form, but details of the molecular mechanism remained unclear. Here we demonstrated that Humanin d-Ser14 exhibited potent inhibitory activity against fibrillation of amyloid-β and remarkably higher binding affinity for amyloid-β than that of the Humanin wild-type and S14G mutant. In addition, we determined the solution structure of Humanin d-Ser14 by nuclear magnetic resonance (NMR) and showed that d-isomerization of the Ser14 residue enables drastic conformational rearrangement of Humanin. Furthermore, we identified an amyloid-β-binding site on Humanin d-Ser14 at atomic resolution by NMR. These biophysical and high-resolution structural analyses clearly revealed structure-function relationships of Humanin and explained the driving force of the drastic conformational change and molecular basis of the potent anti-amyloid-β fibrillation activity of Humanin caused by d-isomerization of the Ser14 residue. This is the first study to show correlations between the functional activity, tertiary structure, and partner recognition mode of Humanin and may lead to elucidation of the molecular mechanisms of the cytoprotective activity of Humanin. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. Impact damage and residual strength analysis of composite panels with bonded stiffeners. [for primary aircraft structures

    Science.gov (United States)

    Madan, Ram C.; Shuart, Mark J.

    1990-01-01

    Blade-stiffened, compression-loaded cover panels were designed, manufactured, analyzed, and tested. All panels were fabricated from IM6/1808I interleafed graphite-epoxy. An orthotropic blade stiffener and an orthotropic skin were selected to satisfy the design requirements for an advanced aircraft configuration. All specimens were impact damaged prior to testing. Experimental results were obtained for three- and five-stiffener panels. Analytical results described interlaminar forces caused by impact and predicted specimen residual strength. The analytical results compared reasonably with the experimental results for residual strength of the specimens.

  16. Determination of sugar structures in solution from residual dipolar coupling constants: methodology and application to methyl beta-D-xylopyranoside.

    Science.gov (United States)

    Pham, Tran N; Hinchley, Sarah L; Rankin, David W H; Liptaj, Tibor; Uhrín, Dusan

    2004-10-13

    We have developed methodology for the determination of solution structures of small molecules from residual dipolar coupling constants measured in dilute liquid crystals. The power of the new technique is demonstrated by the determination of the structure of methyl beta-d-xylopyranoside (I) in solution. An oriented sample of I was prepared using a mixture of C(12)E(5) and hexanol in D(2)O. Thirty residual dipolar coupling constants, ranging from -6.44 to 4.99 Hz, were measured using intensity-based J-modulated NMR techniques. These include 15 D(HH), 4 (1)D(CH), and 11 (n)D(CH) coupling constants. The accuracy of the dipolar coupling constants is estimated to be Comparison with the neutron diffraction structure showed larger differences attributable to crystal packing effects. Reducing the degree of order by using dilute liquid crystalline media in combination with precise measurement of small residual dipolar coupling constants, as shown here, is a way of overcoming the limitation of strongly orienting liquid crystals associated with the complexity of (1)H NMR spectra for molecules with more than 12 protons.

  17. Sequence-specific 1H NMR assignments and secondary structure of the Arc repressor of bacteriophage P22, as determined by two-dimensional 1H NMR spectroscopy

    International Nuclear Information System (INIS)

    Breg, J.N.; Boelens, R.; George, A.V.E.; Kaptein, R.

    1989-01-01

    The Arc repressor of bacteriophage P22 is a DNA binding protein that does not belong to any of the known classes of such proteins. The authors have undertaken a 1 H NMR study of the protein with the aim of elucidating its three-dimensional structure in solution and its mode of binding of operator DNA. Here the authors present the 1 H nuclear magnetic resonance (NMR) assignments of all backbone protons an most of the side-chain protons of Arc repressor. Elements of secondary structure have been identified on the basis of networks of characteristics sequential and medium-range nuclear Overhauser enhancements (NOEs). Two α-helical regions have been found in the peptide regions 16-29 and 35-45. The ends of the helices could not yet be firmly established and could extend to residue 31 for the first helix and to residue 49 for the second. Immediately before the first helix, between residues 8 and 14, a region is present with β-sheet characteristics dominated by a close proximity of the α-protons of residues 9 and 13. Because of the dimeric nature of the protein there are still two possible ways in which the NOEs in the β-sheet region can be interpreted. While the data presently do not allow an unambiguous choice between these two possibilities, some evidence is discussed that favors the latter (β-sheet between monomers). Since the N-terminal region of Arc is responsible for the sequence-specific recognition of its operator, the findings suggest the existence of a DNA binding motif in which a β-sheet region is present

  18. Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be.

    KAUST Repository

    Schaefer, Christian

    2010-01-16

    MOTIVATION: The mutation of amino acids often impacts protein function and structure. Mutations without negative effect sustain evolutionary pressure. We study a particular aspect of structural robustness with respect to mutations: regular protein secondary structure and natively unstructured (intrinsically disordered) regions. Is the formation of regular secondary structure an intrinsic feature of amino acid sequences, or is it a feature that is lost upon mutation and is maintained by evolution against the odds? Similarly, is disorder an intrinsic sequence feature or is it difficult to maintain? To tackle these questions, we in silico mutated native protein sequences into random sequence-like ensembles and monitored the change in predicted secondary structure and disorder. RESULTS: We established that by our coarse-grained measures for change, predictions and observations were similar, suggesting that our results were not biased by prediction mistakes. Changes in secondary structure and disorder predictions were linearly proportional to the change in sequence. Surprisingly, neither the content nor the length distribution for the predicted secondary structure changed substantially. Regions with long disorder behaved differently in that significantly fewer such regions were predicted after a few mutation steps. Our findings suggest that the formation of regular secondary structure is an intrinsic feature of random amino acid sequences, while the formation of long-disordered regions is not an intrinsic feature of proteins with disordered regions. Put differently, helices and strands appear to be maintained easily by evolution, whereas maintaining disordered regions appears difficult. Neutral mutations with respect to disorder are therefore very unlikely.

  19. An evolutionary method for learning HMM structure: prediction of protein secondary structure

    DEFF Research Database (Denmark)

    Won, Kyoung-Jae; Hamelryck, Thomas; Prügel-Bennett, Adam

    2007-01-01

    Therefore, we have developed a method for evolving the structure of HMMs automatically, using Genetic Algorithms (GAs). RESULTS: In the GA procedure, populations of HMMs are assembled from biologically meaningful building blocks. Mutation and crossover operators were designed to explore the space...

  20. Determination of the crystal structure and active residues of FabV, the enoyl-ACP reductase from Xanthomonas oryzae.

    Directory of Open Access Journals (Sweden)

    He Li

    Full Text Available Enoyl-ACP reductase (ENR catalyses the last reduction reaction in the fatty acid elongation cycle in bacteria and is a good antimicrobial target candidate. FabV is the most recently discovered class of ENR, but we lack information about the atomic structure and the key residues involved in reductase activity except for the known conserved tyrosine and lysine residues in the Y-X(8-K active site motif.Here we report the crystal structure of FabV from Xanthomonas oryzae (xoFabV. The crystal structure of this enzyme has been solved to 1.6 Å resolution in space group P2(12(12(1. The model of xoFabV consists of one monomer in the asymmetric unit which is composed of 13 α-helices and 11 β-strands, representing a canonical Rossmann fold architecture. Structural comparison presents that the locations of the conserved tyrosine (Y236 and lysine (K245 residues in the Y-X(8-K active site motif of xoFabV and the Y-X(6-K motif of ecFabI are notably similar. However, the conformations of Y236 in xoFabV and Y156 in ecFabI are distinct. Structure-based site-directed mutagenesis and enzymatic activity assays reveal that in addition to the conserved Y236 and K245 in the Y-X(8-K motif, Y53, D111 and Y226 are key residues implicated in the reductase activity, and F113 and T276 are also important for enzyme function. Moreover, a proposed active lysine located immediately after the Y-X(8-K motif in FabV from Burkholderia mallei (bmFabV is altered to an inactive V246 in xoFabV.We determine the first crystal structure of the FabV enzyme and identify several residues important for its enzymatic activity. These findings lay a solid foundation for the development of specific antibacterial inhibitors of the pathogenic bacteria, such as Vibrio cholerae, Burkholderia species and Xanthomonas species.

  1. SARNA-Predict: accuracy improvement of RNA secondary structure prediction using permutation-based simulated annealing.

    Science.gov (United States)

    Tsang, Herbert H; Wiese, Kay C

    2010-01-01

    Ribonucleic acid (RNA), a single-stranded linear molecule, is essential to all biological systems. Different regions of the same RNA strand will fold together via base pair interactions to make intricate secondary and tertiary structures that guide crucial homeostatic processes in living organisms. Since the structure of RNA molecules is the key to their function, algorithms for the prediction of RNA structure are of great value. In this article, we demonstrate the usefulness of SARNA-Predict, an RNA secondary structure prediction algorithm based on Simulated Annealing (SA). A performance evaluation of SARNA-Predict in terms of prediction accuracy is made via comparison with eight state-of-the-art RNA prediction algorithms: mfold, Pseudoknot (pknotsRE), NUPACK, pknotsRG-mfe, Sfold, HotKnots, ILM, and STAR. These algorithms are from three different classes: heuristic, dynamic programming, and statistical sampling techniques. An evaluation for the performance of SARNA-Predict in terms of prediction accuracy was verified with native structures. Experiments on 33 individual known structures from eleven RNA classes (tRNA, viral RNA, antigenomic HDV, telomerase RNA, tmRNA, rRNA, RNaseP, 5S rRNA, Group I intron 23S rRNA, Group I intron 16S rRNA, and 16S rRNA) were performed. The results presented in this paper demonstrate that SARNA-Predict can out-perform other state-of-the-art algorithms in terms of prediction accuracy. Furthermore, there is substantial improvement of prediction accuracy by incorporating a more sophisticated thermodynamic model (efn2).

  2. The Interplay between Adolescent Needs and Secondary School Structures: Fostering Developmentally Responsive Middle and High School Environments across the Transition

    Science.gov (United States)

    Ellerbrock, Cheryl R.; Kiefer, Sarah M.

    2013-01-01

    Understanding the developmental responsiveness of secondary school environments may be an important factor in supporting students as they make the transition from one school to the next. Students' needs may or may not be met depending on the nature of the fit between their basic and developmental needs and secondary school structures at the middle…

  3. Nanometer-scale structure of alkali-soluble bio-macromolecules of maize plant residues explains their recalcitrance in soil.

    Science.gov (United States)

    Adani, Fabrizio; Salati, Silvia; Spagnol, Manuela; Tambone, Fulvia; Genevini, Pierluigi; Pilu, Roberto; Nierop, Klaas G J

    2009-07-01

    The quantity and quality of plant litter in the soil play an important role in the soil organic matter balance. Besides other pedo-climatic aspects, the content of recalcitrant molecules of plant residues and their chemical composition play a major role in the preservation of plant residues. In this study, we report that intrinsically resistant alkali-soluble bio-macromolecules extracted from maize plant (plant-humic acid) (plant-HA) contribute directly to the soil organic matter (OM) by its addition and conservation in the soil. Furthermore, we also observed that a high syringyl/guaiacyl (S/G) ratio in the lignin residues comprising the plant tissue, which modifies the microscopic structure of the alkali-soluble plant biopolymers, enhances their recalcitrance because of lower accessibility of molecules to degrading enzymes. These results are in agreement with a recent study, which showed that the humic substance of soil consists of a mixture of identifiable biopolymers obtained directly from plant tissues that are added annually by maize plant residues.

  4. A quantitative analysis of secondary RNA structure using domination based parameters on trees

    Directory of Open Access Journals (Sweden)

    Zou Yue

    2006-03-01

    Full Text Available Abstract Background It has become increasingly apparent that a comprehensive database of RNA motifs is essential in order to achieve new goals in genomic and proteomic research. Secondary RNA structures have frequently been represented by various modeling methods as graph-theoretic trees. Using graph theory as a modeling tool allows the vast resources of graphical invariants to be utilized to numerically identify secondary RNA motifs. The domination number of a graph is a graphical invariant that is sensitive to even a slight change in the structure of a tree. The invariants selected in this study are variations of the domination number of a graph. These graphical invariants are partitioned into two classes, and we define two parameters based on each of these classes. These parameters are calculated for all small order trees and a statistical analysis of the resulting data is conducted to determine if the values of these parameters can be utilized to identify which trees of orders seven and eight are RNA-like in structure. Results The statistical analysis shows that the domination based parameters correctly distinguish between the trees that represent native structures and those that are not likely candidates to represent RNA. Some of the trees previously identified as candidate structures are found to be "very" RNA like, while others are not, thereby refining the space of structures likely to be found as representing secondary RNA structure. Conclusion Search algorithms are available that mine nucleotide sequence databases. However, the number of motifs identified can be quite large, making a further search for similar motif computationally difficult. Much of the work in the bioinformatics arena is toward the development of better algorithms to address the computational problem. This work, on the other hand, uses mathematical descriptors to more clearly characterize the RNA motifs and thereby reduce the corresponding search space. These

  5. Change in Glutenin Macropolymer Secondary Structure in Wheat Sourdough Fermentation by FTIR.

    Science.gov (United States)

    Wang, Jinshui; Yue, Yuanyuan; Liu, Tiantian; Zhang, Bin; Wang, Zhenlei; Zhang, Changfu

    2017-06-01

    Wheat sourdough was prepared by fermentation with Lactobacillus plantarum M616 and yeast in the present study. The change in secondary structure of glutenin macropolymer (GMP) in wheat sourdough fermentation for 4 and 12 h was determined using Fourier transform infrared spectroscopy, and then the resultant spectra were Fourier self-deconvoluted of the amide I band in the region from 1600 to 1700 cm -1 . Significant different spectra especially in the amide I band for GMP from sourdough fermented with L. plantarum M616 (SL) and with L. plantarum M616 and yeast (SLY) were found in respect of control dough (CK), dough with acids (SA), and sourdough fermented with yeast (SY) at 4 and 12 h of fermentation. The loss of α-helix structure in SL, SLY, and SA samples was noticed during fermentation. Compared with CK and SY, SL, SLY, and SA samples showed significant decrease (p fermentation. In addition, β-turns in SL sourdough decrease, and the relative areas of random coil increase significantly (p fermentation. The modified secondary structure of GMP makes more sensitive to proteolysis by means of cereal enzymes.

  6. Effects of high hydrostatic pressure on secondary structure and emulsifying behavior of sweet potato protein

    Science.gov (United States)

    Mehmood Khan, Nasir; Mu, Tai-Hua; Sun, Hong-Nan; Zhang, Miao; Chen, Jing-Wang

    2015-04-01

    In this study, secondary structures of sweet potato protein (SPP) after high hydrostatic pressure (HHP) treatment (200-600 MPa) were evaluated and emulsifying properties of emulsions with HHP-treated SPP solutions in different pH values (3, 6, and 9) were investigated. Circular dichroism analysis confirmed the modification of the SPP secondary structure. Surface hydrophobicity increased at pH 3 and decreased at 6 and 9. Emulsifying activity index at pH 6 increased with an increase in pressure, whereas emulsifying stability index increased at pH 6 and 9. Oil droplet sizes decreased, while volume frequency distribution of the smaller droplets increased at pH 3 and 6 with the HHP treatment. Emulsion viscosity increased at pH 6 and 9 and pseudo-plastic flow behaviors were not altered for all emulsions produced with HHP-treated SPP. These results suggested that HHP could modify the SPP structure for better emulsifying properties, which could increase the use of SPP emulsion in the food industry.

  7. D-amino acid residue in a defensin-like peptide from platypus venom: effect on structure and chromatographic properties.

    Science.gov (United States)

    Torres, Allan M; Tsampazi, Chryssanthi; Geraghty, Dominic P; Bansal, Paramjit S; Alewood, Paul F; Kuchel, Philip W

    2005-10-15

    The recent discovery that the natriuretic peptide OvCNPb (Ornithorhynchus venom C-type natriuretic peptide B) from platypus (Ornithorynchus anatinus) venom contains a D-amino acid residue suggested that other D-amino-acid-containing peptides might be present in the venom. In the present study, we show that DLP-2 (defensin-like peptide-2), a 42-amino-acid residue polypeptide in the platypus venom, also contains a D-amino acid residue, D-methionine, at position 2, while DLP-4, which has an identical amino acid sequence, has all amino acids in the L-form. These findings were supported further by the detection of isomerase activity in the platypus gland venom extract that converts DLP-4 into DLP-2. In the light of this new information, the tertiary structure of DLP-2 was recalculated using a new structural template with D-Met2. The structure of DLP-4 was also determined in order to evaluate the effect of a D-amino acid at position 2 on the structure and possibly to explain the large retention time difference observed for the two molecules in reverse-phase HPLC. The solution structures of the DLP-2 and DLP-4 are very similar to each other and to the earlier reported structure of DLP-2, which assumed that all amino acids were in the L-form. Our results suggest that the incorporation of the D-amino acid at position 2 has minimal effect on the overall fold in solution.

  8. Structure of the secondary xylem of Aniba Aubl. species from the Brazilian Amazon

    Directory of Open Access Journals (Sweden)

    Cláudia Viana Urbinati

    2014-09-01

    Full Text Available The aim of this study was to characterize the wood of Aniba species from the Brazilian Amazon, on the basis of specimens in the wood collection of the Herbarium of the Museu Paraense Emílio Goeldi, in the city of Belém, Brazil. The species were found to present a homogeneous structure in the secondary xylem, as defined by the location of oil cells; the presence of tyloses and crystals; and singularities of the radial and axial parenchyma.

  9. Secondary Structure Prediction of Protein using Resilient Back Propagation Learning Algorithm

    Directory of Open Access Journals (Sweden)

    Jyotshna Dongardive

    2015-12-01

    Full Text Available The paper proposes a neural network based approach to predict secondary structure of protein. It uses Multilayer Feed Forward Network (MLFN with resilient back propagation as the learning algorithm. Point Accepted Mutation (PAM is adopted as the encoding scheme and CB396 data set is used for the training and testing of the network. Overall accuracy of the network has been experimentally calculated with different window sizes for the sliding window scheme and by varying the number of units in the hidden layer. The best results were obtained with eleven as the window size and seven as the number of units in the hidden layer.

  10. Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins

    DEFF Research Database (Denmark)

    Kushon, S A; Jordan, J P; Seifert, J L

    2001-01-01

    structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic......-DNA and DNA-DNA duplexes can be formed with these target hairpins, even when the melting temperatures for the resulting duplexes are up to 50 degrees C lower than that of the hairpin target. Both hairpin/single-stranded and hairpin/hairpin interactions are considered in the scope of these studies. Secondary...

  11. Pitch accent alignment in romance: primary and secondary associations with metrical structure.

    Science.gov (United States)

    Prieto, Pilar; D'Imperio, Mariapaola; Fivela, Barbara Gili

    2005-01-01

    The article describes the contrastive possibilities of alignment of high accents in three Romance varieties, namely, Central Catalan, Neapolitan Italian, and Pisa Italian. The Romance languages analyzed in this article provide crucial evidence that small differences in alignment in rising accents should be encoded phonologically. To account for such facts within the AM model, the article develops the notion of "phonological anchoring" as an extension of the concept of secondary association originally proposed by Pierrehumbert and Beckman (1988), and later adopted by Grice (1995), Grice, Ladd, and Arvaniti (2000), and others to explain the behavior of edge tones. The Romance data represent evidence that not only peripheral edge tones seek secondary associations. We claim that the phonological representation of pitch accents should include two independent mechanisms to encode alignment properties with metrical structure: (1) encoding of the primary phonological association (or affiliation) between the tone and its tone-bearing unit; and (2), for some specific cases, encoding of the secondary phonological anchoring of tones to prosodic edges (moras, syllables, and prosodic words). The Romance data described in the article provide crucial evidence of mora-edge, syllable-edge, and word-edge H tonal associations.

  12. Structural insights into cellulolytic and chitinolytic enzymes revealing crucial residues of insect β-N-acetyl-D-hexosaminidase.

    Directory of Open Access Journals (Sweden)

    Tian Liu

    Full Text Available The chemical similarity of cellulose and chitin supports the idea that their corresponding hydrolytic enzymes would bind β-1,4-linked glucose residues in a similar manner. A structural and mutational analysis was performed for the plant cellulolytic enzyme BGlu1 from Oryza sativa and the insect chitinolytic enzyme OfHex1 from Ostrinia furnacalis. Although BGlu1 shows little amino-acid sequence or topological similarity with OfHex1, three residues (Trp(490, Glu(328, Val(327 in OfHex1, and Trp(358, Tyr(131 and Ile(179 in BGlu1 were identified as being conserved in the +1 sugar binding site. OfHex1 Glu(328 together with Trp(490 was confirmed to be necessary for substrate binding. The mutant E328A exhibited a 8-fold increment in K(m for (GlcNAc(2 and a 42-fold increment in K(i for TMG-chitotriomycin. A crystal structure of E328A in complex with TMG-chitotriomycin was resolved at 2.5 Å, revealing the obvious conformational changes of the catalytic residues (Glu(368 and Asp(367 and the absence of the hydrogen bond between E328A and the C3-OH of the +1 sugar. V327G exhibited the same activity as the wild-type, but acquired the ability to efficiently hydrolyse β-1,2-linked GlcNAc in contrast to the wild-type. Thus, Glu(328 and Val(327 were identified as important for substrate-binding and as glycosidic-bond determinants. A structure-based sequence alignment confirmed the spatial conservation of these three residues in most plant cellulolytic, insect and bacterial chitinolytic enzymes.

  13. Structural insights into cellulolytic and chitinolytic enzymes revealing crucial residues of insect β-N-acetyl-D-hexosaminidase.

    Science.gov (United States)

    Liu, Tian; Zhou, Yong; Chen, Lei; Chen, Wei; Liu, Lin; Shen, Xu; Zhang, Wenqing; Zhang, Jianzhen; Yang, Qing

    2012-01-01

    The chemical similarity of cellulose and chitin supports the idea that their corresponding hydrolytic enzymes would bind β-1,4-linked glucose residues in a similar manner. A structural and mutational analysis was performed for the plant cellulolytic enzyme BGlu1 from Oryza sativa and the insect chitinolytic enzyme OfHex1 from Ostrinia furnacalis. Although BGlu1 shows little amino-acid sequence or topological similarity with OfHex1, three residues (Trp(490), Glu(328), Val(327) in OfHex1, and Trp(358), Tyr(131) and Ile(179) in BGlu1) were identified as being conserved in the +1 sugar binding site. OfHex1 Glu(328) together with Trp(490) was confirmed to be necessary for substrate binding. The mutant E328A exhibited a 8-fold increment in K(m) for (GlcNAc)(2) and a 42-fold increment in K(i) for TMG-chitotriomycin. A crystal structure of E328A in complex with TMG-chitotriomycin was resolved at 2.5 Å, revealing the obvious conformational changes of the catalytic residues (Glu(368) and Asp(367)) and the absence of the hydrogen bond between E328A and the C3-OH of the +1 sugar. V327G exhibited the same activity as the wild-type, but acquired the ability to efficiently hydrolyse β-1,2-linked GlcNAc in contrast to the wild-type. Thus, Glu(328) and Val(327) were identified as important for substrate-binding and as glycosidic-bond determinants. A structure-based sequence alignment confirmed the spatial conservation of these three residues in most plant cellulolytic, insect and bacterial chitinolytic enzymes.

  14. Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification

    DEFF Research Database (Denmark)

    Buslje, Cristina Marino; Teppa, Elin; Di Doménico, Tomas

    2010-01-01

    to significantly outperform both the Shannon entropy and maximal frequency measurements. Residues in the proximity of catalytic sites were shown to be rich in shared MI. A structural proximity MI average score (termed pMI) was demonstrated to be a strong predictor for CR, thus confirming the proposed hypothesis....... A structural proximity conservation average score (termed pC) was also calculated and demonstrated to carry distinct information from pMI. A catalytic likeliness score (Cls), combining the KL, pC and pMI measures, was shown to lead to significantly improved prediction accuracy. At a specificity of 0...

  15. Residual thermal stress control in composite reinforced metal structures. [by mechanical loading of metal component prior to bonding

    Science.gov (United States)

    Kelly, J. B.; June, R. R.

    1972-01-01

    Advanced composite materials, composed of boron or graphite fibers and a supporting matrix, make significant structural efficiency improvements available to aircraft and aerospace designers. Residual stress induced during bonding of composite reinforcement to metal structural elements can be reduced or eliminated through suitable modification to the manufacturing processes. The most successful method employed during this program used a steel tool capable of mechanically loading the metal component in compression prior to the adhesive bonding cycle. Compression loading combined with heating to 350 F during the bond cycle can result in creep deformation in aluminum components. The magnitude of the deformation increases with increasing stress level during exposure to 350 F.

  16. Residue energy and mobility in sequence to global structure and dynamics of a HIV-1 protease (1DIFA) by a coarse-grained Monte Carlo simulation

    Science.gov (United States)

    Pandey, R. B.; Farmer, B. L.

    2009-01-01

    Energy, mobility, and structural profiles of residues in a specific sequence of human immunodeficiency virus (HIV)-1 protease chain and its global conformation and dynamics are studied by a coarse-grained computer simulation model on a cubic lattice. HIV-1 protease is described by a chain of 99 residues (nodes) in a specific sequence (1DIFA) with N- and C-terminals on the lattice, where empty lattice sites represent an effective solvent medium. Internal structures of the residues are ignored but their specificities are captured via an interaction (ɛij) matrix (residue-residue, residue-solvent) of the coefficient (fɛij) of the Lennard-Jones potential. Simulations are performed for a range of interaction strength (f ) with the solvent-residue interaction describing the quality of the solvent. Snapshots of the protein show considerable changes in the conformation of the protein on varying the interaction. From the mobility and energy profiles of the residues, it is possible to identify the active (and not so active) segments of the protein and consequently their role in proteolysis. Contrary to interaction thermodynamics, the hydrophobic residues possess higher configurational energy and lower mobility while the electrostatic and polar residues are more mobile despite their lower interaction energy. Segments of hydrophobic core residues, crucial for the structural evolution of the protein are identified—some of which are consistent with recent molecular dynamics simulation in context to possible clinical observations. Global energy and radius of gyration of the protein exhibit nonmonotonic dependence on the interaction strength (f) with opposite trends, e.g., rapid transition into globular structure with higher energy. Variations of the rms displacement of the protein and that of a tracer residue, Gly49, with the time steps show how they slow down on increasing the interaction strength.

  17. High cycle fatigue analysis of vortex suppression plate and secondary core support structures

    International Nuclear Information System (INIS)

    Xue Guohong; Li Yuan; Zhao Feiyun; Feng Shaodong; Yu Hao

    2013-01-01

    Background: Reactor internals are important equipment s in the reactor coolant system, its structure design needs high reliability in the entire lifetime, Reactor internals have occurred breakdown and the damage event due to flow induced vibrations in the domestic and foreign nuclear power plants, which make immediate influence on reactor safe operation and economic efficiency. Purpose: In this work, the dynamic response of reactor internals-vortex suppression plate and secondary core support structure (SCSS) under the loading from pump induced vibrations and flow induced vibrations are studied. Methods: Based on the finite element model of SCSS, Spectrum analysis and the harmonious analysis are performed, in order to get the response of the structure under flow induced vibrations. Then, the high fatigue of the structure is assessed according to the ASME B and PV Code. Results: The results indicate that alternate stresses of all the components satisfy the limiting value in the correlative requirements. Conclusions: The structure of SCSS could bear the vibration induced from the flow and the pump, and the method used in this article provides the reference for other reactor internals structure analysis like this. (authors)

  18. Comparison of primary and secondary 26S rRNA structures in two Tetrahymena species: evidence for a strong evolutionary and structural constraint in expansion segments

    DEFF Research Database (Denmark)

    Engberg, J; Nielsen, Henrik; Lenaers, G

    1990-01-01

    . These are regions within the common core of secondary structure where expansions have taken place during the evolution of the rRNA of higher eukaryotes. The dispensable nature of some of the expansion segments has been taken as evidence of their non-functionality. However, our data show that a considerable...... selective constraint has operated to preserve the secondary structure of these segments. Especially in the case of the D2 and D8 segments, the presence of a considerable number of compensatory base changes suggests that the secondary structure of these regions is of functional importance. Alternatively...

  19. Secondary structure in solution of two anti-HIV-1 hammerhead ribozymes as investigated by two-dimensional 1H 500 MHz NMR spectroscopy in water

    Science.gov (United States)

    Sarma, R. H.; Sarma, M. H.; Rein, R.; Shibata, M.; Setlik, R. S.; Ornstein, R. L.; Kazim, A. L.; Cairo, A.; Tomasi, T. B.

    1995-01-01

    Two hammerhead chimeric RNA/DNA ribozymes (HRz) were synthesized in pure form. Both were 30 nucleotides long, and the sequences were such that they could be targeted to cleave the HIV-1 gag RNA. Named HRz-W and HRz-M, the former had its invariable core region conserved, the latter had a uridine in the invariable region replaced by a guanine. Their secodary structures were determined by 2D NOESY 1H 500 MHz NMR spectroscopy in 90% water and 10% D2(0), following the imino protons. The data show that both HRz-M and HRz-W form identical secondary structures with stem regions consisting of continuous stacks of AT and GT pairs. An energy minimized computer model of this stem region is provided. The results suggest that the loss of catalytic activity that is known to result when an invariant core residue is replaced is not related to the secondary structure of the ribozymes in the absence of substrate.

  20. Exploring cross-species-related miRNAs based on sequence and secondary structure.

    Science.gov (United States)

    Chen, Feng; Chen, Yi-Ping Phoebe

    2010-07-01

    MicroRNA (miRNA) plays an important role as a regulator of mRNA. But how miRNAs relate with each other in gene regulation network is still remaining. Understanding the reactions between miRNAs can be very significant for exploring miRNA target, gene regulation mechanism, and gene conservation in evolution process. We explore cross-species-related miRNAs to find out how miRNAs regulate each other by using joint entropy and mutual information, respectively. Our contribution includes the following: 1) our algorithms are based on the combination of sequence and secondary structure analysis because miRNAs are conserved much better in the secondary structure; and 2) when we consider if two miRNAs A and B are related, we consider the relationship between A (B) and other miRNAs in their own species too. If A (B) has a very close relationship with other miRNAs in its own species and the relationship of A and B is close too, then the relationship between A and B is more important. Therefore, this related miRNA pair is more significant. So, our algorithms confirm to the reality that genes regulate each other as a network. Through experiments on miRNAMap 2.0, it has been proven that we can not only find out the known related miRNA pairs but also predict some novel ones.

  1. Evolutionary conservation of sequence and secondary structures inCRISPR repeats

    Energy Technology Data Exchange (ETDEWEB)

    Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

    2006-09-01

    Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.

  2. Structure and formation of convection of secondary rainbands in a simulated typhoon Jangmi (2008)

    Science.gov (United States)

    Xiao, Jing; Tan, Zhe-Min; Chow, Kim-Chiu

    2018-04-01

    Secondary rainbands in tropical cyclone are relatively transient compared with the quasi-stationary principle rainbands. To have a better understanding on their convective structure, a cloud-resolving scale numerical simulation of the super typhoon Jangmi (2008) was performed. The results suggest that the convections in secondary rainbands have some distinctive features that may not be seen in other types of rainbands in tropical cyclone. First, they have a front-like structure and are triggered to form above the boundary layer by the convergence of the above-boundary outflow from the inner side (warmer) and the descending inflow (colder) from the outer side. These elevated convections can be further confirmed by the three-dimensional backward trajectory calculations. Second, due to the release in baroclinic energy, the lower portion of the mid-level inflow from outside may penetrate into the bottom of the convection tower and may help accelerate the boundary layer inflow in the inner side. Third, the local maximum tangential wind is concentrated in the updraft region, with a lower portion which is dipping inward. Tangential wind budget analysis also suggests that the maxima are mainly contributed by the updraft advection, and can be advected cyclonically downstream by the tangential advection.

  3. Electromagnetic Fields Effects on the Secondary Structure of Lysozyme and Bioprotective Effectiveness of Trehalose

    Directory of Open Access Journals (Sweden)

    Emanuele Calabrò

    2012-01-01

    Full Text Available FTIR spectroscopy was used to investigate the effects of extremely low frequency (50 Hz electromagnetic field and of microwaves at 900 MHz on the secondary structure of a typical protein, the lysozyme, evaluating the bioprotective effectiveness of trehalose. Lysozyme in D2O solution (60 mg/ml was exposed to 50 Hz frequency electromagnetic field at 180 μT. The FTIR spectra indicated an increase of CH2 group at 1921 and 1853 cm−1 after 3 h of exposure. Such effect was not observed after the addition of trehalose (150 mg/mL at the same exposure conditions. Lysozyme dissolved in D2O at the concentration of 100 mg/mL was exposed up to 4 h to 900 MHz mobile phone microwaves at 25 mA/m. A significant increase in intensity of the amide I vibration band in the secondary structure of the protein was observed after 4 h exposure to microwaves. This effect was inhibited by the presence of trehalose at the concentration of 150 mg/mL. Fourier self-deconvolution spectral analysis of lysozyme in D2O solution after exposure to microwaves revealed an increase in intensity of the conformational components of amide I mode, particularly of β-sheet and turn that can be attributed to disorder and unfolding processes of the protein.

  4. Perturbation of the Secondary Structure of the Scrapie Prion Protein Under Conditions that Alter Infectivity

    Science.gov (United States)

    Gasset, Maria; Baldwin, Michael A.; Fletterick, Robert J.; Prusiner, Stanley B.

    1993-01-01

    Limited proteolysis of the scrapie prion protein (PrPSc) generates PrP 27-30, which polymerizes into amyloid. By attenuated total reflection-Fourier transform infrared spectroscopy, PrP 27-30 polymers contained 54% β-sheet, 25% α-helix, 10% turns, and 11% random coil; dispersion into detergent-lipid-protein-complexes preserved infectivity and secondary structure. Almost 60% of the β-sheet was low-frequency infrared-absorbing, reflecting intermolecular aggregation. Decreased low-frequency β-sheet and increased turn content were found after SDS/PAGE, which disassembled the amyloid polymers, denatured PrP 27-30, and diminished scrapie infectivity. Acid-induced transitions were reversible, whereas alkali produced an irreversible transition centered at pH 10 under conditions that diminished infectivity. Whether PrPSc synthesis involves a transition in the secondary structure of one or more domains of the cellular prion protein from α-helical, random coil, or turn into β-sheet remains to be established.

  5. Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding

    Directory of Open Access Journals (Sweden)

    Adami Christoph

    2003-02-01

    Full Text Available Background The rate at which fitness declines as an organism's genome accumulates random mutations is an important variable in several evolutionary theories. At an intuitive level, it might seem natural that random mutations should tend to interact synergistically, such that the rate of mean fitness decline accelerates as the number of random mutations is increased. However, in a number of recent studies, a prevalence of antagonistic epistasis (the tendency of multiple mutations to have a mitigating rather than reinforcing effect has been observed. Results We studied in silico the net amount and form of epistatic interactions in RNA secondary structure folding by measuring the fraction of neutral mutants as a function of mutational distance d. We found a clear prevalence of antagonistic epistasis in RNA secondary structure folding. By relating the fraction of neutral mutants at distance d to the average neutrality at distance d, we showed that this prevalence derives from the existence of many compensatory mutations at larger mutational distances. Conclusions Our findings imply that the average direction of epistasis in simple fitness landscapes is directly related to the density with which fitness peaks are distributed in these landscapes.

  6. Study of structure and residual stresses in cold rotary swaged tungsten heavy alloy

    Czech Academy of Sciences Publication Activity Database

    Kunčická, L.; Kocich, R.; Hervoches, Charles; Macháčková, A.

    2017-01-01

    Roč. 705, č. 9 (2017), s. 25-31 ISSN 0921-5093 R&D Projects: GA MŠk LM2015056 Institutional support: RVO:61389005 Keywords : Tungsten heavy alloy * residual stresses * neutron scattering * electron microscopy * work hardening Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 3.094, year: 2016

  7. Short Oligonucleotides Aligned in Stretched Humid Matrix: Secondary DNA Structure in Poly(vinyl alcohol) Environment

    KAUST Repository

    Hanczyc, Piotr

    2012-04-24

    We report that short, synthetic, double- as well as single-stranded DNA can be aligned in stretched humid poly(vinyl alcohol) (PVA) matrix, and the secondary structure (nucleobase orientation) can be characterized with linear dichroism (LD) spectroscopy. Oligonucleotides of lengths varying between 10 (3.4 nm) and 60 bases (20.4 nm) were investigated with respect to structural properties in the gel-like polymer environment. The DNA conformation as a function of relative humidity reveals a strong dependence of helical structure of DNA on PVA hydration level, results of relevance for nanotechnical studies of DNA-based supramolecular systems. Also, the PVA gel could provide possibilities to test models for nucleic acid interactions and distribution in cell contexts, including structural stability of genetic material in the cell and PVA-packaging for gene delivery. A method by which duplex oligonucleotides, with sequences designed to provide specific binding sites, become amenable to polarized-light spectroscopy opens up new possibilities for studying structure in DNA complexes with small adduct molecules as well as proteins. © 2012 American Chemical Society.

  8. Secondary Structure Prediction of Protein Constructs Using Random Incremental Truncation and Vacuum-Ultraviolet CD Spectroscopy

    Science.gov (United States)

    Pukáncsik, Mária; Orbán, Ágnes; Nagy, Kinga; Matsuo, Koichi; Gekko, Kunihiko; Maurin, Damien; Hart, Darren; Kézsmárki, István; Vertessy, Beata G.

    2016-01-01

    A novel uracil-DNA degrading protein factor (termed UDE) was identified in Drosophila melanogaster with no significant structural and functional homology to other uracil-DNA binding or processing factors. Determination of the 3D structure of UDE is excepted to provide key information on the description of the molecular mechanism of action of UDE catalysis, as well as in general uracil-recognition and nuclease action. Towards this long-term aim, the random library ESPRIT technology was applied to the novel protein UDE to overcome problems in identifying soluble expressing constructs given the absence of precise information on domain content and arrangement. Nine constructs of UDE were chosen to decipher structural and functional relationships. Vacuum ultraviolet circular dichroism (VUVCD) spectroscopy was performed to define the secondary structure content and location within UDE and its truncated variants. The quantitative analysis demonstrated exclusive α-helical content for the full-length protein, which is preserved in the truncated constructs. Arrangement of α-helical bundles within the truncated protein segments suggested new domain boundaries which differ from the conserved motifs determined by sequence-based alignment of UDE homologues. Here we demonstrate that the combination of ESPRIT and VUVCD spectroscopy provides a new structural description of UDE and confirms that the truncated constructs are useful for further detailed functional studies. PMID:27273007

  9. Secondary Structure Prediction of Protein Constructs Using Random Incremental Truncation and Vacuum-Ultraviolet CD Spectroscopy.

    Directory of Open Access Journals (Sweden)

    Mária Pukáncsik

    Full Text Available A novel uracil-DNA degrading protein factor (termed UDE was identified in Drosophila melanogaster with no significant structural and functional homology to other uracil-DNA binding or processing factors. Determination of the 3D structure of UDE is excepted to provide key information on the description of the molecular mechanism of action of UDE catalysis, as well as in general uracil-recognition and nuclease action. Towards this long-term aim, the random library ESPRIT technology was applied to the novel protein UDE to overcome problems in identifying soluble expressing constructs given the absence of precise information on domain content and arrangement. Nine constructs of UDE were chosen to decipher structural and functional relationships. Vacuum ultraviolet circular dichroism (VUVCD spectroscopy was performed to define the secondary structure content and location within UDE and its truncated variants. The quantitative analysis demonstrated exclusive α-helical content for the full-length protein, which is preserved in the truncated constructs. Arrangement of α-helical bundles within the truncated protein segments suggested new domain boundaries which differ from the conserved motifs determined by sequence-based alignment of UDE homologues. Here we demonstrate that the combination of ESPRIT and VUVCD spectroscopy provides a new structural description of UDE and confirms that the truncated constructs are useful for further detailed functional studies.

  10. The formation of a native-like structure containing eight conserved hydrophobic residues is rate limiting in two-state protein folding of ACBP

    DEFF Research Database (Denmark)

    Kragelund, Birthe Brandt; Osmark, Peter; Neergaard, Thomas B.

    1999-01-01

    probed, that are critical for fast productive folding. The residues are all hydrophobic and located in the interface between the N- and C-terminal helices. The results suggest that one specific site dominated by conserved hydrophobic residues forms the structure of the productive rate-determining folding...

  11. Structural model of a putrescine-cadaverine permease from Trypanosoma cruzi predicts residues vital for transport and ligand binding.

    Science.gov (United States)

    Soysa, Radika; Venselaar, Hanka; Poston, Jacqueline; Ullman, Buddy; Hasne, Marie-Pierre

    2013-06-15

    The TcPOT1.1 gene from Trypanosoma cruzi encodes a high affinity putrescine-cadaverine transporter belonging to the APC (amino acid/polyamine/organocation) transporter superfamily. No experimental three-dimensional structure exists for any eukaryotic member of the APC family, and thus the structural determinants critical for function of these permeases are unknown. To elucidate the key residues involved in putrescine translocation and recognition by this APC family member, a homology model of TcPOT1.1 was constructed on the basis of the atomic co-ordinates of the Escherichia coli AdiC arginine/agmatine antiporter crystal structure. The TcPOT1.1 homology model consisted of 12 transmembrane helices with the first ten helices organized in two V-shaped antiparallel domains with discontinuities in the helical structures of transmembrane spans 1 and 6. The model suggests that Trp241 and a Glu247-Arg403 salt bridge participate in a gating system and that Asn245, Tyr148 and Tyr400 contribute to the putrescine-binding pocket. To test the validity of the model, 26 site-directed mutants were created and tested for their ability to transport putrescine and to localize to the parasite cell surface. These results support the robustness of the TcPOT1.1 homology model and reveal the importance of specific aromatic residues in the TcPOT1.1 putrescine-binding pocket.

  12. Secondary structure and dynamics study of the intrinsically disordered silica-mineralizing peptide P 5 S 3 during silicic acid condensation and silica decondensation

    Energy Technology Data Exchange (ETDEWEB)

    Zerfass, Christian; Buchko, Garry W.; Shaw, Wendy J.; Hobe, Stephan; Paulsen, Harold

    2017-08-24

    The silica forming repeat R5 of sil1 from Cylindrotheca fusiformis was the blueprint for the design of P5S3, a 50-residue peptide which can be produced in large amounts by recombinant bacterial expression. It contains five protein kinase A target sites and is highly cationic due to 10 lysine and 10 arginine residues. In the presence of supersaturated ortho silicic acid P5S3 strongly enhances silica-formation whereas it retards the dissolution of amorphous silica (SiO2) at globally undersaturated concentrations. The secondary structure of P5S3 during these different functions was studied by circular dichroism (CD), complemented by nuclear magnetic resonance (NMR) studies of the peptide in the absence of silicate. The NMR studies of dual-labeled (13C, 15N) P5S3 revealed a disordered structure at pH 2.8 and 4.5. Within the pH range of 4.5 to 9.5, the CD data verified the disordered secondary structure but also suggested the presence of some polyproline II character in the absence of silicic acid. Upon silicic acid polymerization and during dissolution of preformed silica, the CD spectrum of P5S3 indicated partial transition into an α-helical conformation which was transient during silica-dissolution. Consequently, the secondary structural changes observed for P5S3 correlate with the presence of oli-gomeric/polymeric silicic acid, presumably due to P5S3-silicic acid interactions. These interactions appear, at least in part, ionic in nature since dodecylsulfate micelles, which are negatively charged, cause similar conformational shifts to P5S3 in the absence of silica while ß-D-dodecyl maltoside micelles, which are neutral, do not. Thus, P5S3 influences both the condensation of silicic acid into silica and its decondensation back to silicic acid. Moreover, the dynamics of these pro-cesses may be indirectly monitored by following structural changes to P5S3 with CD spectroscopy.

  13. SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data.

    Science.gov (United States)

    Ouyang, Zhengqing; Snyder, Michael P; Chang, Howard Y

    2013-02-01

    We present an integrative approach, SeqFold, that combines high-throughput RNA structure profiling data with computational prediction for genome-scale reconstruction of RNA secondary structures. SeqFold transforms experimental RNA structure information into a structure preference profile (SPP) and uses it to select stable RNA structure candidates representing the structure ensemble. Under a high-dimensional classification framework, SeqFold efficiently matches a given SPP to the most likely cluster of structures sampled from the Boltzmann-weighted ensemble. SeqFold is able to incorporate diverse types of RNA structure profiling data, including parallel analysis of RNA structure (PARS), selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), fragmentation sequencing (FragSeq) data generated by deep sequencing, and conventional SHAPE data. Using the known structures of a wide range of mRNAs and noncoding RNAs as benchmarks, we demonstrate that SeqFold outperforms or matches existing approaches in accuracy and is more robust to noise in experimental data. Application of SeqFold to reconstruct the secondary structures of the yeast transcriptome reveals the diverse impact of RNA secondary structure on gene regulation, including translation efficiency, transcription initiation, and protein-RNA interactions. SeqFold can be easily adapted to incorporate any new types of high-throughput RNA structure profiling data and is widely applicable to analyze RNA structures in any transcriptome.

  14. Comparison of primary and secondary 26S rRNA structures in two Tetrahymena species: evidence for a strong evolutionary and structural constraint in expansion segments

    DEFF Research Database (Denmark)

    Engberg, J; Nielsen, Henrik; Lenaers, G

    1990-01-01

    . These are regions within the common core of secondary structure where expansions have taken place during the evolution of the rRNA of higher eukaryotes. The dispensable nature of some of the expansion segments has been taken as evidence of their non-functionality. However, our data show that a considerable......We have determined the nucleotide sequence of the 26S large subunit (LSU) rRNA genes for two Tetrahymena species, T. thermophila and T. pyriformis. The inferred rRNA sequences are presented in their most probable secondary structures based on compensatory mutations, energy, and conservation...... selective constraint has operated to preserve the secondary structure of these segments. Especially in the case of the D2 and D8 segments, the presence of a considerable number of compensatory base changes suggests that the secondary structure of these regions is of functional importance. Alternatively...

  15. Solution NMR structure and inhibitory effect against amyloid-β fibrillation of Humanin containing a D-isomerized serine residue

    Energy Technology Data Exchange (ETDEWEB)

    Alsanousi, Nesreen [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Sugiki, Toshihiko, E-mail: sugiki@protein.osaka-u.ac.jp [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Furuita, Kyoko; So, Masatomo; Lee, Young-Ho; Fujiwara, Toshimichi [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Kojima, Chojiro, E-mail: kojima-chojiro-xk@ynu.ac.jp [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama 240-8501 (Japan)

    2016-09-02

    Humanin comprising 24 amino acid residues is a bioactive peptide that has been isolated from the brain tissue of patients with Alzheimer's disease. Humanin reportedly suppressed aging-related death of various cells due to amyloid fibrils and oxidative stress. There are reports that the cytoprotective activity of Humanin was remarkably enhanced by optical isomerization of the Ser14 residue from L to D form, but details of the molecular mechanism remained unclear. Here we demonstrated that Humanin D-Ser14 exhibited potent inhibitory activity against fibrillation of amyloid-β and remarkably higher binding affinity for amyloid-β than that of the Humanin wild-type and S14G mutant. In addition, we determined the solution structure of Humanin D-Ser14 by nuclear magnetic resonance (NMR) and showed that D-isomerization of the Ser14 residue enables drastic conformational rearrangement of Humanin. Furthermore, we identified an amyloid-β-binding site on Humanin D-Ser14 at atomic resolution by NMR. These biophysical and high-resolution structural analyses clearly revealed structure–function relationships of Humanin and explained the driving force of the drastic conformational change and molecular basis of the potent anti-amyloid-β fibrillation activity of Humanin caused by D-isomerization of the Ser14 residue. This is the first study to show correlations between the functional activity, tertiary structure, and partner recognition mode of Humanin and may lead to elucidation of the molecular mechanisms of the cytoprotective activity of Humanin. - Highlights: • Humanin D-Ser14 showed the strongest inhibitory activity against Aβ40 fibrillation. • NMR structure of Humanin D-Ser14 was determined in alcohol/water mixture solution. • Humanin D-Ser14 directly bound Aβ40 stronger than Humanin wild-type and Humanin S14G. • Aβ40 and zinc ion binding sites of Humanin D-Ser14 were identified. • Structure around Ser14 of Humanin is critical for Aβ40 binding and

  16. Cadmium and Secondary Structure-dependent Function of a Degron in the Pca1p Cadmium Exporter.

    Science.gov (United States)

    Smith, Nathan; Wei, Wenzhong; Zhao, Miaoyun; Qin, Xiaojuan; Seravalli, Javier; Kim, Heejeong; Lee, Jaekwon

    2016-06-03

    Protein turnover is a critical cellular process regulating biochemical pathways and destroying terminally misfolded or damaged proteins. Pca1p, a cadmium exporter in the yeast Saccharomyces cerevisiae, is rapidly degraded by the endoplasmic reticulum-associated degradation (ERAD) system via a cis-acting degron that exists at the 250-350 amino acid region of Pca1p and is transferable to other proteins to serve as a degradation signal. Cadmium stabilizes Pca1p in a manner dependent on the degron. This suggested that cadmium-mediated masking of the degron impedes its interaction with the molecular factors involved in the ERAD. The characteristics and mechanisms of action of the degron in Pca1p and most of those in other proteins however remain to be determined. The results presented here indicate that specific cysteine residues in a degron of Pca1p sense cadmium. An unbiased approach selecting non-functional degrons indicated a critical role of hydrophobic amino acids in the degron for its function. A secondary structure modeling predicted the formation of an amphipathic helix. Site-directed mutagenesis confirmed the functional significance of the hydrophobic patch. Last, hydrophobic amino acids in the degron- and cadmium-binding region affected the interaction of Pca1p with the Ssa1p molecular chaperone, which is involved in ERAD. These results reveal the mechanism of action of the degron, which might be useful for the identification and characterization of other degrons. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Salient design features of secondary containment structure of Narora Atomic Power Project

    International Nuclear Information System (INIS)

    Rahalkar, B.D.

    1975-01-01

    Design of the secondary containment structure for Narora Atomic Power Project is an improvement over the two earlier structures at of Rajasthan and Kalpakkam wherein Candu-type of reactors are involved. The major improvements envisaged are : to limit the leakage through the double containment envelope to 0.1% of volume of the building per day as against 0.1% per hour achieved for earlier stations; to separate heavy water atmosphere from that of light water for effective heavy water recovery; and better man-rem budgetting by limiting inner containment structure upto boiler room floor level and making boiler room area accessible during normal operation for servicing of light water system equipment. Narora Atomic Power Station is located in the Indo-Gangetic alluvial plains in seismically active zone IV. Comprehensive soil investigation, including dynamic properties of soil is required to be undertaken as the foundation level of the containment structure is 17 M below the ground level. The salient results of this investigation relevant to the foundations as well as type of foundation proposed are presented in brief. Double containment concept similar to that adopted for Kalpakkam station is provided for this station also. However, necessary changes in design to withstand large earthquake forces are required to be made. These design problems are discussed in brief. (author)

  18. Evidence for the residual tertiary structure in the urea-unfolded form of bacteriophage T5 endolysin.

    Science.gov (United States)

    Kutyshenko, Victor P; Prokhorov, Dmitry A; Mikoulinskaia, Galina V; Molochkov, Nikolai V; Paskevich, Svetlana I; Uversky, Vladimir N

    2017-05-01

    Using high-resolution NMR spectroscopy, we studied peculiarities of the unfolding process of the bacteriophage T5 endolysin (EndoT5) by strong denaturants. It was shown that in the absence of zinc ions this protein is mostly unfolded in the solution of 8 M urea or 6 M guanidine hydrochloride. However, in the presence of zinc ions EndoT5 unfolding can be achieved only in acidic solutions (at pH  4.0 NMR spectra of the metal-bound protein (Zn 2+ -Ca 2+ -EndoT5 or Zn 2+ -EndoT5 complexes) exhibit a few chemical shifts characteristic of the native or native-like proteins. Our data, including the pH-titration curve with the pK of ~5, suggested involvement of the zinc-binding histidines in the stabilization of this protein. Up-field signals that appear in the NMR spectra of apo-EndoT5 in the presence of high concentrations of strong denaturants are probably derived from the amino acid residues included in the formation of structured hydrophobic cluster, which likely corresponds to the 81-93 region of EndoT5 and contains some residual tertiary structure. It is possible also that this hydrophobic fragment serves as a foundation for the formation of structured cluster in the unfolded state.

  19. ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction.

    Science.gov (United States)

    Sahoo, Sudhakar; Świtnicki, Michał P; Pedersen, Jakob Skou

    2016-09-01

    Recently, new RNA secondary structure probing techniques have been developed, including Next Generation Sequencing based methods capable of probing transcriptome-wide. These techniques hold great promise for improving structure prediction accuracy. However, each new data type comes with its own signal properties and biases, which may even be experiment specific. There is therefore a growing need for RNA structure prediction methods that can be automatically trained on new data types and readily extended to integrate and fully exploit multiple types of data. Here, we develop and explore a modular probabilistic approach for integrating probing data in RNA structure prediction. It can be automatically trained given a set of known structures with probing data. The approach is demonstrated on SHAPE datasets, where we evaluate and selectively model specific correlations. The approach often makes superior use of the probing data signal compared to other methods. We illustrate the use of ProbFold on multiple data types using both simulations and a small set of structures with both SHAPE, DMS and CMCT data. Technically, the approach combines stochastic context-free grammars (SCFGs) with probabilistic graphical models. This approach allows rapid adaptation and integration of new probing data types. ProbFold is implemented in C ++. Models are specified using simple textual formats. Data reformatting is done using separate C ++ programs. Source code, statically compiled binaries for x86 Linux machines, C ++ programs, example datasets and a tutorial is available from http://moma.ki.au.dk/prj/probfold/ : jakob.skou@clin.au.dk Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  20. Structure on lower montane secondary forests and shrublands in northern Antioquia, Colombia

    Directory of Open Access Journals (Sweden)

    Héctor Iván Restrepo

    2012-12-01

    Full Text Available Tropical montane forests have the highest biodiversity in the world. However, they are being seriously threatened by deforestation, degradation and climate change. Their conservation is also at risk because we know little about their ecology. We established four permanent plots at two successional stages: secondary forest and cultivated areas. Distribution by diameter was analyzed using Hugershoff non-linear models. We estimated biomass of trees above and below-ground along with liana, under bush, understory and epiphyte biomass. In addition we measured necromass of standing dead trees, litter from wood and litterfall. We estimated total carbon in living and dead organic matter and in the soil. All the diametric distributions were of a J-inverted shape. The Hugershoff models successfully explained the behavior of the secondary forest and shrub structure. The biomass, necromass and total carbon were estimated at 185.7 and 29.8 t ha-1, 9.2 and 3.8 t ha-1 and 151.7 and 78.2 t ha-1 respectively for forests and cultivated areas. An interesting finding is the high biomass of trees below-ground, lianas and epiphytes in tropical montane forest. Tropical montane forests provide important environmental services and therefore we have to search for better ways to conserve them.

  1. Impact of Microscale and Pilot-Scale Freeze-Drying on Protein Secondary Structures: Sucrose Formulations of Lysozyme and Catalase.

    Science.gov (United States)

    Peters, Björn-Hendrik; Leskinen, Jari T T; Molnár, Ferdinand; Ketolainen, Jarkko

    2015-11-01

    Microscale (MS) freeze-drying offers rapid process cycles for early-stage formulation development. The effects of the MS approach on the secondary structures of two model proteins, lysozyme and catalase, were compared with pilot-scale (PS) vial freeze-drying. The secondary structures were assessed by attenuated total reflection Fourier transformed infrared spectroscopy. Formulations were made with increasing sucrose-protein ratios. Freeze-drying protocols involved regular cooling without thermal treatment and annealing with MS and PS equipment, and cooling rate variations with the MS. Principal component analysis of smoothed second-derivative amide I spectra revealed sucrose-protein ratio-dependent shifts toward α-helical structures. Transferability of sucrose-protein formulations from MS to PS vial freeze-drying was evidenced at regular cooling rates. Local differences in protein secondary structures between the bottom and top of sucrose-catalase samples could be detected at the sucrose-catalase ratios of 1 and 2, this being related to the initial filling height and ice crystal morphology. Annealing revealed temperature, protein, formulation, and sample location-dependent effects influencing surface morphology at the top, or causing protein secondary structure perturbation at the bottom. With the MS approach, protein secondary structure differences at different cooling rates could be detected for sucrose-lysozyme samples at the sucrose-lysozyme ratio of 1. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

  2. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations.

    Science.gov (United States)

    Lees, Jonathan G; Janes, Robert W

    2008-01-15

    A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.

  3. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

    Directory of Open Access Journals (Sweden)

    Lees Jonathan G

    2008-01-01

    Full Text Available Abstract Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. Results In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Conclusion Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.

  4. Residual deposits (residual soil)

    International Nuclear Information System (INIS)

    Khasanov, A.Kh.

    1988-01-01

    Residual soil deposits is accumulation of new formate ore minerals on the earth surface, arise as a result of chemical decomposition of rocks. As is well known, at the hyper genes zone under the influence of different factors (water, carbonic acid, organic acids, oxygen, microorganism activity) passes chemical weathering of rocks. Residual soil deposits forming depends from complex of geologic and climatic factors and also from composition and physical and chemical properties of initial rocks

  5. Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.

    Directory of Open Access Journals (Sweden)

    Huiying Zhao

    Full Text Available As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most existing techniques do. The method first predicts protein-DNA complex structure by utilizing the template-based structure prediction technique HHblits, followed by binding affinity prediction based on a knowledge-based energy function (Distance-scaled finite ideal-gas reference state for protein-DNA interactions. A leave-one-out cross validation of the method based on 179 DNA-binding and 3797 non-binding protein domains achieves a Matthews correlation coefficient (MCC of 0.77 with high precision (94% and high sensitivity (65%. We further found 51% sensitivity for 82 newly determined structures of DNA-binding proteins and 56% sensitivity for the human proteome. In addition, the method provides a reasonably accurate prediction of DNA-binding residues in proteins based on predicted DNA-binding complex structures. Its application to human proteome leads to more than 300 novel DNA-binding proteins; some of these predicted structures were validated by known structures of homologous proteins in APO forms. The method [SPOT-Seq (DNA] is available as an on-line server at http://sparks-lab.org.

  6. Residue Modification and Mass Spectrometry for the Investigation of Structural and Metalation Properties of Metallothionein and Cysteine-Rich Proteins.

    Science.gov (United States)

    Irvine, Gordon W; Stillman, Martin J

    2017-04-26

    Structural information regarding metallothioneins (MTs) has been hard to come by due to its highly dynamic nature in the absence of metal-thiolate cluster formation and crystallization difficulties. Thus, typical spectroscopic methods for structural determination are limited in their usefulness when applied to MTs. Mass spectrometric methods have revolutionized our understanding of protein dynamics, structure, and folding. Recently, advances have been made in residue modification mass spectrometry in order to probe the hard-to-characterize structure of apo- and partially metalated MTs. By using different cysteine specific alkylation reagents, time dependent electrospray ionization mass spectrometry (ESI-MS), and step-wise "snapshot" ESI-MS, we are beginning to understand the dynamics of the conformers of apo-MT and related species. In this review we highlight recent papers that use these and similar techniques for structure elucidation and attempt to explain in a concise manner the data interpretations of these complex methods. We expect increasing resolution in our picture of the structural conformations of metal-free MTs as these techniques are more widely adopted and combined with other promising tools for structural elucidation.

  7. [Partially unfolded state of lysozyme with a developed secondary structure in dimethylsulfoxide].

    Science.gov (United States)

    Timchenko, A A; Kirkitadze, M D; Prokhorov, D A; Potekhin, S A; Serdiuk, I N

    1996-06-01

    The conformation of a chicken egg lysozyme molecule (dimensions, stoichiometry of its associates, and the degree of helicity) in DMSO was studied by small-angle neutron scattering, dynamic light scattering, and optical rotatory dispersion in the visible region of the spectrum. At high DMSO concentrations (70%), the protein was shown to exist as a dimer. The monomer molecules in the dimer adopt a partially unfolded conformation, with dimensions substantially greater than those in the native state and a high content of secondary structure (the degree of helicity is close to that of native lysozyme). This approach provides a unique possibility to assess the compactness of molecules in associates, which may be very useful in studying protein self-organization.

  8. Structural Equations Model (SEM of a questionnaire on the evaluation of intercultural secondary education classrooms

    Directory of Open Access Journals (Sweden)

    Eva María Olmedo Moreno

    2014-12-01

    Full Text Available This research includes the design of a questionnaire for evaluating cultural coexistence in secondary education classrooms (Berrocal, Olmedo & Olmos, 2014; Olmedo et al., 2014, as well as the comparison of its psychometric properties in a multicultural population of schools in southern Spain. An attempt is made to create a valid, reliable and useful tool for teachers to measure conflict situations in the classroom, as well as understanding the nature of the conflict from the point of view of all those involved. The metric aspects show a maximized content and construct validity (Muñiz, 2010 using a Structural Equation Model (SEM and Confirmatory Factor Analysis (CFA analysis, checking and modifying its model by Wald and Lagrange indicators (Bentler, 2007, to obtain the most adjusted model to the theoretical and goodness criteria.

  9. Molecular and crystal structure of the antibiotic enniatin B, a secondary microbial metabolite

    International Nuclear Information System (INIS)

    Zhukhlistova, N.E.; Tishchenko, G.N.; Tolstykh, I.V.; Zenkova, V.A.

    1999-01-01

    Single crystals of the secondary microbial metabolite C 33 H 57 N 3 O 9 ·1(2/3)H 2 O with the known molecular weight were studied by the method of X-ray diffraction analysis, where a=b=15.102(3) A, c=14.548(3) A, sp. gr.R3, R=0.057. In the course of the structure determination, it was established that the substance is a natural antibiotic, namely, enniatin B. The conformation of its molecule is similar to that of the known synthetic antibiotic. The main difference between the natural and synthesized forms reduces to the different numbers of water molecules and their arrangement in the cavity of the antibiotic molecule

  10. Examining the dimensional structure models of secondary traumatic stress based on DSM-5 symptoms.

    Science.gov (United States)

    Mordeno, Imelu G; Go, Geraldine P; Yangson-Serondo, April

    2017-02-01

    Latent factor structure of Secondary Traumatic Stress (STS) has been examined using Diagnostic Statistic Manual-IV (DSM-IV)'s Posttraumatic Stress Disorder (PTSD) nomenclature. With the advent of Diagnostic Statistic Manual-5 (DSM-5), there is an impending need to reexamine STS using DSM-5 symptoms in light of the most updated PTSD models in the literature. The study investigated and determined the best fitted PTSD models using DSM-5 PTSD criteria symptoms. Confirmatory factor analysis (CFA) was conducted to examine model fit using the Secondary Traumatic Stress Scale in 241 registered and practicing Filipino nurses (166 females and 75 males) who worked in the Philippines and gave direct nursing services to patients. Based on multiple fit indices, the results showed the 7-factor hybrid model, comprising of intrusion, avoidance, negative affect, anhedonia, externalizing behavior, anxious arousal, and dysphoric arousal factors has excellent fit to STS. This model asserts that: (1) hyperarousal criterion needs to be divided into anxious and dysphoric arousal factors; (2) symptoms characterizing negative and positive affect need to be separated to two separate factors, and; (3) a new factor would categorize externalized, self-initiated impulse and control-deficit behaviors. Comparison of nested and non-nested models showed Hybrid model to have superior fit over other models. The specificity of the symptom structure of STS based on DSM-5 PTSD criteria suggests having more specific interventions addressing the more elaborate symptom-groupings that would alleviate the condition of nurses exposed to STS on a daily basis. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Linker histone partial phosphorylation: effects on secondary structure and chromatin condensation

    Science.gov (United States)

    Lopez, Rita; Sarg, Bettina; Lindner, Herbert; Bartolomé, Salvador; Ponte, Inma; Suau, Pedro; Roque, Alicia

    2015-01-01

    Linker histones are involved in chromatin higher-order structure and gene regulation. We have successfully achieved partial phosphorylation of linker histones in chicken erythrocyte soluble chromatin with CDK2, as indicated by HPCE, MALDI-TOF and Tandem MS. We have studied the effects of linker histone partial phosphorylation on secondary structure and chromatin condensation. Infrared spectroscopy analysis showed a gradual increase of β-structure in the phosphorylated samples, concomitant to a decrease in α-helix/turns, with increasing linker histone phosphorylation. This conformational change could act as the first step in the phosphorylation-induced effects on chromatin condensation. A decrease of the sedimentation rate through sucrose gradients of the phosphorylated samples was observed, indicating a global relaxation of the 30-nm fiber following linker histone phosphorylation. Analysis of specific genes, combining nuclease digestion and qPCR, showed that phosphorylated samples were more accessible than unphosphorylated samples, suggesting local chromatin relaxation. Chromatin aggregation was induced by MgCl2 and analyzed by dynamic light scattering (DLS). Phosphorylated chromatin had lower percentages in volume of aggregated molecules and the aggregates had smaller hydrodynamic diameter than unphosphorylated chromatin, indicating that linker histone phosphorylation impaired chromatin aggregation. These findings provide new insights into the effects of linker histone phosphorylation in chromatin condensation. PMID:25870416

  12. Interaction Of Calcium Phosphate Nanoparticles With Human Chorionic Gonadotropin Modifies Secondary And Tertiary Protein Structure

    Directory of Open Access Journals (Sweden)

    Al-Hakeim Hussein K

    2015-12-01

    Full Text Available Calcium phosphate nanoparticles (CaPNP have good biocompatibility and bioactivity inside human body. In this study, the interaction between CaPNP and human chorionic gonadotropin (hCG was analyzed to determine the changes in the protein structure in the presence of CaPNP and the quantity of protein adsorbed on the CaPNP surface. The results showed a significant adsorption of hCG on the CaPNP nanoparticle surface. The optimal fit was achieved using the Sips isotherm equation with a maximum adsorption capacity of 68.23 µg/mg. The thermodynamic parameters, including ∆H° and ∆G°, of the adsorption process are positive, whereas ∆S° is negative. The circular dichroism results of the adsorption of hCG on CaPNP showed the changes in its secondary structure; such changes include the decomposition of α-helix strand and the increase in β-pleated sheet and random coil percentages. Fluorescence study indicated minimal changes in the tertiary structure near the microenvironment of the aromatic amino acids such as tyrosine and phenyl alanine caused by the interaction forces between the CaPNP and hCG protein. The desorption process showed that the quantity of the hCG desorbed significantly increases as temperature increases, which indicates the weak forces between hCG and the surface.

  13. Phosphorylation regulates the secondary structure and function of dentin phosphoprotein peptides

    Energy Technology Data Exchange (ETDEWEB)

    Villarreal-Ramirez, Eduardo; Eliezer, David; Garduño-Juarez, Ramon; Gericke, Arne; Perez-Aguilar, Jose Manuel; Boskey, Adele

    2017-02-01

    Dentin phosphoprotein (DPP) is the most acidic protein in vertebrates and structurally is classified as an intrinsically disordered protein. Functionally, DPP is related to dentin and bone formation, however the specifics of such association remain unknown. Here, we used atomistic molecular dynamics simulations to screen selected binding domains of DPP onto hydroxyapatite (HA), which is one of its important interacting partners. From these results, we selected a functionally relevant peptide, Ace-SSDSSDSSDSSDSSD-NH2 (named P5) and its phosphorylated form (named P5P), for experimental characterization. SAXS experiments indicated that in solution P5 was disordered, possibly in an extended conformation while P5P displayed more compact globular conformations. Circular dichroism and FTIR confirmed that, either in the presence or absence of Ca2 +/HA, P5 adopts a random coil structure, whereas its phosphorylated counterpart, P5P, has a more compact arrangement associated with conformations that display β-sheet and α-helix motifs when bound to HA. In solution, P5 inhibited HA crystal growth, whereas at similar concentrations, P5P stimulated it. These findings suggest that phosphorylation controls the transient formation of secondary and tertiary structure of DPP peptides, and, most likely of DPP itself, which in turn controls HA growth in solution and possibly HA growth in mineralized tissues.

  14. FPGA accelerator for protein secondary structure prediction based on the GOR algorithm.

    Science.gov (United States)

    Xia, Fei; Dou, Yong; Lei, Guoqing; Tan, Yusong

    2011-02-15

    Protein is an important molecule that performs a wide range of functions in biological systems. Recently, the protein folding attracts much more attention since the function of protein can be generally derived from its molecular structure. The GOR algorithm is one of the most successful computational methods and has been widely used as an efficient analysis tool to predict secondary structure from protein sequence. However, the execution time is still intolerable with the steep growth in protein database. Recently, FPGA chips have emerged as one promising application accelerator to accelerate bioinformatics algorithms by exploiting fine-grained custom design. In this paper, we propose a complete fine-grained parallel hardware implementation on FPGA to accelerate the GOR-IV package for 2D protein structure prediction. To improve computing efficiency, we partition the parameter table into small segments and access them in parallel. We aggressively exploit data reuse schemes to minimize the need for loading data from external memory. The whole computation structure is carefully pipelined to overlap the sequence loading, computing and back-writing operations as much as possible. We implemented a complete GOR desktop system based on an FPGA chip XC5VLX330. The experimental results show a speedup factor of more than 430x over the original GOR-IV version and 110x speedup over the optimized version with multi-thread SIMD implementation running on a PC platform with AMD Phenom 9650 Quad CPU for 2D protein structure prediction. However, the power consumption is only about 30% of that of current general-propose CPUs.

  15. Structure and properties of silver sulfate complexes derived from dipyridyl methylthio ligands with secondary donor site

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Wen-Hua; Yan, Hao-Jie; Chen, Hui; Liu, Rui-Heng; Li, Ai-Min; Wang, Guo [Beijing Key Laboratory for Optical Materials and Photonic Devices, Department of Chemistry, Capital Normal University, Beijing 100048 (China); Wan, Chong-Qing, E-mail: wancq@cnu.edu.cn [Beijing Key Laboratory for Optical Materials and Photonic Devices, Department of Chemistry, Capital Normal University, Beijing 100048 (China); State Key Laboratory of Structural Chemistry in China, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002 (China)

    2017-06-15

    Dipyridyl sulphide ligands 4-(pyridin-4-ylmethylthio)pyridine (abbreviated as L1) and 3-(pyridin-4-ylmethylthio)pyridine (abbreviated as L2) have been designed and used as μ-{sub N},{sub N}-bridging linkages to construct coordination polymers with free –S–CH{sub 2}– groups as secondary donor sites. By use solvent control method, coordination polymers ([Ag{sub 3}SO{sub 4}(L1){sub 3}](Cl)·4.5H{sub 2}O){sub ∞}(1), ([Ag{sub 2}SO{sub 4}(L1){sub 2}]·6H{sub 2}O·2CH{sub 3}OH){sub ∞}(2), ([Ag{sub 2}SO{sub 4}(L2){sub 2}]·H{sub 2}O){sub ∞}(3) and ([Ag{sub 4}(SO{sub 4}){sub 2}(L2){sub 4}]·5H{sub 2}O){sub ∞}(4) with different architectures were obtained. Complexes 1, 3 and 4 feature 1D channel with different sizes and structures. Complex 1 exhibits guest exchange by THF and 1,4-dioxane, and Hg{sup 2+} sorption ability from solution due to its relative larger channel and available bonding sites of –S– exposed to the channel region. All complexes have been characterized through single-crystal and powder X-ray diffraction (PXRD), FT-IR spectra, X-ray photoelectron spectroscopy (XPS), elemental and thermogravimetric analyses. The guest exchange and Hg{sup 2+} sorption were monitored and identified, and the structure-property relationship of coordination polymers 1–4 are discussed. - Graphical abstract: Coordination polymers of silver(I) sulfate with secondary donor sites are shown guest exchange property and Hg{sup 2+} absorb ability from solution. This work provides a new method to construct functional materials with potential application. - Highlights: • New example of constructing functional coordination polymer with secondary donor methylthio group. • Guest exchange and interesting Hg(II) absorb ability from solution are investigated. • New method to construct functional materials with potential application.

  16. In-situ measurements for assessment of residual radiation field on incore structural components of research reactor Cirus

    International Nuclear Information System (INIS)

    Chaudhary, P.B.; Varughese, A.; Gopalakrishnan, R.K.; Mishra, S.G.; Prasad, S.K.; Vakharwala, K.J.

    2003-01-01

    In-situ radiation field measurements on in-core components of Cirus reactor were carried out during the refurbishing outage of the reactor. The data aided in characterization studies for evaluation of residual activity in the structural components of the reactor after four decades of its operation. The study led to the generation of a database which served as a primary input in decision making for various refurbishing activities related to in-core components of the reactor. The measurements also helped in dose budgeting during the refurbishing activities. The radiation field measurements were repeated in near identical conditions to asses the decay pattern of the residual activity. It was observed that the reduction of 35-40% in radiation field over a period of ∼-1200 days can be correlated to the half-life of radionuclides produced by neutron activation of structural components. This paper describes, in detail, the radiation field measurements carried out and the measurement technique employed for in-situ measurements in generating a reliable database for planning of the future decommissioning activities of the reactor. (author)

  17. Role of cysteine residues in the structure, stability, and alkane producing activity of cyanobacterial aldehyde deformylating oxygenase.

    Directory of Open Access Journals (Sweden)

    Yuuki Hayashi

    Full Text Available Aldehyde deformylating oxygenase (AD is a key enzyme for alkane biosynthesis in cyanobacteria, and it can be used as a catalyst for alkane production in vitro and in vivo. However, three free Cys residues in AD may impair its catalytic activity by undesired disulfide bond formation and oxidation. To develop Cys-deficient mutants of AD, we examined the roles of the Cys residues in the structure, stability, and alkane producing activity of AD from Nostoc punctiforme PCC 73102 by systematic Cys-to-Ala/Ser mutagenesis. The C71A/S mutations reduced the hydrocarbon producing activity of AD and facilitated the formation of a dimer, indicating that the conserved Cys71, which is located in close proximity to the substrate-binding site, plays crucial roles in maintaining the activity, structure, and stability of AD. On the other hand, mutations at Cys107 and Cys117 did not affect the hydrocarbon producing activity of AD. Therefore, we propose that the C107A/C117A double mutant is preferable to wild type AD for alkane production and that the double mutant may be used as a pseudo-wild type protein for further improvement of the alkane producing activity of AD.

  18. Assessment of Residual Life of concrete structures affected by reinforcement corrosion

    Directory of Open Access Journals (Sweden)

    Néstor F. Ortega

    2016-08-01

    The reinforcement corrosion is an electrochemical process that can be quantified by measuring the intensity of the current on the concrete surface. In this paper, to simulate the corrosion process, a current is externally applied to the studied structure reinforcement and then crack widths and vibration natural frequencies are measured. Based on these measurements a mathematical model is proposed to predict structure remaining life.

  19. Structure of non-(1-84) PTH fragments secreted by parathyroid glands in primary and secondary hyperparathyroidism.

    Science.gov (United States)

    D'Amour, Pierre; Brossard, Jean-Hugues; Rousseau, Louise; Nguyen-Yamamoto, Loan; Nassif, Edgard; Lazure, Claude; Gauthier, Dany; Lavigne, Jeffrey R; Zahradnik, Richard J

    2005-09-01

    Non-(1-84) parathyroid hormone (PTH) fragments are large circulating carboxyl-terminal (C) fragments with a partially preserved amino-terminal (N) structure. hPTH (7-84), a synthetic surrogate, has been demonstrated to exert biologic effects in vivo and in vitro which are opposite to those of hPTH (1-34) on the PTH/PTHrP type I receptor through a C-PTH receptor. We wanted to determine the N structure of non-(1-84) PTH fragments. Parathyroid cells isolated from glands obtained at surgery from three patients with primary hyperparathyroidism and three patients with secondary hyperparathyroidism were incubated with 35S-methionine to internally label their secretion products. Incubations were performed for 8 hours at the patient-ionized calcium concentration and in the presence of various protease inhibitors. The supernatant was fractionated by high-performance liquid chromatography (HPLC) and fractions were analyzed with PTH assays having (1 to 4) and (12 to 23) epitopes, respectively. The serum of each patient was similarly analyzed. Peaks of immunoreactivity identified were submitted to sequence analysis to recover the 35S-methionine residues in positions 8 and 18. Three regions of interest were identified with PTH assays. They corresponded to non-(1-84) PTH fragments (further divided in regions 3 and 4), a peak of N-PTH migrating in front of hPTH (1-84) (region 2) and a peak of immunoreactivity corresponding to the elution position of hPTH (1-84) (region 1). The last corresponded to a single sequence starting at position 1. Region 2 gave similar results in all cases (a major signal starting at position 1) but also sometimes minor sequences starting at position 4 or 7. Regions 3 and 4 always identified a major sequence starting at positions 7 and minor sequences starting at positions 8, 10, and 15. Surprisingly, a major signal starting at position 1 was also present in region 3. The HPLC profile obtained from a given patient's parathyroid cells was qualitatively

  20. Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.

    Science.gov (United States)

    Wu, Yang; Shi, Binbin; Ding, Xinqiang; Liu, Tong; Hu, Xihao; Yip, Kevin Y; Yang, Zheng Rong; Mathews, David H; Lu, Zhi John

    2015-09-03

    Recently, several experimental techniques have emerged for probing RNA structures based on high-throughput sequencing. However, most secondary structure prediction tools that incorporate probing data are designed and optimized for particular types of experiments. For example, RNAstructure-Fold is optimized for SHAPE data, while SeqFold is optimized for PARS data. Here, we report a new RNA secondary structure prediction method, restrained MaxExpect (RME), which can incorporate multiple types of experimental probing data and is based on a free energy model and an MEA (maximizing expected accuracy) algorithm. We first demonstrated that RME substantially improved secondary structure prediction with perfect restraints (base pair information of known structures). Next, we collected structure-probing data from diverse experiments (e.g. SHAPE, PARS and DMS-seq) and transformed them into a unified set of pairing probabilities with a posterior probabilistic model. By using the probability scores as restraints in RME, we compared its secondary structure prediction performance with two other well-known tools, RNAstructure-Fold (based on a free energy minimization algorithm) and SeqFold (based on a sampling algorithm). For SHAPE data, RME and RNAstructure-Fold performed better than SeqFold, because they markedly altered the energy model with the experimental restraints. For high-throughput data (e.g. PARS and DMS-seq) with lower probing efficiency, the secondary structure prediction performances of the tested tools were comparable, with performance improvements for only a portion of the tested RNAs. However, when the effects of tertiary structure and protein interactions were removed, RME showed the highest prediction accuracy in the DMS-accessible regions by incorporating in vivo DMS-seq data. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Determination of Endosperm Protein Secondary Structure in Hard Wheat Breeding Lines using Synchrotron Infrared Microspectroscopy

    International Nuclear Information System (INIS)

    Bonwell, E.; Fisher, T.; Fritz, A.; Wetzel, D.

    2008-01-01

    One molecular aspect of mature hard wheat protein quality for breadmaking is the relative amount of endosperm protein in the a-helix form compared with that in other secondary structure forms including β-sheet. Modeling of a-helix and β-sheet absorption bands that contribute to the amide I band at 1650 cm-1 was applied to more than 1500 spectra in this study. The microscopic view of wheat endosperm is dominated by many large starch granules with protein in between. The spectrum produced from in situ microspectroscopy of this mixture is dominated by carbohydrate bands from the large starch granules that fill up the field. The high spatial resolution achievable with synchrotron infrared microspectroscopy enables revealing good in situ spectra of the protein located interstitially. Synchrotron infrared microspectroscopic mapping of 4 μm thick frozen sections of endosperm in the subaleurone region provides spectra from a large number of pixels. Pixels with protein-dominated spectra are sorted out from among adjacent pixels to minimize the starch absorption and scattering contributions. Subsequent data treatment to extract information from the amide I band requires a high signal to noise ratio. Although spectral interference of the carbohydrate band on the amide band is not a problem, the scattering produced by the large starch granules diminishes the signal to noise ratio throughout the spectrum. High density mapping was done on beamlines U2B and U10B at the National Synchrotron Light Source at Brookhaven National Laboratory, Upton, NY. Mapping with a single masked spot size of 5.5 μm diameter or confocal 5 μm x 5 μm spot size, respectively, on the two beamlines used produced spectra for new breeding lines under current consideration. Appropriate data treatment allows calculation of a numerical estimate of the a-helix population relative to other secondary protein structures from the position and shape of the amide I absorption band. Current breeding lines show a

  2. Protein-associated water and secondary structure effect removal of blood proteins from metallic substrates.

    Science.gov (United States)

    Anand, Gaurav; Zhang, Fuming; Linhardt, Robert J; Belfort, Georges

    2011-03-01

    Removing adsorbed protein from metals has significant health and industrial consequences. There are numerous protein-adsorption studies using model self-assembled monolayers or polymeric substrates but hardly any high-resolution measurements of adsorption and removal of proteins on industrially relevant transition metals. Surgeons and ship owners desire clean metal surfaces to reduce transmission of disease via surgical instruments and minimize surface fouling (to reduce friction and corrosion), respectively. A major finding of this work is that, besides hydrophobic interaction adhesion energy, water content in an adsorbed protein layer and secondary structure of proteins determined the access and hence ability to remove adsorbed proteins from metal surfaces with a strong alkaline-surfactant solution (NaOH and 5 mg/mL SDS in PBS at pH 11). This is demonstrated with three blood proteins (bovine serum albumin, immunoglobulin, and fibrinogen) and four transition metal substrates and stainless steel (platinum (Pt), gold (Au), tungsten (W), titanium (Ti), and 316 grade stainless steel (SS)). All the metallic substrates were checked for chemical contaminations like carbon and sulfur and were characterized using X-ray photoelectron spectroscopy (XPS). While Pt and Au surfaces were oxide-free (fairly inert elements), W, Ti, and SS substrates were associated with native oxide. Difference measurements between a quartz crystal microbalance with dissipation (QCM-D) and surface plasmon resonance spectroscopy (SPR) provided a measure of the water content in the protein-adsorbed layers. Hydrophobic adhesion forces, obtained with atomic force microscopy, between the proteins and the metals correlated with the amount of the adsorbed protein-water complex. Thus, the amount of protein adsorbed decreased with Pt, Au, W, Ti and SS, in this order. Neither sessile contact angle nor surface roughness of the metal substrates was useful as predictors here. All three globular proteins

  3. Secondary structure of 5S RNA: NMR experiments on RNA molecules partially labeled with Nitrogen-15

    International Nuclear Information System (INIS)

    Gewirth, D.T.; Abo, S.R.; Leontis, N.B.; Moore, P.B.

    1987-01-01

    A method has been found for reassembling fragment 1 of Escherichia coli 5S RNA from mixtures containing strand III (bases 69-87) and the complex consisting of strand II (bases 89-120) and strand IV (bases 1-11). The reassembled molecule is identical with unreconstituted fragment 1. With this technique, fragment 1 molecules have been constructed 15 N-labeled either in strand III or in the strand II-strand IV complex. Spectroscopic data obtained with these partially labeled molecules show that the terminal helix of 5S RNA includes the GU and GC base pairs at positions 9 and 10 which the standard model for 5S secondary structure predicts but that these base pairs are unstable both in the fragment and in native 5S RNA. The data also assign three resonances to the helix V region of the molecule (bases 70-77 and 99-106). None of these resonances has a normal chemical shift even though two of them correspond to AU or GU base pairs in the standard model. The implications of these findings for the authors understanding of the structure of 5S RNA and its complex with ribosomal protein L25 are discussed

  4. Interrelation between in-service inspection and structural integrity in reactors residual lifetime assessment

    Energy Technology Data Exchange (ETDEWEB)

    Karzov, Georgy; Timofeev, Boris; Rozina, Marina [Central Research Inst. of Structural Materials ' Prometey' , St. Petersburg (Russian Federation)

    1999-07-01

    The object of this paper is to show that in-service inspection (ISI) is of a great importance in structural integrity provision of NPP equipment as it permits: to assess material properties degradation during operation, to describe production flaws propagation under operating factors influence, to detect flaws appearance from structural concentrators and corrosion damages and to observe their development, to verify material loading conditions in structure depending on operating damages. It is presented the detailed scheme of possible production and operating flaws development during structure lifetime. The following flaws distribution function are considered in the schema: distribution probability of detected flaws (detectability), distribution density of actual flaws, distribution density of detected flaws. On the basis of stated above functions it is performed the selection of reference flow size and its outline (surface and internal flaws, cracks in cladding). (author)

  5. Ensuring Structural Integrity through Reliable Residual Stress Measurement: From Crystals to Crankshafts

    International Nuclear Information System (INIS)

    Edwards, Lyndon

    2005-01-01

    Full text: The determination of accurate, reliable stresses is critical to many fields of engineering and, in particular, the structural integrity and hence, safety, of many systems. Neutron stress measurement is a non-destructive technique that uniquely provides insights into stress fields deep within components and structures. As such, it has become an increasingly important tool within the engineering community leading to improved manufacturing processes to reduce stress and distortion as well as to the definition of more precise structural integrity lifting procedures. This talk describes the current state of the art and identifies the key opportunities for improved structural integrity provided by the 2nd generation dedicated engineering stress diffractometers currently being designed and commissioned world-wide. Examples are provided covering a range of industrially relevant problems from the fields. (author)

  6. Residual Stress and Fracture of PECVD Thick Oxide Films for Power MEMS Structures and Devices

    National Research Council Canada - National Science Library

    Zhang, Xin

    2007-01-01

    ...) in MEMS devices and structures. In this project, PECVD SiOx is chosen as an example for the systematic study of mechanical behavior and underlying casual mechanisms of amorphous thin films for MEMS applications, which are generally...

  7. Bidet toilet seats with warm-water tanks: residual chlorine, microbial community, and structural analyses.

    Science.gov (United States)

    Iyo, Toru; Asakura, Keiko; Nakano, Makiko; Yamada, Mutsuko; Omae, Kazuyuki

    2016-02-01

    Despite the reported health-related advantages of the use of warm water in bidets, there are health-related disadvantages associated with the use of these toilet seats, and the bacterial research is sparse. We conducted a survey on the hygienic conditions of 127 warm-water bidet toilet seats in restrooms on a university campus. The spray water from the toilet seats had less residual chlorine than their tap water sources. However, the total viable microbial count was below the water-quality standard for tap water. In addition, the heat of the toilet seats' warm-water tanks caused heterotrophic bacteria in the source tap water to proliferate inside the nozzle pipes and the warm-water tanks. Escherichia coli was detected on the spray nozzles of about 5% of the toilet seats, indicating that the self-cleaning mechanism of the spray nozzles was largely functioning properly. However, Pseudomonas aeruginosa was detected on about 2% of the toilet seats. P. aeruginosa was found to remain for long durations in biofilms that formed inside warm-water tanks. Infection-prevention measures aimed at P. aeruginosa should receive full consideration when managing warm-water bidet toilet seats in hospitals in order to prevent opportunistic infections in intensive care units, hematology wards, and other hospital locations.

  8. Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Janssen Stefan

    2011-11-01

    Full Text Available Abstract Background Many bioinformatics tools for RNA secondary structure analysis are based on a thermodynamic model of RNA folding. They predict a single, "optimal" structure by free energy minimization, they enumerate near-optimal structures, they compute base pair probabilities and dot plots, representative structures of different abstract shapes, or Boltzmann probabilities of structures and shapes. Although all programs refer to the same physical model, they implement it with considerable variation for different tasks, and little is known about the effects of heuristic assumptions and model simplifications used by the programs on the outcome of the analysis. Results We extract four different models of the thermodynamic folding space which underlie the programs RNAFOLD, RNASHAPES, and RNASUBOPT. Their differences lie within the details of the energy model and the granularity of the folding space. We implement probabilistic shape analysis for all models, and introduce the shape probability shift as a robust measure of model similarity. Using four data sets derived from experimentally solved structures, we provide a quantitative evaluation of the model differences. Conclusions We find that search space granularity affects the computed shape probabilities less than the over- or underapproximation of free energy by a simplified energy model. Still, the approximations perform similar enough to implementations of the full model to justify their continued use in settings where computational constraints call for simpler algorithms. On the side, we observe that the rarely used level 2 shapes, which predict the complete arrangement of helices, multiloops, internal loops and bulges, include the "true" shape in a rather small number of predicted high probability shapes. This calls for an investigation of new strategies to extract high probability members from the (very large level 2 shape space of an RNA sequence. We provide implementations of all four

  9. Fine Structure in the Secondary Electron Emission Peak for Diamond Crystal with (100) Negative Electron Affinity Surface

    Science.gov (United States)

    Asnin, V. M.; Krainsky, I. L.

    1998-01-01

    A fine structure was discovered in the low-energy peak of the secondary electron emission spectra of the diamond surface with negative electron affinity. We studied this structure for the (100) surface of the natural type-IIb diamond crystal. We have found that the low-energy peak consists of a total of four maxima. The relative energy positions of three of them could be related to the electron energy minima near the bottom of the conduction band. The fourth peak, having the lowest energy, was attributed to the breakup of the bulk exciton at the surface during the process of secondary electron emission.

  10. Halide salts and their structural properties in presence of secondary amine based molecule: A combined experimental and theoretical analysis

    Science.gov (United States)

    Ghosh, Pritam; Hazra, Abhijit; Ghosh, Meenakshi; Chandra Murmu, Naresh; Banerjee, Priyabrata

    2018-04-01

    Biologically relevant halide salts and its solution state structural properties are always been significant. In general, exposure of halide salts into polar solution medium results in solvation which in turn separates the cationic and anionic part of the salt. However, the conventional behaviour of salts might alter in presence of any secondary amine based compound, i.e.; moderately strong Lewis acid. In its consequence, to investigate the effect of secondary amine based compound in the salt solution, novel (E)-2-(4-bromobenzylidene)-1-(perfluorophenyl) hydrazine has been synthesized and used as secondary amine source. The secondary amine compound interestingly shows a drastic color change upon exposure to fluoride salts owing to hydrogen bonding interaction. Several experimental methods, e.g.; SCXRD, UV-Vis, FT-IR, ESI-MS and DLS together with modern DFT (i.e.; DFT-D3) have been performed to explore the structural properties of the halide salts upon exposure to secondary amine based compound. The effect of counter cation of the fluoride salt in binding with secondary amine source has also been investigated.

  11. Residue-specific description of non-native transient structures in the ensemble of acid-denatured structures of the all-beta protein c-src SH3

    DEFF Research Database (Denmark)

    Rösner, Heike I; Poulsen, Flemming Martin

    2010-01-01

    Secondary chemical shift analysis has been used to characterize the unfolded state of acid-denatured c-src SH3. Even though native c-src SH3 adopts an all-beta fold, we found evidence of transient helicity in regions corresponding to native loops. In particular, residues 40-46, connecting the n-src...

  12. Determinants of residual risk in secondary prevention patients treated with high- versus low-dose statin therapy: the Treating to New Targets (TNT) study

    NARCIS (Netherlands)

    Mora, Samia; Wenger, Nanette K.; Demicco, David A.; Breazna, Andrei; Boekholdt, S. Matthijs; Arsenault, Benoit J.; Deedwania, Prakash; Kastelein, John J. P.; Waters, David D.

    2012-01-01

    Cardiovascular events occur among statin-treated patients, albeit at lower rates. Risk factors for this "residual risk" have not been studied comprehensively. We aimed to identify determinants of this risk above and beyond lipid-related risk factors. A total of 9251 coronary patients with

  13. NMR and biophysical elucidation of structural effects on extra N-terminal methionine residue of recombinant amphibian RNases from Rana catesbeiana.

    Science.gov (United States)

    Hsu, Chun-Hua; Pan, Yun-Ru; Liao, You-Di; Wu, Shih-Hsiung; Chen, Chinpan

    2010-08-01

    The stability, structures and steric hindrances of recombinant RNases 2 and 4 expressed in bacteria were studied by circular dichroism (CD) and NMR techniques, and the results were compared with those of their authentic RNases extracted from oocytes of Rana catesbeiana. Although the overall structures of the recombinant and authentic proteins are almost identical, the extra N-terminal Met residue of the recombinant protein remarkably affects catalytic activity and stability. NMR chemical shift comparison of recombinant RNases and the authentic proteins indicated that the structural differences are mainly confined to the N-terminal helical and S2 anti-parallel beta-sheet regions. Significant shift changes for the residues located on the S2 region indicate that the major influences on the structure around the N terminus is due to the loss of the hydrogen bond between Pyr(1) and Val(95(96)) in recombinant RNases 2 and 4. We concluded the apparent steric hindrances of the extra Met to the binding pocket. As well, the affected conformational changes of active residues are attributed to the reduced activities of recombinant RNases. The structural integrity exerted by the N-terminal Pyr(1) residue may be crucial for amphibian RNases and the greatest structural differences occur on the network of the Pyr(1) residue and S2 beta-sheet region.

  14. Orientation of aromatic residues in amyloid cores: Structural insights into prion fiber diversity

    KAUST Repository

    Reymer, Anna

    2014-11-17

    Structural conversion of one given protein sequence into different amyloid states, resulting in distinct phenotypes, is one of the most intriguing phenomena of protein biology. Despite great efforts the structural origin of prion diversity remains elusive, mainly because amyloids are insoluble yet noncrystalline and therefore not easily amenable to traditional structural-biology methods. We investigate two different phenotypic prion strains, weak and strong, of yeast translation termination factor Sup35 with respect to angular orientation of tyrosines using polarized light spectroscopy. By applying a combination of alignment methods the degree of fiber orientation can be assessed, which allows a relatively accurate determination of the aromatic ring angles. Surprisingly, the strains show identical average orientations of the tyrosines, which are evenly spread through the amyloid core. Small variations between the two strains are related to the local environment of a fraction of tyrosines outside the core, potentially reflecting differences in fibril packing.

  15. Superhard behaviour, low residual stress, and unique structure in diamond-like carbon films by simple bilayer approach

    International Nuclear Information System (INIS)

    Dwivedi, Neeraj; Kumar, Sushil; Malik, Hitendra K.

    2012-01-01

    Simple bilayer approach is proposed for synthesizing hard and superhard diamond-like carbon (DLC) coatings with reduced residual stress. For this, M/DLC bilayer (M = Ti and Cu) structures are grown using hybrid system involving radio frequency (RF)-sputtering and RF-plasma enhanced chemical vapor deposition techniques. Ti/DLC bilayer deposited at negative self bias of 100 V shows superhard behaviour with hardness (H) as 49 GPa. Cu/DLC bilayer grown at self bias of 100 V exhibits hard behaviour with H as 22.8 GPa. The hardness of Ti/DLC (Cu/DLC) bilayer gets changed from superhard (hard) to hard (moderate hard) regime, when the self bias is raised to 300 V. Residual stress in Ti/DLC (Cu/DLC) bilayer is found to be significantly low that varies in the range of 1 GPa-1.65 GPa (0.8 GPa-1.6 GPa). The microstructure and morphology are studied by Raman spectroscopy, scanning electron microscopy (SEM), and atomic force microscopy (AFM). SEM and AFM pictures reveal the creation of nanostructured features in the deposited bilayers. Raman, SEM, and AFM analyses are correlated with the nano-mechanical properties. Owing to excellent nano-mechanical properties, these bilayers can find their direct industrial applications as hard and protective coatings.

  16. Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure.

    Science.gov (United States)

    Reinharz, Vladimir; Major, François; Waldispühl, Jérôme

    2012-06-15

    The prediction of RNA 3D structures from its sequence only is a milestone to RNA function analysis and prediction. In recent years, many methods addressed this challenge, ranging from cycle decomposition and fragment assembly to molecular dynamics simulations. However, their predictions remain fragile and limited to small RNAs. To expand the range and accuracy of these techniques, we need to develop algorithms that will enable to use all the structural information available. In particular, the energetic contribution of secondary structure interactions is now well documented, but the quantification of non-canonical interactions-those shaping the tertiary structure-is poorly understood. Nonetheless, even if a complete RNA tertiary structure energy model is currently unavailable, we now have catalogues of local 3D structural motifs including non-canonical base pairings. A practical objective is thus to develop techniques enabling us to use this knowledge for robust RNA tertiary structure predictors. In this work, we introduce RNA-MoIP, a program that benefits from the progresses made over the last 30 years in the field of RNA secondary structure prediction and expands these methods to incorporate the novel local motif information available in databases. Using an integer programming framework, our method refines predicted secondary structures (i.e. removes incorrect canonical base pairs) to accommodate the insertion of RNA 3D motifs (i.e. hairpins, internal loops and k-way junctions). Then, we use predictions as templates to generate complete 3D structures with the MC-Sym program. We benchmarked RNA-MoIP on a set of 9 RNAs with sizes varying from 53 to 128 nucleotides. We show that our approach (i) improves the accuracy of canonical base pair predictions; (ii) identifies the best secondary structures in a pool of suboptimal structures; and (iii) predicts accurate 3D structures of large RNA molecules. RNA-MoIP is publicly available at: http://csb.cs.mcgill.ca/RNAMoIP.

  17. Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions

    Science.gov (United States)

    Heim, Andrew J.; Li, Zhijun

    2012-03-01

    Membrane proteins are of particular biological and pharmaceutical importance, and computational modeling and structure prediction approaches play an important role in studies of membrane proteins. Developing an accurate model quality assessment program is of significance to the structure prediction of membrane proteins. Few such programs are proposed that can be applied to a broad range of membrane protein classes and perform with high accuracy. We developed a new model scoring function Interaction-based Quality assessment (IQ), based on the analysis of four types of inter-residue interactions within the transmembrane domains of helical membrane proteins. This function was tested using three high-quality model sets: all 206 models of GPCR Dock 2008, all 284 models of GPCR Dock 2010, and all 92 helical membrane protein models of the HOMEP set. For all three sets, the scoring function can select the native structures among all of the models with the success rates of 93, 85, and 100% respectively. For comparison, these three model sets were also adopted for a recently published model assessment program for membrane protein structures, ProQM, which gave the success rates of 85, 79, and 92% separately. These results suggested that IQ outperforms ProQM when only the transmembrane regions of the models are considered. This scoring function should be useful for the computational modeling of membrane proteins.

  18. Understanding the effect of secondary structure on molecular interactions of poly-L-lysine with different substrates by SFA.

    Science.gov (United States)

    Binazadeh, Mojtaba; Faghihnejad, Ali; Unsworth, Larry D; Zeng, Hongbo

    2013-10-14

    Nonspecific adsorption of proteins on biomaterial surfaces challenges the widespread application of engineered materials, and understanding the impact of secondary structure of proteins and peptides on their adsorption process is of both fundamental and practical importance in bioengineering. In this work, poly-L-lysine (PLL)-based α-helices and β-sheets were chosen as a model system to investigate the effect of secondary structure on peptide interactions with substrates of various surface chemistries. Circular dichroism (CD) was used to confirm the presence of both α-helix and β-sheet structured PLL in aqueous solutions and upon adsorption to quartz, where these secondary structures seemed to be preserved. Atomic force microscopy (AFM) imaging showed different surface patterns for adsorbed α-helix and β-sheet PLL. Interactions between PLL of different secondary structures and various substrates (i.e., PLL, Au, mica, and poly(ethylene glycol) (PEG)) were directly measured using a surface forces apparatus (SFA). It was found that β-sheet PLL films showed higher adsorbed layer thicknesses in general. Adhesion energies of β-sheet versus Au and β-sheet versus β-sheet were considerably higher than that of α-helix versus Au and α-helix versus α-helix systems, respectively. Au and β-sheet PLL interactions seemed to be more dependent on the salt concentration than that of α-helix, while the presence of a grafted PEG layer greatly diminished any attraction with either PLL structure. The molecular interaction mechanism of peptide in different secondary structures is discussed in terms of Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, Alexander-de Gennes (AdG) steric model and hydrogen bonding, which provides important insight into the fundamental understanding of the interaction mechanism between proteins and biomaterials.

  19. ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins.

    Science.gov (United States)

    de Castro, Edouard; Sigrist, Christian J A; Gattiker, Alexandre; Bulliard, Virginie; Langendijk-Genevaux, Petra S; Gasteiger, Elisabeth; Bairoch, Amos; Hulo, Nicolas

    2006-07-01

    ScanProsite--http://www.expasy.org/tools/scanprosite/--is a new and improved version of the web-based tool for detecting PROSITE signature matches in protein sequences. For a number of PROSITE profiles, the tool now makes use of ProRules--context-dependent annotation templates--to detect functional and structural intra-domain residues. The detection of those features enhances the power of function prediction based on profiles. Both user-defined sequences and sequences from the UniProt Knowledgebase can be matched against custom patterns, or against PROSITE signatures. To improve response times, matches of sequences from UniProtKB against PROSITE signatures are now retrieved from a pre-computed match database. Several output modes are available including simple text views and a rich mode providing an interactive match and feature viewer with a graphical representation of results.

  20. Buffalo Leukemia Inhibitory Factor Induces Differentiation and Dome-Like Secondary Structures in COS-1 Cells.

    Science.gov (United States)

    Kaur, Gurjeet; Ali, Syed Azmal; Pachauri, Shikha; Malakar, Dhruba; Kaushik, Jai K; Mohanty, Ashok K; Kumar, Sudarshan

    2017-01-01

    This study aimed to understand the molecular characteristics of buffalo leukemia inhibitory factor (BuLIF) and the generation of a stably transfected COS-1_BuLIF cell line for its functional characterization. Cumulus cells, isolated from oocytes, were separated, and total cDNA was prepared. The BuLIF gene was ligated into the cloning vector pJET1.2/blunt and expression vector pAcGFP-N1 which was transfected into COS-1 cells and confirmed by qRT-PCR and Western blot. BuLIF was immunoprecipitated and evaluated through a MTT assay. qRT-PCR of STAT3 was performed. The multiple sequence alignment of BuLIF showed high similarity with sheep (98.77%) and cattle (96.62%) compared with other species. The BuLIF gene has an open reading frame of 609 nucleotides coding for 202 amino acids. BuLIF was integrated into the genome of COS-1 cells and resulted in the formation of dome-like secondary structures which are indicative of its functional role mediated through STAT3 proteins. In conclusion, this cell line is suitable for understanding LIF-mediated biological functions. © 2017 S. Karger AG, Basel.

  1. Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

    Energy Technology Data Exchange (ETDEWEB)

    Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang; Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinlzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

    2013-01-24

    The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.

  2. Seborrheic dermatitis: predisposing factors and ITS2 secondary structure for Malassezia phylogenic analysis.

    Science.gov (United States)

    Amado, Yulien; Patiño-Uzcátegui, Anelvi; Cepero de García, Maria C; Tabima, Javier; Motta, Adriana; Cárdenas, Martha; Bernal, Adriana; Restrepo, Silvia; Celis, Adriana

    2013-11-01

    Seborrheic dermatitis (SD) is a chronic, widespread skin condition, which is considered a multifactorial disease influenced, in part, by Malassezia spp. opportunistic activities, as well as various endogenous and exogenous factors. Malassezia species are lipophilic, lipid-dependent yeasts that are members of the normal mycobiota of the human skin. Their isolation from SD lesions varies around the world and the study of the relationship among factors such as gender, age, immunosuppressive condition of the patient and SD development, can lead to a better understanding of this disease. To elucidate the association of age and gender with the development of SD and to precisely determine the Malassezia species involved in the disease, samples were obtained from 134 individuals, including individuals without lesions, human immunodeficiency virus positive patients, individuals with seborrheic dermatitis, and HIV patients with seborrheic dermatitis. Malassezia spp. were identified by phenotypic and genotypic methods and a phylogenetic analysis was performed using Bayesian inference. This study revealed that age and gender are not predisposing factors for SD development, and that the most frequent species of Malassezia related to SD development among the Colombian population is M. restricta. We also report the isolation of M. yamatoensis for the first time in Colombia, and propose an ITS2 secondary structure from Malassezia taxa that can be used for precise identification and to establish more robust phylogenetic relationships.

  3. Secondary structure of the HIV reverse transcription initiation complex by NMR.

    Science.gov (United States)

    Puglisi, Elisabetta Viani; Puglisi, Joseph D

    2011-07-29

    Initiation of reverse transcription of genomic RNA is a key early step in replication of the human immunodeficiency virus (HIV) upon infection of a host cell. Viral reverse transcriptase initiates from a specific RNA-RNA complex formed between a host transfer RNA (tRNA(Lys)(3)) and a region at the 5' end of genomic RNA; the 3' end of the tRNA acts as a primer for reverse transcription of genomic RNA. We report here the secondary structure of the HIV genomic RNA-human tRNA(Lys)(3) initiation complex using heteronuclear nuclear magnetic resonance methods. We show that both RNAs undergo large-scale conformational changes upon complex formation. Formation of the 18-bp primer helix with the 3' end of tRNA(Lys)(3) drives large conformational rearrangements of the tRNA at the 5' end while maintaining the anticodon loop for potential loop-loop interactions. HIV RNA forms an intramolecular helix adjacent to the intermolecular primer helix. This helix, which must be broken by reverse transcription, likely acts as a kinetic block to reverse transcription. Copyright © 2011 Elsevier Ltd. All rights reserved.

  4. Fine-grained parallelism accelerating for RNA secondary structure prediction with pseudoknots based on FPGA.

    Science.gov (United States)

    Xia, Fei; Jin, Guoqing

    2014-06-01

    PKNOTS is a most famous benchmark program and has been widely used to predict RNA secondary structure including pseudoknots. It adopts the standard four-dimensional (4D) dynamic programming (DP) method and is the basis of many variants and improved algorithms. Unfortunately, the O(N(6)) computing requirements and complicated data dependency greatly limits the usefulness of PKNOTS package with the explosion in gene database size. In this paper, we present a fine-grained parallel PKNOTS package and prototype system for accelerating RNA folding application based on FPGA chip. We adopted a series of storage optimization strategies to resolve the "Memory Wall" problem. We aggressively exploit parallel computing strategies to improve computational efficiency. We also propose several methods that collectively reduce the storage requirements for FPGA on-chip memory. To the best of our knowledge, our design is the first FPGA implementation for accelerating 4D DP problem for RNA folding application including pseudoknots. The experimental results show a factor of more than 50x average speedup over the PKNOTS-1.08 software running on a PC platform with Intel Core2 Q9400 Quad CPU for input RNA sequences. However, the power consumption of our FPGA accelerator is only about 50% of the general-purpose micro-processors.

  5. A New Criterion to Evaluate Water Vapor Interference in Protein Secondary Structural Analysis by FTIR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Ye Zou

    2014-06-01

    Full Text Available Second derivative and Fourier self-deconvolution (FSD are two commonly used techniques to resolve the overlapped component peaks from the often featureless amide I band in Fourier transform infrared (FTIR curve-fitting approach for protein secondary structural analysis. Yet, the reliability of these two techniques is greatly affected by the omnipresent water vapor in the atmosphere. Several criteria are currently in use as quality controls to ensure the protein absorption spectrum is negligibly affected by water vapor interference. In this study, through a second derivative study of liquid water, we first argue that the previously established criteria cannot guarantee a reliable evaluation of water vapor interference due to a phenomenon that we refer to as sample’s absorbance-dependent water vapor interference. Then, through a comparative study of protein and liquid water, we show that a protein absorption spectrum can still be significantly affected by water vapor interference even though it satisfies the established criteria. At last, we propose to use the comparison between the second derivative spectra of protein and liquid water as a new criterion to better evaluate water vapor interference for more reliable second derivative and FSD treatments on the protein amide I band.

  6. Flammability of self-extinguishing kenaf/ABS nanoclays composite for aircraft secondary structure

    Science.gov (United States)

    Karunakaran, S.; Majid, D. L.; Mohd Tawil, M. L.

    2016-10-01

    This study investigates the flammability properties of kenaf fiber reinforced acrylonitrile butadiene styrene (ABS) with nanoclays composites. Natural fiber is one of the potential materials to be used with thermoplastic as a composite due to its attractive properties such as lightweight and strong. In this paper, flammability properties of this material are evaluated through Underwriters Laboratory 94 Horizontal Burning (UL94 HB), which has been conducted for both controlled and uncontrolled conditions, smoke density and limiting oxygen index tests (LOI). These flammability tests are in compliance with the Federal Aviation Regulation (FAR) requirement. The results from UL94 HB and smoke density tests show that the presence of nanoclays with effective composition of kenaf fiber reinforced ABS has enhanced the burning characteristics of the material by hindering propagation of flame spread over the surface of the material through char formation. Consequently, this decreases the burning rate and produces low amount of smoke during burning. On contrary, through LOI test, this material requires less oxygen to burn when exposed to fire, which hinders the enhancement of burning characteristics. This is due to burning mechanism exhibited by nanoclays that catalyzes barrier formation and flame propagation rate over the surface of the biocomposite material. Overall, these experimental results suggest that this biocomposite material is capable of self-extinguishing and possesses effective fire extinction. The observed novel synergism from the result obtained is promising to be implemented in secondary structures of aircraft with significant benefits such as cost-effective, lightweight and biodegradable self-extinguishing biocomposite.

  7. Temperature Effects on Mechanical Properties of Woven Thermoplastic Composites for Secondary Aircraft Structure Applications

    Directory of Open Access Journals (Sweden)

    Wang Yue

    2017-01-01

    Full Text Available The effect of temperature on the mechanical behavior of 8-H satin woven glass fabric/polyethylene sulfide (GF/PPS was investigated in this paper. Static-tensile tests were both conducted on notched and unnotched specimens at typical temperatures (ambient, 95°C and 125°C based on the glass transition temperatures (Tg of the neat resin and composite, their strength and moduli were obtained and compared. The damage patterns of failed specimens of notched and unnotched were examined with the aid of high-definition camera and stereomicroscope. The results of stress-strain relationships showed that the slight nonlinearity of the curves were observed for these two specimens, which was associated with the plastic deformation of localized resin. The damage patterns of notched and unnotched specimens at different temperatures proved that damage and plastic deformation were two simultaneous mechanisms and it was prominent in the notched. It was the overstress accommodation mechanism that led to a relative high strength rentention for the notched and a reduction of the hole sensitivity. The results obtained in this paper indicated that GF/PPS can be used as secondary aircraft structures at elevated temperatures higher than its Tg.

  8. Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens.

    Directory of Open Access Journals (Sweden)

    Bradford J Condon

    Full Text Available The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus, and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI. The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS, polyketide synthase (PKS, and SSP-encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.

  9. Fold classification based on secondary structure – how much is gained by including loop topology?

    Directory of Open Access Journals (Sweden)

    Przytycka Teresa

    2006-03-01

    Full Text Available Abstract Background It has been proposed that secondary structure information can be used to classify (to some extend protein folds. Since this method utilizes very limited information about the protein structure, it is not surprising that it has a higher error rate than the approaches that use full 3D fold description. On the other hand, the comparing of 3D protein structures is computing intensive. This raises the question to what extend the error rate can be decreased with each new source of information, especially if the new information can still be used with simple alignment algorithms. We consider the question whether the information about closed loops can improve the accuracy of this approach. While the answer appears to be obvious, we had to overcome two challenges. First, how to code and to compare topological information in such a way that local alignment of strings will properly identify similar structures. Second, how to properly measure the effect of new information in a large data sample. We investigate alternative ways of computing and presenting this information. Results We used the set of beta proteins with at most 30% pairwise identity to test the approach; local alignment scores were used to build a tree of clusters which was evaluated using a new log-odd cluster scoring function. In particular, we derive a closed formula for the probability of obtaining a given score by chance.Parameters of local alignment function were optimized using a genetic algorithm. Of 81 folds that had more than one representative in our data set, log-odds scores registered significantly better clustering in 27 cases and significantly worse in 6 cases, and small differences in the remaining cases. Various notions of the significant change or average change were considered and tried, and the results were all pointing in the same direction. Conclusion We found that, on average, properly presented information about the loop topology improves noticeably

  10. Molecular structure impacts on secondary organic aerosol formation from glycol ethers

    Science.gov (United States)

    Li, Lijie; Cocker, David R.

    2018-05-01

    Glycol ethers, a class of widely used solvents in consumer products, are often considered exempt as volatile organic compounds based on their vapor pressure or boiling points by regulatory agencies. However, recent studies found that glycol ethers volatilize at ambient conditions nearly as rapidly as the traditional high-volatility solvents indicating the potential of glycol ethers to form secondary organic aerosol (SOA). This is the first work on SOA formation from glycol ethers. The impact of molecular structure, specifically -OH, on SOA formation from glycol ethers and related ethers are investigated in the work. Ethers with and without -OH, with methyl group hindrance on -OH and with -OH at different location are studied in the presence of NOX and under "NOX free" conditions. Photooxidation experiments under different oxidation conditions confirm that the processing of ethers is a combination of carbonyl formation, cyclization and fragmentation. Bulk SOA chemical composition analysis and oxidation products identified in both gas and particle phase suggests that the presence and location of -OH in the carbon bond of ethers determine the occurrence of cyclization mechanism during ether oxidation. The cyclization is proposed as a critical SOA formation mechanism to prevent the formation of volatile compounds from fragmentation during the oxidation of ethers. Glycol ethers with -CH2-O-CH2CH2OH structure is found to readily form cyclization products, especially with the presence of NOx, which is more relevant to urban atmospheric conditions than without NOx. Glycol ethers are evaluated as dominating SOA precursors among all ethers studied. It is estimated that the contribution of glycol ethers to anthropogenic SOA is roughly 1% of the current organic aerosol from mobile sources. The contribution of glycol ethers to anthropogenic SOA is roughly 1% of the current organic aerosol from mobile sources and will play a more important role in future anthropogenic SOA

  11. Structural characteristics and forage mass of Tifton 85 pastures managed under three post-grazing residual leaf areas

    Directory of Open Access Journals (Sweden)

    Wilton Ladeira da Silva

    2013-04-01

    Full Text Available The experiment was carried out on Cynodon spp cv. Tifton 85 pastures grazed by sheep under rotational stocking, with the objective of evaluating the structural characteristics as well as the forage mass of the pastures subjected to three grazing intensities in successive cycles. Treatments were composed of three residual leaf area indices (rLAI; 2.4; 1.6 and 0.8, allocated in completely randomized blocks with seven replications, totaling 21 experimental units. Tiller population density, pasture height, leaf area index, forage morphological composition and pasture forage mass were evaluated. The rLAI modified the tiller population density, which increased linearly with decrease in the rLAI of the pastures. Dry masses of leaf blade, stem and dead material were inferior when the rLAI imposed were lower, which resulted in differentiated forage production among the treatments. Tifton 85 pastures grazed by sheep in rotational stocking under tropical conditions with different rLAI show a modified sward structure over successive grazing cycles, mainly by alteration in the height and LAI of the plants at pre-grazing and by light interception post-grazing, which change the tiller population density. The residual leaf area index of 1.6 is the most suitable for pasture management for being equivalent to the heights of entrance and exit of animals on and from paddocks of 33 and 19 cm, respectively, which avoid great accumulation of dead material and excessive stem elongation, in addition to ensuring tillering in the sward.

  12. Structure of bovine pancreatic trypsin inhibitor at 125 K definition of carboxyl-terminal residues Gly57 and Ala58.

    Science.gov (United States)

    Parkin, S; Rupp, B; Hope, H

    1996-01-01

    The structure of bovine pancreatic trypsin inhibitor has been refined to a resolution of 1.1 A against data collected at 125 K. The space group of the form II crystal is P2(1)2(1)2(1) with a = 75.39(3), b = 22.581(7), c = 28.606 (9) A (cf. a = 74.1, b = 23.4, c = 28.9 A at room temperature). The structure was refined by restrained least-squares minimization of summation operator w(F (o)(2)- F (c)(2))(2) with the SHELXL93 program. As the model improved, water molecules were included and exceptionally clear electron density was found for two residues, Gly57 and Ala58, that had been largely obscured at room temperature. The side chains of residues Glu7 and Arg53 were modelled over two positions with refined occupancy factors. The final model contains 145.6 water molecules distributed over 167 sites, and a single phosphate group disordered over two sites. The root-mean-square discrepancy between Calpha atoms in residues Arg1-Gly56 at room and low temperatures is 0.4 A. A comparison of models refined with anisotropic and isotropic thermal parameters revealed that there were no significant differences in atomic positions. The final weighted R-factor on F(2) (wR(2)) for data in the range 10-1.1 A was 35.9% for the anisotropic model and 40.9% for the isotropic model. Conventional R-factors based on F for F > 4sigma(F) were 12.2 and 14.6%, respectively, corresponding to 16.1 and 18.7% on all data. These large R-factor differences were not reflected in values of R(free), which were not significantly different at 21.5(5) and 21.8(4)%, respectively. These results, along with the relatively straightforward nature of the refinement, clearly highlight the benefits of low-temperature data collection.

  13. Effect of conditioning by PAM polymers with different charges on the structural and characteristic evolutions of water treatment residuals.

    Science.gov (United States)

    Yan, W L; Wang, Y L; Chen, Y J

    2013-11-01

    Three types of polyacrylamide (PAM) flocculants with different charges (cationic PAM WD4960, nonionic PAM M351, and anionic PAM WDA110) were used for water treatment residuals (WTRs) conditioning, and the physicochemical, morphological and structural characteristics of raw and conditioned WTRs were investigated. Rheological methods were employed to analyze the internal structural transition between the raw and conditioned WTRs under a typical dosage of WD4960. Results showed that when the raw WTRs were conditioned with the polymers, the optimum dosage of WD4960 was 4.82 g/kg total suspended solid (TSS) while that of both M351 and WDA110 was 7.24 g/kg TSS. The residual PAM content in the supernatant of the WTR matrix conditioned at the optimum WD4960 dosage was 5.59 mg/L, which is the least among the supernatants obtained with the three types of PAM. Furthermore, the visible fulvic acid (FA) in the supernatant disappeared and the intensity of the ultraviolet FA decreased. The average diameter of irregularly shaped aggregates in the WTR suspensions increased from 35.73 μm to several hundred micrometers with increasing PAM dosage. The size of WTR aggregates conditioned at the optimum WD4960 dosage was much larger than that of aggregates obtained at the optimum M351 or WDA110 dosages. Two-dimensional fractal dimension (D2) values presented an increasing trend with increasing PAM dosage. D2 values of the conditioned WTR aggregates were 1.87, 1.76, and 1.83 at optimum WD4960, M351, and WDA110 dosages, respectively. The cationic PAM (CPAM) WD4960 thus appears to be a more ideal conditioner for WTRs. Consistent relationships were observed among the capillary suction time (CST), average particle size, and D2 values of the conditioned WTR aggregates at the optimum WD4960 dosage. Mass fractal dimensions (D(f)) indicated that both the raw and WD4960-conditioned WTRs behave like weak-link flocs/aggregates. D(f) values (log G'-log TSS) of the WTR aggregates before and after

  14. Novel evolutionary lineages revealed in the Chaetothyriales (Fungi) based on multigene phylogenetic analyses and comparison of ITS secondary structure

    Czech Academy of Sciences Publication Activity Database

    Réblová, Martina; Untereiner, W. A.; Réblová, K.

    2013-01-01

    Roč. 8, č. 5 (2013), e63547 E-ISSN 1932-6203 R&D Projects: GA ČR GAP506/12/0038 Institutional support: RVO:67985939 Keywords : Cyphelophora * Phialophora * secondary structure Subject RIV: EF - Botanics Impact factor: 3.534, year: 2013

  15. Observed lesson structure during the first year of secondary education : Exploration of change and link with academic engagement

    NARCIS (Netherlands)

    Maulana, Ridwan; Opdenakker, Marie-Christine; Stroet, Kim; Bosker, Roel

    This study investigates whether lesson structure (LS) matters and which components are important for academic engagement during the first grade of secondary education. Data from videoed lessons of 10 Dutch and 12 Indonesian teachers analyzed using an observation protocol show that six LS components

  16. Projection Structure by Single-Particle Electron Microscopy of Secondary Transport Proteins GItT, Cits, and GltS

    NARCIS (Netherlands)

    Moscicka, Katarzyna B.; Krupnik, Tomasz; Boekema, Egbert J.; Lolkema, Juke S.; Mościcka, Katarzyna B.

    2009-01-01

    The structure of three secondary transporter proteins, GltT of Bacillus stearothermophilus, CitS of Klebsiella pneumoniae, and GltS of Escherichia coli, was studied. The proteins were purified to homogeneity ill detergent solution by Ni(2+)-NTA affinity chromatography, and the complexes were

  17. Investigation 8th Grade Students Secondary School Cognitive Structure about Principles of Ataturk through Word Association Test

    Science.gov (United States)

    Akman, Ozkan; Koçoglu, Erol

    2016-01-01

    The purpose of this study is to present the connections between the concepts in perception and cognitive structures of secondary school 8th grade students for principles of Ataturk. Word association test is used in data collection. The number of the total participants in this research is 190. A frequency table is formed for the data obtained in…

  18. Effect of Programmed Instruction on Students' Attitude towards Structure of the Atom and the Periodic Table among Kenyan Secondary Schools

    Science.gov (United States)

    Wangila, M. J.; Martin, W.; Ronald, M.

    2015-01-01

    This study examined the effect of Programmed Instruction on students' attitude towards Structure of the Atom and the Periodic Table (SAPT) among mixed (co-educational) secondary schools of Butere district, Kakamega county, Kenya. The quasi-experimental research design was adopted, using the nonrandomized Solomon four-group as a model. The sample…

  19. Variation in secondary structure of the 16S rRNA molecule in cyanobacteria with implications for phylogenetic analysis

    Czech Academy of Sciences Publication Activity Database

    Řeháková, Klára; Johansen, J. R.; Bowen, M.B.; Martin, M.P.; Sheil, C.A.

    2014-01-01

    Roč. 14, č. 2 (2014), s. 161-178 ISSN 1802-5439 Institutional support: RVO:60077344 Keywords : 16S rRNA secondary structure * cyanobacteria * phylogeny Subject RIV: EE - Microbiology, Virology Impact factor: 1.930, year: 2014

  20. Making Sense of Abstract Algebra: Exploring Secondary Teachers' Understandings of Inverse Functions in Relation to Its Group Structure

    Science.gov (United States)

    Wasserman, Nicholas H.

    2017-01-01

    This article draws on semi-structured, task-based interviews to explore secondary teachers' (N = 7) understandings of inverse functions in relation to abstract algebra. In particular, a concept map task is used to understand the degree to which participants, having recently taken an abstract algebra course, situated inverse functions within its…

  1. Secondary structure and (1)H, (13)C, (15)N resonance assignments of the endosomal sorting protein sorting nexin 3

    OpenAIRE

    Overduin Michael; Rajesh Sandya; Gruenberg Jean; Lenoir Marc

    2015-01-01

    Sorting nexin 3 (SNX3) belongs to a sub family of sorting nexins that primarily contain a single Phox homology domain capable of binding phosphoinositides and membranes. We report the complete (1)H (13)C and (15)N resonance assignments of the full length human SNX3 protein and identification of its secondary structure elements revealing a canonical fold and unstructured termini.

  2. Secondary structure and (1)H, (13)C, (15)N resonance assignments of the endosomal sorting protein sorting nexin 3.

    Science.gov (United States)

    Overduin, Michael; Rajesh, Sandya; Gruenberg, Jean; Lenoir, Marc

    2015-10-01

    Sorting nexin 3 (SNX3) belongs to a sub-family of sorting nexins that primarily contain a single Phox homology domain capable of binding phosphoinositides and membranes. We report the complete (1)H, (13)C and (15)N resonance assignments of the full-length human SNX3 protein and identification of its secondary structure elements, revealing a canonical fold and unstructured termini.

  3. DNA secondary structure of the released strand stimulates WRN helicase action on forked duplexes without coordinate action of WRN exonuclease

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, Byungchan, E-mail: bbccahn@mail.ulsan.ac.kr [Department of Life Sciences, University of Ulsan, Ulsan (Korea, Republic of); Bohr, Vilhelm A. [Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, Baltimore, MD (United States)

    2011-08-12

    Highlights: {yields} In this study, we investigated the effect of a DNA secondary structure on the two WRN activities. {yields} We found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. {yields} These results imply that WRN helicase and exonuclease activities can act independently. -- Abstract: Werner syndrome (WS) is an autosomal recessive premature aging disorder characterized by aging-related phenotypes and genomic instability. WS is caused by mutations in a gene encoding a nuclear protein, Werner syndrome protein (WRN), a member of the RecQ helicase family, that interestingly possesses both helicase and exonuclease activities. Previous studies have shown that the two activities act in concert on a single substrate. We investigated the effect of a DNA secondary structure on the two WRN activities and found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. These results imply that WRN helicase and exonuclease activities can act independently, and we propose that the uncoordinated action may be relevant to the in vivo activity of WRN.

  4. The secondary structure of large-subunit rRNA divergent domains, a marker for protist evolution

    DEFF Research Database (Denmark)

    Lenaers, G; Nielsen, Henrik; Engberg, J

    1988-01-01

    The secondary structure of the large-subunit ribosomal RNA (24-26S rRNA) has been studied with emphasis on comparative analysis of the folding patterns of the divergent domains in the available protist sequences, that is Prorocentrum micans (dinoflagellate), Saccharomyces carlsbergensis (yeast), ...

  5. A stretch of residues within the protease-resistant core is not necessary for prion structure and infectivity.

    Science.gov (United States)

    Munoz-Montesino, Carola; Sizun, Christina; Moudjou, Mohammed; Herzog, Laetitia; Reine, Fabienne; Igel-Egalon, Angelique; Barbereau, Clément; Chapuis, Jérôme; Ciric, Danica; Laude, Hubert; Béringue, Vincent; Rezaei, Human; Dron, Michel

    2017-01-02

    Mapping out regions of PrP influencing prion conversion remains a challenging issue complicated by the lack of prion structure. The portion of PrP associated with infectivity contains the α-helical domain of the correctly folded protein and turns into a β-sheet-rich insoluble core in prions. Deletions performed so far inside this segment essentially prevented the conversion. Recently we found that deletion of the last C-terminal residues of the helix H2 was fully compatible with prion conversion in the RK13-ovPrP cell culture model, using 3 different infecting strains. This was in agreement with preservation of the overall PrP C structure even after removal of up to one-third of this helix. Prions with internal deletion were infectious for cells and mice expressing the wild-type PrP and they retained prion strain-specific characteristics. We thus identified a piece of the prion domain that is neither necessary for the conformational transition of PrP C nor for the formation of a stable prion structure.

  6. Free energy determinants of secondary structure formation: I. alpha-Helices.

    Science.gov (United States)

    Yang, A S; Honig, B

    1995-09-22

    The Zimm-Bragg parameters s and sigma are calculated for the helix-coil transition of poly-L-alanine. The theoretical approach involves evaluating gas phase conformational energies for both coil and helical states using the CHARMM potential function and accounting for solvation effects with various continuum solvation models. Conformational free energies are then incorporated into a formalism developed by Go et al. for the calculation of s and sigma. Calculated values for both s and sigma as well as the enthalpy change associated with helix formation are in good agreement with experimental data when the Finite Difference Poisson-Boltzmann (FDPB) method is used to treat solvent effects. The driving force for the helix-coil transition is analyzed in terms of individual free energy components. Hydrogen bond formation is found to contribute little to helix stability because the internal hydrogen bonding energy is largely canceled by the large free energy cost associated with removing polar groups from water. The entropic cost associated with fixing backbone dihedral angles in the helical conformation is found to be approximately 7 e.u./residue (about 2 kcal/mol at room temperature). The major driving force favoring helix formation can be associated with interactions including enhanced van der Waals interactions in the close-packed helix conformation and the hydrophobic effect. These contribute about 2 kcal/mol favoring the helical state. The differences in helical propensities between alanine and glycine are attributed primarily to hydrophobic and packing interactions involving the C beta with a smaller contribution arising from increased conformational freedom for glycine in the coil state. The description of helix formation presented here is consistent with previous conclusions regarding tertiary structure formation which suggest that hydrophobic and close-packed interactions provide stability while hydrogen bond formation constitutes a structural constraint imposed

  7. DipoCoup: A versatile program for 3D-structure homology comparison based on residual dipolar couplings and pseudocontact shifts

    International Nuclear Information System (INIS)

    Meiler, Jens; Peti, Wolfgang; Griesinger, Christian

    2000-01-01

    A program, DipoCoup, is presented that allows to search the protein data bank for proteins which have a three dimensional fold that is at least partially homologous to a protein under investigation. The three dimensional homology search uses secondary structure alignment based on chemical shifts and dipolar couplings or pseudocontact shifts for the three dimensional orientation of secondary structure elements. Moreover, the program offers additional tools for handling and analyzing dipolar couplings

  8. Residual life and strength estimates of aircraft structural components with MSD/MED

    Science.gov (United States)

    Singh, Ripudaman; Park, Jai H.; Atluri, Satya N.

    1994-01-01

    Economic and safe operation of the flight vehicles flying beyond their initial design life calls for an in-depth structural integrity evaluation of all components with potential for catastrophic damages. Fuselage panels with cracked skin and/or stiffening elements is one such example. A three level analytical approach is developed to analyze the pressurized fuselage stiffened shell panels with damaged skin or stiffening elements. A global finite element analysis is first carried out to obtain the load flow pattern through the damaged panel. As an intermediate step, the damaged zone is treated as a spatially three-dimensional structure modeled by plate and shell finite elements, with all the neighboring elements that can alter the stress state at the crack tip. This is followed by the Schwartz-Neumann alternating method for local analysis to obtain the relevant crack tip parameters that govern the onset of fracture and the crack growth. The methodology developed is generic in nature and aims at handling a large fraction of problem areas identified by the Industry Committee on Wide-Spread Fatigue Damage.

  9. Relationship between mRNA secondary structure and sequence variability in Chloroplast genes: possible life history implications

    Directory of Open Access Journals (Sweden)

    Seligmann Hervé

    2008-01-01

    Full Text Available Abstract Background Synonymous sites are freer to vary because of redundancy in genetic code. Messenger RNA secondary structure restricts this freedom, as revealed by previous findings in mitochondrial genes that mutations at third codon position nucleotides in helices are more selected against than those in loops. This motivated us to explore the constraints imposed by mRNA secondary structure on evolutionary variability at all codon positions in general, in chloroplast systems. Results We found that the evolutionary variability and intrinsic secondary structure stability of these sequences share an inverse relationship. Simulations of most likely single nucleotide evolution in Psilotum nudum and Nephroselmis olivacea mRNAs, indicate that helix-forming propensities of mutated mRNAs are greater than those of the natural mRNAs for short sequences and vice-versa for long sequences. Moreover, helix-forming propensity estimated by the percentage of total mRNA in helices increases gradually with mRNA length, saturating beyond 1000 nucleotides. Protection levels of functionally important sites vary across plants and proteins: r-strategists minimize mutation costs in large genes; K-strategists do the opposite. Conclusion Mrna length presumably predisposes shorter mRNAs to evolve under different constraints than longer mRNAs. The positive correlation between secondary structure protection and functional importance of sites suggests that some sites might be conserved due to packing-protection constraints at the nucleic acid level in addition to protein level constraints. Consequently, nucleic acid secondary structure a priori biases mutations. The converse (exposure of conserved sites apparently occurs in a smaller number of cases, indicating a different evolutionary adaptive strategy in these plants. The differences between the protection levels of functionally important sites for r- and K-strategists reflect their respective molecular adaptive

  10. Dissecting and analyzing key residues in protein-DNA complexes.

    Science.gov (United States)

    Kulandaisamy, A; Srivastava, Ambuj; Nagarajan, R; Gromiha, M Michael

    2018-04-01

    Protein-DNA interactions are involved in various fundamental biological processes such as replication, transcription, DNA repair, and gene regulation. To understand the interaction in protein-DNA complexes, the integrative study of binding and stabilizing residues is important. In the present study, we have identified key residues that play a dual role in both binding and stability from a nonredundant dataset of 319 protein-DNA complexes. We observed that key residues are identified in very less number of complexes (29%) and only about 4% of stabilizing/binding residues are identified as key residues. Specifically, stabilizing residues have higher preference to be key residues than binding residues. These key residues include polar, nonpolar, aliphatic, aromatic, and charged amino acids. Moreover, we have analyzed and discussed the key residues in different protein-DNA complexes, which are classified based on protein structural class, function, DNA strand, and their conformations. Especially, Ser, Thr, Tyr, Arg, and Lys residues are commonly found in most of the subclasses of protein-DNA complexes. Further, we analyzed atomic contacts, which show that polar-nonpolar is more enriched than other types of contacts. In addition, the charged contacts are highly preferred in protein-DNA complexes compared with protein-protein and protein-RNA complexes. Finally, we have discussed the sequence and structural features of key residues such as conservation score, surrounding hydrophobicity, solvent accessibility, secondary structure, and long-range order. This study will be helpful to understand the recognition mechanism and structural and functional aspects of protein-DNA complexes. Copyright © 2017 John Wiley & Sons, Ltd.

  11. Analysis of energy-based algorithms for RNA secondary structure prediction.

    Science.gov (United States)

    Hajiaghayi, Monir; Condon, Anne; Hoos, Holger H

    2012-02-01

    RNA molecules play critical roles in the cells of organisms, including roles in gene regulation, catalysis, and synthesis of proteins. Since RNA function depends in large part on its folded structures, much effort has been invested in developing accurate methods for prediction of RNA secondary structure from the base sequence. Minimum free energy (MFE) predictions are widely used, based on nearest neighbor thermodynamic parameters of Mathews, Turner et al. or those of Andronescu et al. Some recently proposed alternatives that leverage partition function calculations find the structure with maximum expected accuracy (MEA) or pseudo-expected accuracy (pseudo-MEA) methods. Advances in prediction methods are typically benchmarked using sensitivity, positive predictive value and their harmonic mean, namely F-measure, on datasets of known reference structures. Since such benchmarks document progress in improving accuracy of computational prediction methods, it is important to understand how measures of accuracy vary as a function of the reference datasets and whether advances in algorithms or thermodynamic parameters yield statistically significant improvements. Our work advances such understanding for the MFE and (pseudo-)MEA-based methods, with respect to the latest datasets and energy parameters. We present three main findings. First, using the bootstrap percentile method, we show that the average F-measure accuracy of the MFE and (pseudo-)MEA-based algorithms, as measured on our largest datasets with over 2000 RNAs from diverse families, is a reliable estimate (within a 2% range with high confidence) of the accuracy of a population of RNA molecules represented by this set. However, average accuracy on smaller classes of RNAs such as a class of 89 Group I introns used previously in benchmarking algorithm accuracy is not reliable enough to draw meaningful conclusions about the relative merits of the MFE and MEA-based algorithms. Second, on our large datasets, the

  12. Analysis of energy-based algorithms for RNA secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Hajiaghayi Monir

    2012-02-01

    Full Text Available Abstract Background RNA molecules play critical roles in the cells of organisms, including roles in gene regulation, catalysis, and synthesis of proteins. Since RNA function depends in large part on its folded structures, much effort has been invested in developing accurate methods for prediction of RNA secondary structure from the base sequence. Minimum free energy (MFE predictions are widely used, based on nearest neighbor thermodynamic parameters of Mathews, Turner et al. or those of Andronescu et al. Some recently proposed alternatives that leverage partition function calculations find the structure with maximum expected accuracy (MEA or pseudo-expected accuracy (pseudo-MEA methods. Advances in prediction methods are typically benchmarked using sensitivity, positive predictive value and their harmonic mean, namely F-measure, on datasets of known reference structures. Since such benchmarks document progress in improving accuracy of computational prediction methods, it is important to understand how measures of accuracy vary as a function of the reference datasets and whether advances in algorithms or thermodynamic parameters yield statistically significant improvements. Our work advances such understanding for the MFE and (pseudo-MEA-based methods, with respect to the latest datasets and energy parameters. Results We present three main findings. First, using the bootstrap percentile method, we show that the average F-measure accuracy of the MFE and (pseudo-MEA-based algorithms, as measured on our largest datasets with over 2000 RNAs from diverse families, is a reliable estimate (within a 2% range with high confidence of the accuracy of a population of RNA molecules represented by this set. However, average accuracy on smaller classes of RNAs such as a class of 89 Group I introns used previously in benchmarking algorithm accuracy is not reliable enough to draw meaningful conclusions about the relative merits of the MFE and MEA-based algorithms

  13. The respiratory arsenite oxidase: structure and the role of residues surrounding the rieske cluster.

    Directory of Open Access Journals (Sweden)

    Thomas P Warelow

    Full Text Available The arsenite oxidase (Aio from the facultative autotrophic Alphaproteobacterium Rhizobium sp. NT-26 is a bioenergetic enzyme involved in the oxidation of arsenite to arsenate. The enzyme from the distantly related heterotroph, Alcaligenes faecalis, which is thought to oxidise arsenite for detoxification, consists of a large α subunit (AioA with bis-molybdopterin guanine dinucleotide at its active site and a 3Fe-4S cluster, and a small β subunit (AioB which contains a Rieske 2Fe-2S cluster. The successful heterologous expression of the NT-26 Aio in Escherichia coli has resulted in the solution of its crystal structure. The NT-26 Aio, a heterotetramer, shares high overall similarity to the heterodimeric arsenite oxidase from A. faecalis but there are striking differences in the structure surrounding the Rieske 2Fe-2S cluster which we demonstrate explains the difference in the observed redox potentials (+225 mV vs. +130/160 mV, respectively. A combination of site-directed mutagenesis and electron paramagnetic resonance was used to explore the differences observed in the structure and redox properties of the Rieske cluster. In the NT-26 AioB the substitution of a serine (S126 in NT-26 for a threonine as in the A. faecalis AioB explains a -20 mV decrease in redox potential. The disulphide bridge in the A. faecalis AioB which is conserved in other betaproteobacterial AioB subunits and the Rieske subunit of the cytochrome bc 1 complex is absent in the NT-26 AioB subunit. The introduction of a disulphide bridge had no effect on Aio activity or protein stability but resulted in a decrease in the redox potential of the cluster. These results are in conflict with previous data on the betaproteobacterial AioB subunit and the Rieske of the bc 1 complex where removal of the disulphide bridge had no effect on the redox potential of the former but a decrease in cluster stability was observed in the latter.

  14. Sequence analysis and structure prediction of enoyl-CoA hydratase from Avicennia marina: implication of various amino acid residues on substrate-enzyme interactions.

    Science.gov (United States)

    Jabeen, Uzma; Salim, Asmat

    2013-10-01

    Enoyl-CoA hydratase catalyzes the hydration of 2-trans-enoyl-CoA into 3-hydroxyacyl-CoA. The present study focuses on the correlation between the functional and structural aspects of enoyl-CoA hydratase from Avicennia marina. We have used bioinformatics tools to construct and analyze 3D homology models of A. marina enoyl-CoA hydratase (AMECH) bound to different substrates and inhibitors and studied the residues involved in the ligand-enzyme interaction. Structural information obtained from the models was compared with those of the reported crystal structures. We observed that the overall folds were similar; however, AMECH showed few distinct structural changes which include structural variation in the mobile loop, formation and loss of certain interactions between the active site residues and substrates. Some changes were also observed within specific regions of the enzyme. Glu106 is almost completely conserved in sequences of the isomerases/hydratases including AMECH while Glu86 which is the other catalytic residue in most of the isomerases/hydratases is replaced by Gly and shows no interaction with the substrate. Asp114 is located within 4Å distance of the catalytic water which makes it a probable candidate for the second catalytic residue in AMECH. Another prominent feature of AMECH is the presence of structurally distinct mobile loop having a completely different coordination with the hydrophobic binding pocket of acyl portion of the substrate. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Two-dimensional sup 1 H NMR studies on HPr protein from Staphylococcus aureus: Complete sequential assignments and secondary structure

    Energy Technology Data Exchange (ETDEWEB)

    Kalbitzer, H.R.; Neidig, K.P. (Max-Planck-Inst. for Medical Research, Heidelberg (West Germany)); Hengstenberg, W. (Univ. of Bochum (West Germany))

    1991-11-19

    Complete sequence-specific assignments of the {sup 1}H NMR spectrum of HPr protein from Staphylococcus aureus were obtained by two-dimensional NMR methods. Important secondary structure elements that can be derived from the observed nuclear Overhauser effects are a large antiparallel {beta}-pleated sheet consisting of four strands, A, B, C, D, a segment S{sub AB} consisting of an extended region around the active-center histidine (His-15) and an {alpha}-helix, a half-turn between strands B and C, a segment S{sub CD} which shows no typical secondary structure, and the {alpha}-helical, C-terminal segment S{sub term}. These general structural features are similar to those found earlier in HPr proteins from different microorganisms such as Escherichia coli, Bacillus subtilis, and Streptococcus faecalis.

  16. Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations.

    Science.gov (United States)

    Hu, Xihao; Wu, Yang; Lu, Zhi John; Yip, Kevin Y

    2016-11-01

    High-throughput sequencing has been used to study posttranscriptional regulations, where the identification of protein-RNA binding is a major and fast-developing sub-area, which is in turn benefited by the sequencing methods for whole-transcriptome probing of RNA secondary structures. In the study of RNA secondary structures using high-throughput sequencing, bases are modified or cleaved according to their structural features, which alter the resulting composition of sequencing reads. In the study of protein-RNA binding, methods have been proposed to immuno-precipitate (IP) protein-bound RNA transcripts in vitro or in vivo By sequencing these transcripts, the protein-RNA interactions and the binding locations can be identified. For both types of data, read counts are affected by a combination of confounding factors, including expression levels of transcripts, sequence biases, mapping errors and the probing or IP efficiency of the experimental protocols. Careful processing of the sequencing data and proper extraction of important features are fundamentally important to a successful analysis. Here we review and compare different experimental methods for probing RNA secondary structures and binding sites of RNA-binding proteins (RBPs), and the computational methods proposed for analyzing the corresponding sequencing data. We suggest how these two types of data should be integrated to study the structural properties of RBP binding sites as a systematic way to better understand posttranscriptional regulations. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  17. iDC: A comprehensive toolkit for the analysis of residual dipolar couplings for macromolecular structure determination

    International Nuclear Information System (INIS)

    Wei Yufeng; Werner, Milton H.

    2006-01-01

    Measurement of residual dipolar couplings (RDCs) has become an important method for the determination and validation of protein or nucleic acid structures by NMRf spectroscopy. A number of toolkits have been devised for the handling of RDC data which run in the Linux/Unix operating environment and require specifically formatted input files. The outputs from these programs, while informative, require format modification prior to the incorporation of this data into commonly used personal computer programs for manuscript preparation. To bridge the gap between analysis and publication, an easy-to-use, comprehensive toolkit for RDC analysis has been created, iDC. iDC is written for the WaveMetrics Igor Pro mathematics program, a widely used graphing and data analysis software program that runs on both Windows PC and Mac OS X computers. Experimental RDC values can be loaded into iDC using simple data formats accessible to Igor's tabular data function. The program can perform most useful RDC analyses, including alignment tensor estimation from a histogram of RDC occurrence versus values and order tensor analysis by singular value decomposition (SVD). SVD analysis can be performed on an entire structure family at once, a feature missing in other applications of this kind. iDC can also import from and export to several different commonly used programs for the analysis of RDC data (DC, PALES, REDCAT) and can prepare formatted files for RDC-based refinement of macromolecular structures using XPLOR-NIH, CNS and ARIA. The graphical user interface provides an easy-to-use I/O for data, structures and formatted outputs

  18. Structural Basis for Recognizing Phosphoarginine and Evolving Residue-Specific Protein Phosphatases in Gram-Positive Bacteria

    Directory of Open Access Journals (Sweden)

    Jakob Fuhrmann

    2013-06-01

    Full Text Available Many cellular pathways are regulated by the competing activity of protein kinases and phosphatases. The recent identification of arginine phosphorylation as a protein modification in bacteria prompted us to analyze the molecular basis of targeting phospho-arginine. In this work, we characterize an annotated tyrosine phosphatase, YwlE, that counteracts the protein arginine kinase McsB. Strikingly, structural studies of YwlE reaction intermediates provide a direct view on a captured arginine residue. Together with biochemical data, the crystal structures depict the evolution of a highly specific phospho-arginine phosphatase, with the use of a size-and-polarity filter for distinguishing phosphorylated arginine from other phosphorylated side chains. To confirm the proposed mechanism, we performed bioinformatic searches for phosphatases, employing a similar selectivity filter, and identified a protein in Drosophila melanogaster exhibiting robust arginine phosphatase activity. In sum, our findings uncover the molecular framework for specific targeting of phospho-arginine and suggest that protein arginine (dephosphorylation may be relevant in eukaryotes.

  19. Effect of linker length and residues on the structure and stability of a fusion protein with malaria vaccine application.

    Science.gov (United States)

    Shamriz, Shabnam; Ofoghi, Hamideh; Moazami, Nasrin

    2016-09-01

    Recombinant protein technology has revolutionized the world of biology and medicine. Following this progress, fusion protein technology, as a novel innovation, has opened new horizons for the development of proteins that do not naturally exist. Fusion proteins are generated via genetically fusing two or more genes coding for separate proteins, thus the product is a single protein having functional properties of both proteins. As an indispensable element in fusion protein construction, linkers are used to separate the functional domains in order to improve their expression, folding and stability. We computationally fused an antigen and an adjuvant together using different linkers to obtain a two-domain fusion construct which can potentially act as an oral vaccine candidate against malaria. We then predicted the structures computationally to find out the probable folding of each domain in the designed construct. One of the fusion constructs was selected based on the highest value for C-score. Ramchandran Plot analysis represented that most residues were fallen in favorable regions. Our in silico analysis showed that (GGGGS)3 linker confers the best structure and stability for our target fusion protein. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Immunoglobulin-G Glycation by Fructose Leads to Structural Perturbations and Drop Off in Free Lysine and Arginine Residues.

    Science.gov (United States)

    Faisal, Mohammad; Alatar, Abdulrahman A; Ahmad, Saheem

    2017-01-01

    Non-enzymatic glycation is the addition of free carbonyl group of reducing sugar to the free amino groups of proteins and leads to the formation of early glycation products and further into advanced glycation end products (AGEs). Fructose reacts rapidly with the free amino groups of proteins to form AGEs. AGEs are believed to be involved in the pathogenesis of several diseases, particularly in diabetic complications. In this study, IgG was glycated with fructose monosaccharide at 10 mM concentration for varying time interval. The reaction mixture was kept at 37ºC. The early glycation of IgG was done by nitroblue tetrazolium assay (NBT), and the generation of AGEs was done by the extent of side chain modifications (lysine and arginine), Nε-carboxymethyl lysine, pentosidine and carbonyl content. The decrease in free lysine and arginine residues suggests that protein 'IgG' has undergone modification specifically on epsilon amino groups of lysine and arginine. Additionally, their fluorescence and absorbance characteristics were also systematically studied. The results suggest that the maximum Amadori product (ketoamine content) was formed on sixth day of the incubation. The conformational structural perturbation was observed within the glycated IgG protein as studied by using various physicochemical techniques. This study reports structural perturbation, formation of various intermediates and AGEs. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  1. Use of residues proceeding from marbles and granites finishing and manufacturing processes as raw material for structural ceramic

    International Nuclear Information System (INIS)

    Mello, Roberta Monteiro de

    2006-01-01

    In order to decrease environmental impact, caused by mud discarding and clay extraction in the ceramic industry, it was used residual mud from marble and granite companies for structural ceramic. Samples were collected in twelve different marble companies located at the metropolitan region of Sao Paulo. However, only four samples were selected, based on its different characteristics. Clay stone was the raw material chosen to prepare the structural ceramic, considering its high use in this segment. Samples and clay stone were both analysed by the following procedures: granulometric analysis, x-rays fluorescent chemical analysis and x-rays diffraction mineralogical analysis, besides, tests in the samples were conducted following NBR 10004 standards. Once raw materials were characterized, the plasticity test was conducted. Test specimen were molded with different levels of mud, then burned and submitted to technological tests, such as: mechanical resistance, water absorption, porosity, specific gravity and retraction, material dilation before burning process and scanning electron microscopy. The final results have shown the viability of using this kind of mud, and pointed some advantages on its usage, but taking in consideration some previous conditions to be adopted. (author)

  2. Effect of deuteration on some structural parameters of methyl groups in proteins as evaluated by residual dipolar couplings

    International Nuclear Information System (INIS)

    Mittermaier, Anthony; Kay, Lewis E.

    2002-01-01

    One bond methyl 1 H- 13 C and 13 C methyl - 13 C scalar and residual dipolar couplings have been measured at sites in an 15 N, 13 C, ∼ 50% 2 H labeled sample of the B1 immunoglobulin binding domain of peptostreptococcal protein L to investigate changes in the structure of methyl groups in response to deuterium substitution. Both one bond methyl 1 H- 13 C and 13 C methyl - 13 C scalar coupling constants have been found to decrease slightly with increasing deuterium content. Previous studies have shown that 1 H- 13 C couplings in methyl groups are exquisitely sensitive to electronic structure, with decreases in coupling values as a function of deuteration consistent with a slight lengthening of the remaining H-C bonds. Changes in the H methyl C methyl C angle are found to be small, with average differences on the order of 0.3 ± 0.1 deg. and 0.4 ± 0.2 deg. between CH 3 , CH 2 D and CH 3 , CHD 2 isotopomers, respectively. Knowledge of methyl geometry is a prerequisite for the extraction of accurate dynamics parameters from spin relaxation studies involving these groups

  3. Effect of Resonant Magnetic Perturbations on secondary structures in Drift-Wave turbulence

    Science.gov (United States)

    Leconte, Michael

    2011-10-01

    In this work, we study the effects of RMPs on turbulence, flows and confinement, in the framework of two paradigmatic models, resistive ballooning and resistive drift waves. For resistive ballooning turbulence, we use 3D global numerical simulations, including RMP fields and (externally-imposed) sheared rotation profile. Without RMPs, relaxation oscillations of the pressure profile occur. With RMPs, results show that long-lived convection cells are generated by the combined effects of pressure modulation and toroidal curvature coupling. These modify the global structure of the turbulence and eliminate relaxation oscillations. This effect is due mainly to a modification of the pressure profile linked to the presence of residual magnetic island chains. Hence convection-cell generation increases for increasing δBr/B0. For RMP effect on zonal flows in drift wave turbulence, we extend the Hasegawa-Wakatani model to include RMP fields. The effect of the RMPs is to induce a linear coupling between the zonal electric field and the zonal density gradient, which drives the system to a state of electron radial force balance for large δBr/B0. Both the vorticity flux (Reynolds stress), and particle flux are modulated. We derive an extended predator prey model which couples zonal potential and density dynamics to the evolution of turbulence intensity. This model has both turbulence drive and RMP amplitude as control parameters, and predicts a novel type of transport bifurcation in the presence of RMPs. We find a novel set of system states that are similar to the Hmode-like state of the standard predator-prey model, but for which the power threshold is now a function of the RMP strength. For small RMP amplitude and low collisionality, both the ambient turbulence and zonal flow energy increase with δBr/B0. For larger RMP strength, the turbulence energy increases, but the energy of zonal flows decreases with δBr/B0, corresponding to a damping of zonal flows. At high

  4. PSP_MCSVM: brainstorming consensus prediction of protein secondary structures using two-stage multiclass support vector machines.

    Science.gov (United States)

    Chatterjee, Piyali; Basu, Subhadip; Kundu, Mahantapas; Nasipuri, Mita; Plewczynski, Dariusz

    2011-09-01

    Secondary structure prediction is a crucial task for understanding the variety of protein structures and performed biological functions. Prediction of secondary structures for new proteins using their amino acid sequences is of fundamental importance in bioinformatics. We propose a novel technique to predict protein secondary structures based on position-specific scoring matrices (PSSMs) and physico-chemical properties of amino acids. It is a two stage approach involving multiclass support vector machines (SVMs) as classifiers for three different structural conformations, viz., helix, sheet and coil. In the first stage, PSSMs obtained from PSI-BLAST and five specially selected physicochemical properties of amino acids are fed into SVMs as features for sequence-to-structure prediction. Confidence values for forming helix, sheet and coil that are obtained from the first stage SVM are then used in the second stage SVM for performing structure-to-structure prediction. The two-stage cascaded classifiers (PSP_MCSVM) are trained with proteins from RS126 dataset. The classifiers are finally tested on target proteins of critical assessment of protein structure prediction experiment-9 (CASP9). PSP_MCSVM with brainstorming consensus procedure performs better than the prediction servers like Predator, DSC, SIMPA96, for randomly selected proteins from CASP9 targets. The overall performance is found to be comparable with the current state-of-the art. PSP_MCSVM source code, train-test datasets and supplementary files are available freely in public domain at: http://sysbio.icm.edu.pl/secstruct and http://code.google.com/p/cmater-bioinfo/

  5. Characterizing the secondary protein structure of black widow dragline silk using solid-state NMR and X-ray diffraction.

    Science.gov (United States)

    Jenkins, Janelle E; Sampath, Sujatha; Butler, Emily; Kim, Jihyun; Henning, Robert W; Holland, Gregory P; Yarger, Jeffery L

    2013-10-14

    This study provides a detailed secondary structural characterization of major ampullate dragline silk from Latrodectus hesperus (black widow) spiders. X-ray diffraction results show that the structure of black widow major ampullate silk fibers is comprised of stacked β-sheet nanocrystallites oriented parallel to the fiber axis and an amorphous region with oriented (anisotropic) and isotropic components. The combination of two-dimensional (2D) (13)C-(13)C through-space and through-bond solid-state NMR experiments provide chemical shifts that are used to determine detailed information about the amino acid motif secondary structure in black widow spider dragline silk. Individual amino acids are incorporated into different repetitive motifs that make up the majority of this protein-based biopolymer. From the solid-state NMR measurements, we assign distinct secondary conformations to each repetitive amino acid motif and, hence, to the amino acids that make up the motifs. Specifically, alanine is incorporated in β-sheet (poly(Alan) and poly(Gly-Ala)), 3(1)-helix (poly(Gly-Gly-Xaa), and α-helix (poly(Gln-Gln-Ala-Tyr)) components. Glycine is determined to be in β-sheet (poly(Gly-Ala)) and 3(1)-helical (poly(Gly-Gly-X(aa))) regions, while serine is present in β-sheet (poly(Gly-Ala-Ser)), 3(1)-helix (poly(Gly-Gly-Ser)), and β-turn (poly(Gly-Pro-Ser)) structures. These various motif-specific secondary structural elements are quantitatively correlated to the primary amino acid sequence of major ampullate spidroin 1 and 2 (MaSp1 and MaSp2) and are shown to form a self-consistent model for black widow dragline silk.

  6. Identification of protein secondary structures by laser induced autofluorescence: A study of urea and GnHCl induced protein denaturation

    Science.gov (United States)

    Siddaramaiah, Manjunath; Satyamoorthy, Kapaettu; Rao, Bola Sadashiva Satish; Roy, Suparna; Chandra, Subhash; Mahato, Krishna Kishore

    2017-03-01

    In the present study an attempt has been made to interrogate the bulk secondary structures of some selected proteins (BSA, HSA, lysozyme, trypsin and ribonuclease A) under urea and GnHCl denaturation using laser induced autofluorescence. The proteins were treated with different concentrations of urea (3 M, 6 M, 9 M) and GnHCl (2 M, 4 M, 6 M) and the corresponding steady state autofluorescence spectra were recorded at 281 nm pulsed laser excitations. The recorded fluorescence spectra of proteins were then interpreted based on the existing PDB structures of the proteins and the Trp solvent accessibility (calculated using "Scratch protein predictor" at 30% threshold). Further, the influence of rigidity and conformation of the indole ring (caused by protein secondary structures) on the intrinsic fluorescence properties of proteins were also evaluated using fluorescence of ANS-HSA complexes, CD spectroscopy as well as with trypsin digestion experiments. The outcomes obtained clearly demonstrated GnHCl preferably disrupt helix as compared to the beta β-sheets whereas, urea found was more effective in disrupting β-sheets as compared to the helices. The other way round the proteins which have shown detectable change in the intrinsic fluorescence at lower concentrations of GnHCl were rich in helices whereas, the proteins which showed detectable change in the intrinsic fluorescence at lower concentrations of urea were rich in β-sheets. Since high salt concentrations like GnHCl and urea interfere in the secondary structure analysis by circular dichroism Spectrometry, the present method of analyzing secondary structures using laser induced autofluorescence will be highly advantageous over existing tools for the same.

  7. Structural polymorphism of human islet amyloid polypeptide (hIAPP) oligomers highlights the importance of interfacial residue interactions.

    Science.gov (United States)

    Zhao, Jun; Yu, Xiang; Liang, Guizhao; Zheng, Jie

    2011-01-10

    A 37-residue of human islet amyloid polypeptide (hIAPP or amylin) is a main component of amyloid plaques found in the pancreas of ∼90% of type II diabetes patients. It is reported that hIAPP oligomers, rather than mature fibrils, are major toxic species responsible for pancreatic islet β-cell dysfunction and even cell death, but molecular structures of these oligomers remain elusive. In this work, on the basis of recent solid-state NMR and mass-per-length (MPL) data, we model a series of hIAPP oligomers with different β-layers (one, two, and three layers), symmetries (symmetry and asymmetry), and associated interfaces using molecular dynamics simulations. Three distinct interfaces formed by C-terminal β-sheet and C-terminal β-sheet (CC), N-terminal β-sheet and N-terminal β-sheet (NN), and C-terminal β-sheet and N-terminal β-sheet (CN) are identified to drive multiple cross-β-layers laterally associated together to form different amyloid organizations via different intermolecular interactions, in which the CC interface is dominated by polar interactions, the NN interface is dominated by hydrophobic interactions, and the CN interface is dominated by mixed polar and hydrophobic interactions. Overall, the structural stability of the proposed hIAPP oligomers is a result of delicate balance between maximization of favorable peptide-peptide interactions at the interfaces and optimization of solvation energy with globular structure. Different hIAPP oligomeric models indicate a general and intrinsic nature of amyloid polymorphism, driven by different interfacial side-chain interactions. The proposed models are compatible with recent experimental data in overall size, cross-section area, and molecular weight. A general hIAPP aggregation mechanism is proposed on the basis of our simulated models and experimental data.

  8. Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development

    Science.gov (United States)

    Bandyopadhyay, Deepak; Huan, Jun; Prins, Jan; Snoeyink, Jack; Wang, Wei; Tropsha, Alexander

    2009-11-01

    Protein function prediction is one of the central problems in computational biology. We present a novel automated protein structure-based function prediction method using libraries of local residue packing patterns that are common to most proteins in a known functional family. Critical to this approach is the representation of a protein structure as a graph where residue vertices (residue name used as a vertex label) are connected by geometrical proximity edges. The approach employs two steps. First, it uses a fast subgraph mining algorithm to find all occurrences of family-specific labeled subgraphs for all well characterized protein structural and functional families. Second, it queries a new structure for occurrences of a set of motifs characteristic of a known family, using a graph index to speed up Ullman's subgraph isomorphism algorithm. The confidence of function inference from structure depends on the number of family-specific motifs found in the query structure compared with their distribution in a large non-redundant database of proteins. This method can assign a new structure to a specific functional family in cases where sequence alignments, sequence patterns, structural superposition and active site templates fail to provide accurate annotation.

  9. Very high resolution structure of a trematode hemoglobin displaying a TyrB10-TyrE7 heme distal residue pair and high oxygen affinity.

    Science.gov (United States)

    Pesce, A; Dewilde, S; Kiger, L; Milani, M; Ascenzi, P; Marden, M C; Van Hauwaert, M L; Vanfleteren, J; Moens, L; Bolognesi, M

    2001-06-22

    Monomeric hemoglobin from the trematode Paramphistomum epiclitum displays very high oxygen affinity (P(50)hemoglobin, solved at 1.17 A resolution via multiwavelength anomalous dispersion techniques (R-factor=0.121), shows that the heme distal site pocket residue TyrB10 is engaged in hydrogen bonding to the iron-bound ligand. By contrast, residue TyrE7 is unexpectedly locked next to the CD globin region, in a conformation unsuitable for heme-bound ligand stabilisation. Such structural organization of the E7 distal residue differs strikingly from that observed in the nematode Ascaris suum hemoglobin (bearing TyrB10 and GlnE7 residues), which also displays very high oxygen affinity. The oxygenation and carbonylation parameters of wild-type P. epiclitum Hb as well as of single- and double-site mutants, with residue substitutions at positions B10, E7 and E11, have been determined and are discussed here in the light of the protein atomic resolution crystal structure. Copyright 2001 Academic Press.

  10. Amyloid β-Sheet Secondary Structure Identified in UV-Induced Cataracts of Porcine Lenses using 2D IR Spectroscopy.

    Science.gov (United States)

    Zhang, Tianqi O; Alperstein, Ariel M; Zanni, Martin T

    2017-06-02

    Cataracts are formed by the aggregation of crystallin proteins in the eye lens. Many in vitro studies have established that crystallin proteins precipitate into aggregates that contain amyloid fibers when denatured, but there is little evidence that ex vivo cataracts contain amyloid. In this study, we collect two-dimensional infrared (2D IR) spectra on tissue slices of porcine eye lenses. As shown in control experiments on in vitro αB- and γD-crystallin, 2D IR spectroscopy can identify the highly ordered β-sheets typical of amyloid secondary structure even if the fibers themselves are too short to be resolved with TEM. In ex vivo experiments of acid-treated tissues, characteristic 2D IR features are observed and fibers >50nm in length are resolved by transmission electron microscopy (TEM), consistent with amyloid fibers. In UV-irradiated lens tissues, fibers are not observed with TEM, but highly ordered β-sheets of amyloid secondary structure is identified from the 2D IR spectra. The characteristic 2D IR features of amyloid β-sheet secondary structure are created by as few as four or five strands and so identify amyloid secondary structure even if the aggregates themselves are too small to be resolved with TEM. We discuss these findings in the context of the chaperone system of the lens, which we hypothesize sequesters small aggregates, thereby preventing long fibers from forming. This study expands the scope of heterodyned 2D IR spectroscopy to tissues. The results provide a link between in vitro and ex vivo studies and support the hypothesis that cataracts are an amyloid disease. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Alkali solution extraction of rice residue protein isolates: Influence of alkali concentration on protein functional, structural properties and lysinoalanine formation.

    Science.gov (United States)

    Hou, Furong; Ding, Wenhui; Qu, Wenjuan; Oladejo, Ayobami Olayemi; Xiong, Feng; Zhang, Weiwei; He, Ronghai; Ma, Haile

    2017-03-01

    This study evaluated the nutrient property and safety of the rice residue protein isolates (RRPI) product (extracted by different alkali concentrations) by exploring the protein functional, structural properties and lysinoalanine (LAL) formation. The results showed that with the rising of alkali concentration from 0.03M to 0.15M, the solubility, emulsifying and foaming properties of RRPI increased at first and then descended. When the alkali concentration was greater than 0.03M, the RRPI surface hydrophobicity decreased and the content of thiol and disulfide bond, Lys and Cys significantly reduced. By the analysis of HPLC, the content of LAL rose up from 276.08 to 15,198.07mg/kg and decreased to 1340.98mg/kg crude protein when the alkali concentration increased from 0.03 to 0.09M and until to 0.15M. These results indicated that RRPI alkaline extraction concentration above 0.03M may cause severe nutrient or safety problems of protein. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Assessment of residual coronal tooth structure postendodontic cavity preparation using digital dental impressions and micro-computed tomography.

    Science.gov (United States)

    Al-Nuaimi, Nassr; Patel, Shanon; Foschi, Federico; Mannocci, Francesco; Austin, Rupert S

    To evaluate the in vitro accuracy of digital impressions for three-dimensional (3D) volumetric measurement of residual coronal tooth structure postendodontic cavity preparation, with reference to micro-computed tomography (μCT). Quantification of the accuracy and precision of the intraoral digital scanner (3M True Definition Scanner - IOS) was performed using a metrology gauge block and a profilometric calibration model. Thirty-four human extracted molars with endodontic access cavities were scanned using both intraoral scanning (test scanner) in high-resolution mode, and µCT (reference scanner: GE Locus SP μCT scanner) in high- (HiResCT) and low- (LoResCT) resolution modes. Comparisons of volumetric accuracy and 3D profilometric deviations were performed using surface metrology software. One-way repeated measures analysis of variance (ANOVA), in combination with the Bonferroni post hoc test, was implemented to compare the differences in volume measurements between scanning methods. Digital scanning revealed smaller volume measurements by 1.36% and 0.68% compared to HiResCT and LoResCT, respectively. There was a statistically significant difference in the volumetric measurements obtained from the IOS scanner and both HiResCT and LoResCT scans (P digital scanner was able to reliably measure the extra- and intracoronal aspect of the endodontically accessed tooth.

  13. Cholinergic Basal Forebrain Structure Influences the Reconfiguration of White Matter Connections to Support Residual Memory in Mild Cognitive Impairment

    Science.gov (United States)

    Ray, Nicola J.; Metzler-Baddeley, Claudia; Khondoker, Mizanur R.; Grothe, Michel J.; Teipel, Stefan; Wright, Paul; Heinsen, Helmut; Jones, Derek K.; Aggleton, John P.

    2015-01-01

    The fornix and hippocampus are critical to recollection in the healthy human brain. Fornix degeneration is a feature of aging and Alzheimer's disease. In the presence of fornix damage in mild cognitive impairment (MCI), a recognized prodrome of Alzheimer's disease, recall shows greater dependence on other tracts, notably the parahippocampal cingulum (PHC). The current aims were to determine whether this shift is adaptive and to probe its relationship to cholinergic signaling, which is also compromised in Alzheimer's disease. Twenty-five human participants with MCI and 20 matched healthy volunteers underwent diffusion MRI, behavioral assessment, and volumetric measurement of the basal forebrain. In a regression model for recall, there was a significant group × fornix interaction, indicating that the association between recall and fornix structure was weaker in patients. The opposite trend was present for the left PHC. To further investigate this pattern, two regression models were generated to account for recall performance: one based on fornix microstructure and the other on both fornix and left PHC. The realignment to PHC was positively correlated with free recall but not non-memory measures, implying a reconfiguration that is beneficial to residual memory. There was a positive relationship between realignment to PHC and basal forebrain gray matter volume despite this region demonstrating atrophy at a group level, i.e., the cognitive realignment to left PHC was most apparent when cholinergic areas were relatively spared. Therefore, cholinergic systems appear to enable adaptation to injury even as they degenerate, which has implications for functional restoration. PMID:25589767

  14. Secondary structure determination by NMR spectroscopy of an immunoglobulin-like domain from the giant muscle protein titin.

    Science.gov (United States)

    Pfuhl, M; Gautel, M; Politou, A S; Joseph, C; Pastore, A

    1995-07-01

    We present the complete 15N and 1H NMR assignment and the secondary structure of an immunoglobulin-like domain from the giant muscle protein titin. The assignment was obtained using homonuclear and 15N heteronuclear 2D and 3D experiments. The complementarity of 3D TOCSY-NOESY and 3D 15N NOESY-HSQC experiments, using WATERGATE for water suppression, allowed an efficient assignment of otherwise ambiguous cross peaks and was helpful in overcoming poor TOCSY transfer for some amino acids. The secondary structure is derived from specific NOEs between backbone alpha- and amide protons, secondary chemical shifts of alpha-protons and chemical exchange for the backbone amide protons. It consists of eight beta-strands, forming two beta-sheets with four strands each, similar to the classical beta-sandwich of the immunoglobulin superfamily, as previously predicted by sequence analysis. Two of the beta-strands are connected by type II beta-turns; the first beta-strand forms a beta-bulge. The whole topology is very similar to the only intracellular immunoglobulin-like domain for which a structure has been determined so far, i.e., telokin.

  15. Mutations Affecting Keratin 10 Surface-Exposed Residues Highlight the Structural Basis of Phenotypic Variation in Epidermolytic Ichthyosis.

    Science.gov (United States)

    Mirza, Haris; Kumar, Anil; Craiglow, Brittany G; Zhou, Jing; Saraceni, Corey; Torbeck, Richard; Ragsdale, Bruce; Rehder, Paul; Ranki, Annamari; Choate, Keith A

    2015-12-01

    Epidermolytic ichthyosis (EI) due to KRT10 mutations is a rare, typically autosomal dominant, disorder characterized by generalized erythema and cutaneous blistering at birth followed by hyperkeratosis and less frequent blistering later in life. We identified two KRT10 mutations p.Q434del and p.R441P in subjects presenting with a mild EI phenotype. Both occur within the mutational "hot spot" of the keratin 10 (K10) 2B rod domain, adjacent to severe EI-associated mutations. p.Q434del and p.R441P formed collapsed K10 fibers rather than aggregates characteristic of severe EI KRT10 mutations such as p.R156C. Upon differentiation, keratinocytes from p.Q434del showed significantly lower apoptosis (P-value<0.01) compared with p.R156C as assessed by the TUNEL assay. Conversely, the mitotic index of the p.Q434del epidermis was significantly higher compared with that of p.R156C (P-value<0.01) as estimated by the Ki67 assay. Structural basis of EI phenotype variation was investigated by homology-based modeling of wild-type and mutant K1-K10 dimers. Both mild EI mutations were found to affect the surface-exposed residues of the K10 alpha helix coiled-coil and caused localized disorganization of the K1-K10 heterodimer. In contrast, adjacent severe EI mutations disrupt key intermolecular dimer interactions. Our findings provide structural insights into phenotypic variation in EI due to KRT10 mutations.

  16. Structural Insights into TMB-1 and the Role of Residues 119 and 228 in Substrate and Inhibitor Binding.

    Science.gov (United States)

    Skagseth, Susann; Christopeit, Tony; Akhter, Sundus; Bayer, Annette; Samuelsen, Ørjan; Leiros, Hanna-Kirsti S

    2017-08-01

    Metallo-β-lactamases (MBLs) threaten the effectiveness of β-lactam antibiotics, including carbapenems, and are a concern for global public health. β-Lactam/β-lactamase inhibitor combinations active against class A and class D carbapenemases are used, but no clinically useful MBL inhibitor is currently available. Tripoli metallo-β-lactamase-1 (TMB-1) and TMB-2 are members of MBL subclass B1a, where TMB-2 is an S228P variant of TMB-1. The role of S228P was studied by comparisons of TMB-1 and TMB-2, and E119 was investigated through the construction of site-directed mutants of TMB-1, E119Q, E119S, and E119A (E119Q/S/A). All TMB variants were characterized through enzyme kinetic studies. Thermostability and crystallization analyses of TMB-1 were performed. Thiol-based inhibitors were investigated by determining the 50% inhibitory concentrations (IC 50 ) and binding using surface plasmon resonance (SPR) for analysis of TMB-1. Thermostability measurements found TMB-1 to be stabilized by high NaCl concentrations. Steady-state enzyme kinetics analyses found substitutions of E119, in particular, substitutions associated with the penicillins, to affect hydrolysis to some extent. TMB-2 with S228P showed slightly reduced catalytic efficiency compared to TMB-1. The IC 50 levels of the new thiol-based inhibitors were 0.66 μM (inhibitor 2a) and 0.62 μM (inhibitor 2b), and the equilibrium dissociation constant ( K D ) of inhibitor 2a was 1.6 μM; thus, both were more potent inhibitors than l-captopril (IC 50 = 47 μM; K D = 25 μM). The crystal structure of TMB-1 was resolved to 1.75 Å. Modeling of inhibitor 2b in the TMB-1 active site suggested that the presence of the W64 residue results in T-shaped π-π stacking and R224 cation-π interactions with the phenyl ring of the inhibitor. In sum, the results suggest that residues 119 and 228 affect the catalytic efficiency of TMB-1 and that inhibitors 2a and 2b are more potent inhibitors for TMB-1 than l-captopril. Copyright

  17. Crystal structure of Bacillus fastidious uricase reveals an unexpected folding of the C-terminus residues crucial for thermostability under physiological conditions.

    Science.gov (United States)

    Feng, Juan; Wang, Lu; Liu, Hongbo; Yang, Xiaolan; Liu, Lin; Xie, Yanling; Liu, Miaomiao; Zhao, Yunsheng; Li, Xiang; Wang, Deqiang; Zhan, Chang-Guo; Liao, Fei

    2015-10-01

    Bacillus fastidious uricase (BF uricase) containing 322 amino acid residues exhibited high stability under physiological conditions. Its crystal structure was solved to 1.4-Å resolution, showing homotetramer containing two homodimers. After the intersubunit antiparallel β-sheet in its homodimer, each subunit had a total of 18 C-terminus residues forming an α-helix (Q305-A313) and random coil (S314-L322) on surface to bury other two α-helices (I227-T238 and I244-R258). In comparison, reported crystal structures of Arthrobacter globiformis and Aspergillus flavus uricases had atomic coordinates of only some C-terminus residues, while the crystal structures of all the other uricases accessible before September 2014 missed atomic coordinates of all their C-terminus residues, after the intersubunit antiparallel β-sheets. In each homodimer of BF uricase, H-bonds were found between E311 and Y249 and between Y319 and D257; electrostatic interaction networks were found to surround D307 plus R310 and intersubunit R3, K312 plus D257, E318 plus K242, and L322 plus R258. Amino acid mutations that disrupted those interactions when R3 and D307 were reserved caused moderate decreases of activity at pH 9.2 while negligible decreases of activity at pH 7.4, but destroyed stability at pH 7.4 while slightly decreased stability at pH 9.2. Such structural information guided the fusion of 6His-tag to the C-terminus of the mutant L322D with SNSNSN as a linker to reserve the activity and stability. Hence, the folding of the C-terminus residues is