Automated solid-state NMR resonance assignment of protein microcrystals and amyloids

Energy Technology Data Exchange (ETDEWEB)

Schmidt, Elena [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany); Gath, Julia [ETH Zurich, Physical Chemistry (Switzerland); Habenstein, Birgit [UMR 5086 CNRS/Universite de Lyon 1, Institut de Biologie et Chimie des Proteines (France); Ravotti, Francesco; Szekely, Kathrin; Huber, Matthias [ETH Zurich, Physical Chemistry (Switzerland); Buchner, Lena [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany); Boeckmann, Anja, E-mail: a.bockmann@ibcp.fr [UMR 5086 CNRS/Universite de Lyon 1, Institut de Biologie et Chimie des Proteines (France); Meier, Beat H., E-mail: beme@ethz.ch [ETH Zurich, Physical Chemistry (Switzerland); Guentert, Peter, E-mail: guentert@em.uni-frankfurt.de [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany)

2013-07-15

Solid-state NMR is an emerging structure determination technique for crystalline and non-crystalline protein assemblies, e.g., amyloids. Resonance assignment constitutes the first and often very time-consuming step to a structure. We present ssFLYA, a generally applicable algorithm for automatic assignment of protein solid-state NMR spectra. Application to microcrystals of ubiquitin and the Ure2 prion C-terminal domain, as well as amyloids of HET-s(218-289) and {alpha}-synuclein yielded 88-97 % correctness for the backbone and side-chain assignments that are classified as self-consistent by the algorithm, and 77-90 % correctness if also assignments classified as tentative by the algorithm are included.

Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH

International Nuclear Information System (INIS)

Volk, Jochen; Herrmann, Torsten; Wuethrich, Kurt

2008-01-01

MATCH (Memetic Algorithm and Combinatorial Optimization Heuristics) is a new memetic algorithm for automated sequence-specific polypeptide backbone NMR assignment of proteins. MATCH employs local optimization for tracing partial sequence-specific assignments within a global, population-based search environment, where the simultaneous application of local and global optimization heuristics guarantees high efficiency and robustness. MATCH thus makes combined use of the two predominant concepts in use for automated NMR assignment of proteins. Dynamic transition and inherent mutation are new techniques that enable automatic adaptation to variable quality of the experimental input data. The concept of dynamic transition is incorporated in all major building blocks of the algorithm, where it enables switching between local and global optimization heuristics at any time during the assignment process. Inherent mutation restricts the intrinsically required randomness of the evolutionary algorithm to those regions of the conformation space that are compatible with the experimental input data. Using intact and artificially deteriorated APSY-NMR input data of proteins, MATCH performed sequence-specific resonance assignment with high efficiency and robustness

Automated solid-state NMR resonance assignment of protein microcrystals and amyloids

International Nuclear Information System (INIS)

Schmidt, Elena; Gath, Julia; Habenstein, Birgit; Ravotti, Francesco; Székely, Kathrin; Huber, Matthias; Buchner, Lena; Böckmann, Anja; Meier, Beat H.; Güntert, Peter

2013-01-01

Solid-state NMR is an emerging structure determination technique for crystalline and non-crystalline protein assemblies, e.g., amyloids. Resonance assignment constitutes the first and often very time-consuming step to a structure. We present ssFLYA, a generally applicable algorithm for automatic assignment of protein solid-state NMR spectra. Application to microcrystals of ubiquitin and the Ure2 prion C-terminal domain, as well as amyloids of HET-s(218–289) and α-synuclein yielded 88–97 % correctness for the backbone and side-chain assignments that are classified as self-consistent by the algorithm, and 77–90 % correctness if also assignments classified as tentative by the algorithm are included

Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl–methyl nuclear overhauser enhancement spectroscopy

International Nuclear Information System (INIS)

Venditti, Vincenzo; Fawzi, Nicolas L.; Clore, G. Marius

2011-01-01

Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to ∼1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic relaxation enhancement (PRE), induced by nitroxide spin-labels incorporated at only a few surface-exposed engineered cysteines, provides fast, straightforward and robust access to methyl group resonance assignments, including stereoassignments for the methyl groups of leucine and valine. Neither prior assignments, including backbone assignments, for the protein, nor experiments that transfer magnetization between methyl groups and the protein backbone, are required. PRE-derived assignments are refined by 4D methyl–methyl nuclear Overhauser enhancement data, eliminating ambiguities and errors that may arise due to the high sensitivity of PREs to the potential presence of sparsely-populated transient states.

Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear overhauser enhancement spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Venditti, Vincenzo; Fawzi, Nicolas L.; Clore, G. Marius, E-mail: mariusc@mail.nih.gov [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Laboratory of Chemical Physics (United States)

2011-11-15

Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to {approx}1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic relaxation enhancement (PRE), induced by nitroxide spin-labels incorporated at only a few surface-exposed engineered cysteines, provides fast, straightforward and robust access to methyl group resonance assignments, including stereoassignments for the methyl groups of leucine and valine. Neither prior assignments, including backbone assignments, for the protein, nor experiments that transfer magnetization between methyl groups and the protein backbone, are required. PRE-derived assignments are refined by 4D methyl-methyl nuclear Overhauser enhancement data, eliminating ambiguities and errors that may arise due to the high sensitivity of PREs to the potential presence of sparsely-populated transient states.

Automated Bug Assignment: Ensemble-based Machine Learning in Large Scale Industrial Contexts

OpenAIRE

Jonsson, Leif; Borg, Markus; Broman, David; Sandahl, Kristian; Eldh, Sigrid; Runeson, Per

2016-01-01

Bug report assignment is an important part of software maintenance. In particular, incorrect assignments of bug reports to development teams can be very expensive in large software development projects. Several studies propose automating bug assignment techniques using machine learning in open source software contexts, but no study exists for large-scale proprietary projects in industry. The goal of this study is to evaluate automated bug assignment techniques that are based on machine learni...

APSY-NMR for protein backbone assignment in high-throughput structural biology

Energy Technology Data Exchange (ETDEWEB)

Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Herrmann, Torsten [Université de Lyon, Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1 (France); Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

2015-01-15

A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.

Stereospecific assignments of glycine in proteins by stereospecific deuteration and {sup 15}N labeling

Energy Technology Data Exchange (ETDEWEB)

Hansen, A.P.; Curley, R.W. Jr.; Panigot, M.J.; Fesik, S.W. [Ohio State Univ., Columbus, OH (United States)

1994-12-01

Stereospecific assignments are important for accurately determining the three-dimensional structures of proteins through the use of multidimensional NMR techniques. It is especially important to stereospecifically assign the glycine {alpha}-protons in proteins because of the potential for different backbone conformations of this residue. These stereospecific assignments are critical for interpreting the {sup 3}J{sub NH,{alpha}H} coupling constants and NOEs involving the glycine {alpha}-protons that determine the conformation of this part of the protein. However, it is often difficult to unambiguously obtain the stereospecific assignments for glycine residues by using only NOE data. In this poster, we present a method for unambiguous, stereospecific assignment of the {alpha}-protons of glycine residues. This method involves synthesis of stereo-specifically deuterated and {sup 15}N-labeled Gly using a slightly modified procedure originally described by Woodard and coworkers for the stereoselective deuteration of glycine. The stereospecifically deuterated and {sup 15}N-labeled Gy has been incorporated into recombinant proteins expressed in both bacterial systems (FKBP) and mammalian cells (u-PA). Two- and three-dimensional isotope-filtered and isotope-edited NMR experiments were used to obtain the stereospecific assignments of the glycine {alpha}-protons for these proteins.

Organic Chemistry YouTube Writing Assignment for Large Lecture Classes

Science.gov (United States)

Franz, Annaliese K.

2012-01-01

This work describes efforts to incorporate and evaluate the use of a YouTube writing assignment in large lecture classes to personalize learning and improve conceptual understanding of chemistry through peer- and self-explanation strategies. Although writing assignments can be a method to incorporate peer- and self-explanation strategies, this…

Facilitated assignment of large protein NMR signals with covariance sequential spectra using spectral derivatives.

Science.gov (United States)

Harden, Bradley J; Nichols, Scott R; Frueh, Dominique P

2014-09-24

Nuclear magnetic resonance (NMR) studies of larger proteins are hampered by difficulties in assigning NMR resonances. Human intervention is typically required to identify NMR signals in 3D spectra, and subsequent procedures depend on the accuracy of this so-called peak picking. We present a method that provides sequential connectivities through correlation maps constructed with covariance NMR, bypassing the need for preliminary peak picking. We introduce two novel techniques to minimize false correlations and merge the information from all original 3D spectra. First, we take spectral derivatives prior to performing covariance to emphasize coincident peak maxima. Second, we multiply covariance maps calculated with different 3D spectra to destroy erroneous sequential correlations. The maps are easy to use and can readily be generated from conventional triple-resonance experiments. Advantages of the method are demonstrated on a 37 kDa nonribosomal peptide synthetase domain subject to spectral overlap.

Probabilistic validation of protein NMR chemical shift assignments

International Nuclear Information System (INIS)

Dashti, Hesam; Tonelli, Marco; Lee, Woonghee; Westler, William M.; Cornilescu, Gabriel; Ulrich, Eldon L.; Markley, John L.

2016-01-01

Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data. ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/ http://areca.nmrfam.wisc.edu/

Probabilistic validation of protein NMR chemical shift assignments

Energy Technology Data Exchange (ETDEWEB)

Dashti, Hesam [University of Wisconsin-Madison, Graduate Program in Biophysics, Biochemistry Department (United States); Tonelli, Marco; Lee, Woonghee; Westler, William M.; Cornilescu, Gabriel [University of Wisconsin-Madison, Biochemistry Department, National Magnetic Resonance Facility at Madison (United States); Ulrich, Eldon L. [University of Wisconsin-Madison, BioMagResBank, Biochemistry Department (United States); Markley, John L., E-mail: markley@nmrfam.wisc.edu, E-mail: jmarkley@wisc.edu [University of Wisconsin-Madison, Biochemistry Department, National Magnetic Resonance Facility at Madison (United States)

2016-01-15

Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data. ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/ http://areca.nmrfam.wisc.edu/.

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....

A novel strategy for NMR resonance assignment and protein structure determination

International Nuclear Information System (INIS)

Lemak, Alexander; Gutmanas, Aleksandras; Chitayat, Seth; Karra, Murthy; Farès, Christophe; Sunnerhagen, Maria; Arrowsmith, Cheryl H.

2011-01-01

The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution – especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.

Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis

Energy Technology Data Exchange (ETDEWEB)

Harsch, Tobias; Schneider, Philipp; Kieninger, Bärbel; Donaubauer, Harald; Kalbitzer, Hans Robert, E-mail: hans-robert.kalbitzer@biologie.uni-regensburg.de [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany)

2017-02-15

Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB). For a separation of the chemical shifts of the two amide resonance lines with differences ≥0.40 ppm for asparagine and differences ≥0.42 ppm for glutamine, the downfield shifted resonance lines can be assigned to H{sup δ21} and H{sup ε21}, respectively, at a confidence level >95%. A classifier derived from UASCB can also be used to correct the BMRB data. The program tool AssignmentChecker implemented in AUREMOL calculates the Bayesian probability for a given stereospecific assignment and automatically corrects the assignments for a given list of chemical shifts.

CASA: An Efficient Automated Assignment of Protein Mainchain NMR Data Using an Ordered Tree Search Algorithm

International Nuclear Information System (INIS)

Wang Jianyong; Wang Tianzhi; Zuiderweg, Erik R. P.; Crippen, Gordon M.

2005-01-01

Rapid analysis of protein structure, interaction, and dynamics requires fast and automated assignments of 3D protein backbone triple-resonance NMR spectra. We introduce a new depth-first ordered tree search method of automated assignment, CASA, which uses hand-edited peak-pick lists of a flexible number of triple resonance experiments. The computer program was tested on 13 artificially simulated peak lists for proteins up to 723 residues, as well as on the experimental data for four proteins. Under reasonable tolerances, it generated assignments that correspond to the ones reported in the literature within a few minutes of CPU time. The program was also tested on the proteins analyzed by other methods, with both simulated and experimental peaklists, and it could generate good assignments in all relevant cases. The robustness was further tested under various situations

Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm

International Nuclear Information System (INIS)

Yang, Yu; Fritzsching, Keith J.; Hong, Mei

2013-01-01

A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR (SSNMR) spectra with partial resonance overlap and missing peaks due to broad linewidths, molecular motion, and low sensitivity. This non-dominated sorting genetic algorithm II (NSGA-II) aims to identify all possible assignments that are consistent with the spectra and to compare the relative merit of these assignments. Our approach is modeled after the recently introduced Monte-Carlo simulated-annealing (MC/SA) protocol, with the key difference that NSGA-II simultaneously optimizes multiple assignment objectives instead of searching for possible assignments based on a single composite score. The multiple objectives include maximizing the number of consistently assigned peaks between multiple spectra (“good connections”), maximizing the number of used peaks, minimizing the number of inconsistently assigned peaks between spectra (“bad connections”), and minimizing the number of assigned peaks that have no matching peaks in the other spectra (“edges”). Using six SSNMR protein chemical shift datasets with varying levels of imperfection that was introduced by peak deletion, random chemical shift changes, and manual peak picking of spectra with moderately broad linewidths, we show that the NSGA-II algorithm produces a large number of valid and good assignments rapidly. For high-quality chemical shift peak lists, NSGA-II and MC/SA perform similarly well. However, when the peak lists contain many missing peaks that are uncorrelated between different spectra and have chemical shift deviations between spectra, the modified NSGA-II produces a larger number of valid solutions than MC/SA, and is more effective at distinguishing good from mediocre assignments by avoiding the hazard of suboptimal weighting factors for the various objectives. These two advantages, namely diversity and better evaluation, lead to a higher probability of predicting the correct

Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm.

Science.gov (United States)

Yang, Yu; Fritzsching, Keith J; Hong, Mei

2013-11-01

A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR (SSNMR) spectra with partial resonance overlap and missing peaks due to broad linewidths, molecular motion, and low sensitivity. This non-dominated sorting genetic algorithm II (NSGA-II) aims to identify all possible assignments that are consistent with the spectra and to compare the relative merit of these assignments. Our approach is modeled after the recently introduced Monte-Carlo simulated-annealing (MC/SA) protocol, with the key difference that NSGA-II simultaneously optimizes multiple assignment objectives instead of searching for possible assignments based on a single composite score. The multiple objectives include maximizing the number of consistently assigned peaks between multiple spectra ("good connections"), maximizing the number of used peaks, minimizing the number of inconsistently assigned peaks between spectra ("bad connections"), and minimizing the number of assigned peaks that have no matching peaks in the other spectra ("edges"). Using six SSNMR protein chemical shift datasets with varying levels of imperfection that was introduced by peak deletion, random chemical shift changes, and manual peak picking of spectra with moderately broad linewidths, we show that the NSGA-II algorithm produces a large number of valid and good assignments rapidly. For high-quality chemical shift peak lists, NSGA-II and MC/SA perform similarly well. However, when the peak lists contain many missing peaks that are uncorrelated between different spectra and have chemical shift deviations between spectra, the modified NSGA-II produces a larger number of valid solutions than MC/SA, and is more effective at distinguishing good from mediocre assignments by avoiding the hazard of suboptimal weighting factors for the various objectives. These two advantages, namely diversity and better evaluation, lead to a higher probability of predicting the correct assignment for a

Quality Control Test for Sequence-Phenotype Assignments

Science.gov (United States)

Ortiz, Maria Teresa Lara; Rosario, Pablo Benjamín Leon; Luna-Nevarez, Pablo; Gamez, Alba Savin; Martínez-del Campo, Ana; Del Rio, Gabriel

2015-01-01

Relating a gene mutation to a phenotype is a common task in different disciplines such as protein biochemistry. In this endeavour, it is common to find false relationships arising from mutations introduced by cells that may be depurated using a phenotypic assay; yet, such phenotypic assays may introduce additional false relationships arising from experimental errors. Here we introduce the use of high-throughput DNA sequencers and statistical analysis aimed to identify incorrect DNA sequence-phenotype assignments and observed that 10–20% of these false assignments are expected in large screenings aimed to identify critical residues for protein function. We further show that this level of incorrect DNA sequence-phenotype assignments may significantly alter our understanding about the structure-function relationship of proteins. We have made available an implementation of our method at http://bis.ifc.unam.mx/en/software/chispas. PMID:25700273

Specific labeling and assignment strategies of valine methyl groups for NMR studies of high molecular weight proteins

Energy Technology Data Exchange (ETDEWEB)

Mas, Guillaume; Crublet, Elodie [Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS) (France); Hamelin, Olivier [CNRS (France); Gans, Pierre; Boisbouvier, Jérôme, E-mail: jerome.boisbouvier@ibs.fr [Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS) (France)

2013-09-28

The specific protonation of valine and leucine methyl groups in proteins is typically achieved by overexpressing proteins in M9/D{sub 2}O medium supplemented with either labeled α-ketoisovalerate for the labeling of the four prochiral methyl groups or with 2-acetolactate for the stereospecific labeling of the valine and leucine side chains. However, when these labeling schemes are applied to large protein assemblies, significant overlap between the correlations of the valine and leucine methyl groups occurs, hampering the analysis of 2D methyl-TROSY spectra. Analysis of the leucine and valine biosynthesis pathways revealed that the incorporation of labeled precursors in the leucine pathway can be inhibited by the addition of exogenous l-leucine-d{sub 10}. We exploited this property to label stereospecifically the pro-R and pro-S methyl groups of valine with minimal scrambling to the leucine residues. This new labeling protocol was applied to the 468 kDa homododecameric peptidase TET2 to decrease the complexity of its NMR spectra. All of the pro-S valine methyl resonances of TET2 were assigned by combining mutagenesis with this innovative labeling approach. The assignments were transferred to the pro-R groups using an optimally labeled sample and a set of triple resonance experiments. This improved labeling scheme enables us to overcome the main limitation of overcrowding in the NMR spectra of prochiral methyl groups, which is a prerequisite for the site-specific measurement of the structural and dynamic parameters or for the study of interactions in very large protein assemblies.

Smartnotebook: A semi-automated approach to protein sequential NMR resonance assignments

International Nuclear Information System (INIS)

Slupsky, Carolyn M.; Boyko, Robert F.; Booth, Valerie K.; Sykes, Brian D.

2003-01-01

Complete and accurate NMR spectral assignment is a prerequisite for high-throughput automated structure determination of biological macromolecules. However, completely automated assignment procedures generally encounter difficulties for all but the most ideal data sets. Sources of these problems include difficulty in resolving correlations in crowded spectral regions, as well as complications arising from dynamics, such as weak or missing peaks, or atoms exhibiting more than one peak due to exchange phenomena. Smartnotebook is a semi-automated assignment software package designed to combine the best features of the automated and manual approaches. The software finds and displays potential connections between residues, while the spectroscopist makes decisions on which connection is correct, allowing rapid and robust assignment. In addition, smartnotebook helps the user fit chains of connected residues to the primary sequence of the protein by comparing the experimentally determined chemical shifts with expected shifts derived from a chemical shift database, while providing bookkeeping throughout the assignment procedure

Sequential assignment of proline-rich regions in proteins: Application to modular binding domain complexes

International Nuclear Information System (INIS)

Kanelis, Voula; Donaldson, Logan; Muhandiram, D.R.; Rotin, Daniela; Forman-Kay, Julie D.; Kay, Lewis E.

2000-01-01

Many protein-protein interactions involve amino acid sequences containing proline-rich motifs and even poly-proline stretches. The lack of amide protons in such regions complicates assignment, since 1 HN-based triple-resonance assignment strategies cannot be employed. Two such systems that we are currently studying include an SH2 domain from the protein Crk with a region containing 9 prolines in a 14 amino acid sequence, as well as a WW domain that interacts with a proline-rich target. A modified version of the HACAN pulse scheme, originally described by Bax and co-workers [Wang et al. (1995) J. Biomol. NMR, 5, 376-382], and an experiment which correlates the intra-residue 1 H α , 13 C α / 13 C β chemical shifts with the 15 N shift of the subsequent residue are presented and applied to the two systems listed above, allowing sequential assignment of the molecules

A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins

International Nuclear Information System (INIS)

Plevin, Michael J.; Hamelin, Olivier; Boisbouvier, Jérôme; Gans, Pierre

2011-01-01

A new method for stereospecific assignment of prochiral methyl groups in proteins is presented in which protein samples are produced using U-[ 13 C]glucose and subsaturating amounts of 2-[ 13 C]methyl-acetolactate. The resulting non-uniform labeling pattern allows proR and proS methyl groups to be easily distinguished by their different phases in a constant-time two-dimensional 1 H- 13 C correlation spectra. Protein samples are conveniently prepared using the same media composition as the main uniformly-labeled sample and contain higher levels of isotope-enrichment than fractional labeling approaches. This new strategy thus represents an economically-attractive, robust alternative for obtaining isotopically-encoded stereospecific NMR assignments of prochiral methyl groups.

RESCUE: An artificial neural network tool for the NMR spectral assignment of proteins

International Nuclear Information System (INIS)

Pons, J.L.; Delsuc, M.A.

1999-01-01

The assignment of the 1 H spectrum of a protein or a polypeptide is the prerequisite for advanced NMR studies. We present here an assignment tool based on the artificial neural network technology, which determines the type of the amino acid from the chemical shift values observed in the 1 H spectrum. Two artificial neural networks have been trained and extensively tested against a non-redundant subset of the BMRB chemical shift data bank [Seavey, B.R. et al. (1991) J. Biomol. NMR, 1, 217-236]. The most promising of the two accomplishes the analysis in two steps, grouping related amino acids together. It presents a mean rate of success above 80% on the test set. The second network tested separates down to the single amino acid; it presents a mean rate of success of 63%. This tool has been used to assist the manual assignment of peptides and proteins and can also be used as a block in an automated approach to assignment. The program has been called RESCUE and is made publicly available at the following URL: http://www.infobiosud.univ-montp1.fr/rescue

Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm

International Nuclear Information System (INIS)

Hefke, Frederik; Bagaria, Anurag; Reckel, Sina; Ullrich, Sandra Johanna; Dötsch, Volker; Glaubitz, Clemens; Güntert, Peter

2011-01-01

We present a computational method for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional strategies. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273–6279 (1982)), types of amino acids are labeled with 13 C or/and 15 N such that cross peaks between 13 CO(i – 1) and 15 NH(i) result only for pairs of sequentially adjacent amino acids of which the first is labeled with 13 C and the second with 15 N. In this way, unambiguous sequence-specific assignments can be obtained for unique pairs of amino acids that occur exactly once in the sequence of the protein. To be practical, it is crucial to limit the number of differently labeled protein samples that have to be prepared while obtaining an optimal extent of labeled unique amino acid pairs. Our computer algorithm UPLABEL for optimal unique pair labeling, implemented in the program CYANA and in a standalone program, and also available through a web portal, uses combinatorial optimization to find for a given amino acid sequence labeling patterns that maximize the number of unique pair assignments with a minimal number of differently labeled protein samples. Various auxiliary conditions, including labeled amino acid availability and price, previously known partial assignments, and sequence regions of particular interest can be taken into account when determining optimal amino acid type-specific labeling patterns. The method is illustrated for the assignment of the human G-protein coupled receptor bradykinin B2 (B 2 R) and applied as a starting point for the backbone assignment of the membrane protein proteorhodopsin.

A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments

International Nuclear Information System (INIS)

Schubert, Mario; Labudde, Dirk; Leitner, Dietmar; Oschkinat, Hartmut; Schmieder, Peter

2005-01-01

The determination of the three-dimensional structure of a protein or the study of protein-ligand interactions requires the assignment of all relevant nuclei as an initial step. This is nowadays almost exclusively performed using triple-resonance experiments. The conventional strategy utilizes one or more pairs of three dimensional spectra to obtain redundant information and thus reliable assignments. Here, a modified strategy for obtaining sequence specific assignments based on two dimensional amino acid type selective triple-resonance experiments is proposed. These experiments can be recorded with good resolution in a relatively short time. They provide very specific and redundant information, in particular on sequential connectivities, that drastically increases the ease and reliability of the assignment procedure, done either manually or in an automated fashion. The new strategy is demonstrated with the protein domain PB1 from yeast CDC24p

A Temporal Domain Decomposition Algorithmic Scheme for Large-Scale Dynamic Traffic Assignment

Directory of Open Access Journals (Sweden)

Eric J. Nava

2012-03-01

This paper presents a temporal decomposition scheme for large spatial- and temporal-scale dynamic traffic assignment, in which the entire analysis period is divided into Epochs. Vehicle assignment is performed sequentially in each Epoch, thus improving the model scalability and confining the peak run-time memory requirement regardless of the total analysis period. A proposed self-turning scheme adaptively searches for the run-time-optimal Epoch setting during iterations regardless of the characteristics of the modeled network. Extensive numerical experiments confirm the promising performance of the proposed algorithmic schemes.

Backbone assignment and secondary structure of the PsbQ protein from Photosystem II

Czech Academy of Sciences Publication Activity Database

Horničáková, M.; Kohoutová, Jaroslava; Schlagnitweit, J.; Wohlschlager, Ch.; Ettrich, Rüdiger; Fiala, R.; Schoefberger, W.; Müller, N.

2011-01-01

Roč. 5, č. 2 (2011), s. 169-175 ISSN 1874-2718 R&D Projects: GA MŠk(CZ) LC06010 Institutional research plan: CEZ:AV0Z60870520 Keywords : Photosystem II * PsbQ * Missing link * NMR resonance assignment * Protein-protein interaction Subject RIV: BO - Biophysics Impact factor: 0.720, year: 2011 http://www.springerlink.com/content/3n38075w5h1l1082/fulltext.pdf

NMR assignments of juvenile hormone binding protein in complex with JH III.

Science.gov (United States)

Suzuki, Rintaro; Tase, Akira; Fujimoto, Zui; Shiotsuki, Takahiro; Yamazaki, Toshimasa

2009-06-01

A hemolymph juvenile hormone binding protein (JHBP) shuttles hydrophobic JH, a key hormone in regulation of the insect life cycle, from the site of the JH biosynthesis to the cells of target organs. We report complete NMR chemical shift assignments of Bombyx mori JHBP in the JH III-bound state.

Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments

Energy Technology Data Exchange (ETDEWEB)

Motackova, Veronika; Novacek, Jiri [Masaryk University, Faculty of Science, National Centre for Biomolecular Research (Czech Republic); Zawadzka-Kazimierczuk, Anna; Kazimierczuk, Krzysztof [University of Warsaw, Faculty of Chemistry (Poland); Zidek, Lukas, E-mail: lzidek@chemi.muni.c [Masaryk University, Faculty of Science, National Centre for Biomolecular Research (Czech Republic); Sanderova, Hana; Krasny, Libor [Academy of Sciences of the Czech Republic, Laboratory of Molecular Genetics of Bacteria and Department of Bacteriology, Institute of Microbiology (Czech Republic); Kozminski, Wiktor [University of Warsaw, Faculty of Chemistry (Poland); Sklenar, Vladimir [Masaryk University, Faculty of Science, National Centre for Biomolecular Research (Czech Republic)

2010-11-15

A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high dimensionality and long evolution times, allowed by non-uniform sampling in the indirect dimensions. Random distribution of the data points and Sparse Multidimensional Fourier Transform processing were used. Successful application of the assignment procedure to a particularly difficult protein, {delta} subunit of RNA polymerase from Bacillus subtilis, is shown to prove the efficiency of the strategy. The studied protein contains a disordered C-terminal region of 81 amino acids with a highly repetitive sequence. While the conventional assignment methods completely failed due to a very small differences in chemical shifts, the presented strategy provided a complete backbone and side-chain assignment.

Complete sequence-specific 1H NMR assignments for human insulin

International Nuclear Information System (INIS)

Kline, A.D.; Justice, R.M. Jr.

1990-01-01

Solvent conditions where human insulin could be studied by high-resolution NMR were determined. Both low pH and addition of acetonitrile were required to overcome the protein's self-association and to obtain useful spectra. Two hundred eighty-six 1 H resonances were located and assigned to specific sites on the protein by using two-dimensional NMR methods. The presence and position of numerous d NN sequential NOE's indicate that the insulin conformation seen in crystallographic studies is largely retained under these solution conditions. Slowly exchanging protons were observed for seven backbone amide protons and were assigned to positions A15 and A16 and to positions B15-B19. These amides all occur within helical regions of the protein

Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

International Nuclear Information System (INIS)

Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei

2013-01-01

We introduce a Python-based program that utilizes the large database of 13 C and 15 N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13 C– 13 C, 15 N– 13 C, or 3D 15 N– 13 C– 13 C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13 C– 13 C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40–60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO–Cα–Cβ or N–Cα–Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

Main-chain-directed strategy for the assignment of 1H NMR spectra of proteins

International Nuclear Information System (INIS)

Englander, S.W.; Wand, A.J.

1987-01-01

A strategy for assigning the resonances in two-dimensional (2D) NMR spectra of proteins is described. The method emphasizes the analysis of through-space relationships between protons by use of the two-dimensional nuclear Overhauser effect (NOE) experiment. NOE patterns used in the algorithm were derived from a statistical analysis of the combinations of short proton-proton distances observed in the high-resolution crystal structures of 21 proteins. One starts with a search for authentic main-chain NH-C/sub α/H-C/sub β/H J-coupled units, which can be found with high reliability. The many main-chain units of a protein are then placed in their proper juxtaposition by recognition of predefined NOE connectivity patterns. To discover these connectivities, the 2D NOE spectrum is examined, in a prescribed order, for the distinct NOE patterns characteristic of helices, sheets, turns, and extended chain. Finally, the recognition of a few amino acid side-chain types places the discovered secondary structure elements within the polypeptide sequences. Unlike the sequential assignment approach, the main-chain-directed strategy does not rely on the difficult task of recognizing many side-chain spin systems in J-correlated spectra, the assignment process is not in general sequential with the polypeptide chain, and the prescribed connectivity patterns are cyclic rather than linear. The latter characteristic avoids ambiguous branch points in the analysis and imposed an internally confirmatory property on each forward step

Assignment strategies in homonuclear three-dimensional 1H NMR spectra of proteins

International Nuclear Information System (INIS)

Vuister, G.W.; Boelens, R.; Padilla, A.; Kleywegt, G.J.; Kaptein, R.

1990-01-01

The increase in dimensionality of three-dimensional (3D) NMR greatly enhances the spectral resolution in comparison to 2D NMR. It alleviates the problem of resonance overlap and may extend the range of molecules amenable to structure determination by high-resolution NMR spectroscopy. Here, the authors present strategies for the assignment of protein resonances from homonuclear nonselective 3D NOE-HOHAHA spectra. A notation for connectivities between protons, corresponding to cross peaks in 3D spectra, is introduced. They show how spin systems can be identified by tracing cross-peak patterns in cross sections perpendicular to the three frequency axes. The observable 3D sequential connectivities in proteins are tabulated, and estimates for the relative intensities of the corresponding cross peaks are given for α-helical and β-sheet conformations. Intensities of the cross peaks in the 3D spectrum of pike III paravalbumin follow the predictions. The sequential-assignment procedure is illustrated for loop regions, extended and α-helical conformations for the residues Ala 54-Leu 63 of paravalbumin. NOEs that were not previously identified in 2D spectra of paravalbumin due to overlap are found

Application of a fast sorting algorithm to the assignment of mass spectrometric cross-linking data.

Science.gov (United States)

Petrotchenko, Evgeniy V; Borchers, Christoph H

2014-09-01

Cross-linking combined with MS involves enzymatic digestion of cross-linked proteins and identifying cross-linked peptides. Assignment of cross-linked peptide masses requires a search of all possible binary combinations of peptides from the cross-linked proteins' sequences, which becomes impractical with increasing complexity of the protein system and/or if digestion enzyme specificity is relaxed. Here, we describe the application of a fast sorting algorithm to search large sequence databases for cross-linked peptide assignments based on mass. This same algorithm has been used previously for assigning disulfide-bridged peptides (Choi et al., ), but has not previously been applied to cross-linking studies. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

Energy Technology Data Exchange (ETDEWEB)

Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei, E-mail: mhong@iastate.edu [Iowa State University, Department of Chemistry (United States)

2013-06-15

We introduce a Python-based program that utilizes the large database of {sup 13}C and {sup 15}N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D {sup 13}C-{sup 13}C, {sup 15}N-{sup 13}C, or 3D {sup 15}N-{sup 13}C-{sup 13}C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D {sup 13}C-{sup 13}C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the C{alpha} and C{beta} chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-C{alpha}-C{beta} or N-C{alpha}-C{beta}), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

International Nuclear Information System (INIS)

Swain, Monalisa; Atreya, Hanudatta S.

2009-01-01

Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone 1 H α and 13 C' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to α-helical/β-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment

Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks

KAUST Repository

Jang, Richard; Gao, Xin; Li, Ming

2011-01-01

In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data. We propose a novel integer programming framework for structure-based backbone resonance assignment using N-labeled data. The core consists of a pair of integer programming models: one for spin system forming and amino acid typing, and the other for backbone resonance assignment. The goal is to perform the assignment directly from spectra without any manual intervention via automatically picked peaks, which are much noisier than manually picked peaks, so methods must be error-tolerant. In the case of semi-automated/manually processed peak data, we compare our system with the Xiong-Pandurangan-Bailey- Kellogg's contact replacement (CR) method, which is the most error-tolerant method for structure-based resonance assignment. Our system, on average, reduces the error rate of the CR method by five folds on their data set. In addition, by using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for human ubiquitin, where the typing accuracy is 83%, we achieve 91% accuracy, compared to the 59% accuracy obtained without correcting for such errors. In the case of automatically picked peaks, using assignment information from yeast ubiquitin, we achieve a fully automatic assignment with 97% accuracy. To our knowledge, this is the first system that can achieve fully automatic structure-based assignment directly from spectra. This has implications in NMR protein mutant studies, where the assignment step is repeated for each mutant. © Copyright 2011, Mary Ann Liebert, Inc.

Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks

KAUST Repository

Jang, Richard

2011-03-01

In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data. We propose a novel integer programming framework for structure-based backbone resonance assignment using N-labeled data. The core consists of a pair of integer programming models: one for spin system forming and amino acid typing, and the other for backbone resonance assignment. The goal is to perform the assignment directly from spectra without any manual intervention via automatically picked peaks, which are much noisier than manually picked peaks, so methods must be error-tolerant. In the case of semi-automated/manually processed peak data, we compare our system with the Xiong-Pandurangan-Bailey- Kellogg\\'s contact replacement (CR) method, which is the most error-tolerant method for structure-based resonance assignment. Our system, on average, reduces the error rate of the CR method by five folds on their data set. In addition, by using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for human ubiquitin, where the typing accuracy is 83%, we achieve 91% accuracy, compared to the 59% accuracy obtained without correcting for such errors. In the case of automatically picked peaks, using assignment information from yeast ubiquitin, we achieve a fully automatic assignment with 97% accuracy. To our knowledge, this is the first system that can achieve fully automatic structure-based assignment directly from spectra. This has implications in NMR protein mutant studies, where the assignment step is repeated for each mutant. © Copyright 2011, Mary Ann Liebert, Inc.

5D {sup 13}C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion

Energy Technology Data Exchange (ETDEWEB)

Novacek, Jiri [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic); Zawadzka-Kazimierczuk, Anna [University of Warsaw, Faculty of Chemistry (Poland); Papouskova, Veronika; Zidek, Lukas, E-mail: lzidek@chemi.muni.cz [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic); Sanderova, Hana; Krasny, Libor [Institute of Microbiology, Academy of Sciences of the Czech Republic, Laboratory of Molecular Genetics of Bacteria and Department of Bacteriology (Czech Republic); Kozminski, Wiktor [University of Warsaw, Faculty of Chemistry (Poland); Sklenar, Vladimir [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic)

2011-05-15

Two novel 5D NMR experiments (CACONCACO, NCOCANCO) for backbone assignment of disordered proteins are presented. The pulse sequences exploit relaxation properties of the unstructured proteins and combine the advantages of {sup 13}C-direct detection, non-uniform sampling, and longitudinal relaxation optimization to maximize the achievable resolution and minimize the experimental time. The pulse sequences were successfully tested on the sample of partially disordered delta subunit from RNA polymerase from Bacillus subtilis. The unstructured part of this 20 kDa protein consists of 81 amino acids with frequent sequential repeats. A collection of 0.0003% of the data needed for a conventional experiment with linear sampling was sufficient to perform an unambiguous assignment of the disordered part of the protein from a single 5D spectrum.

Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes.

Science.gov (United States)

Lu, Jonathan; Trnka, Michael J; Roh, Soung-Hun; Robinson, Philip J J; Shiau, Carrie; Fujimori, Danica Galonic; Chiu, Wah; Burlingame, Alma L; Guan, Shenheng

2015-12-01

Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise. Graphical Abstract ᅟ.

Backbone resonance assignments for G protein α(i3) subunit in the GDP-bound state.

Science.gov (United States)

Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

2014-10-01

Guanine-nucleotide binding proteins (G proteins) serve as molecular switches in signaling pathways, by coupling the activation of G protein-coupled receptors (GPCRs) at the cell surface to intracellular responses. In the resting state, G protein forms a heterotrimer, consisting of the G protein α subunit with GDP (Gα·GDP) and the G protein βγ subunit (Gβγ). Ligand binding to GPCRs promotes the GDP-GTP exchange on Gα, leading to the dissociation of the GTP-bound form of Gα (Gα·GTP) and Gβγ. Then, Gα·GTP and Gβγ bind to their downstream effector enzymes or ion channels and regulate their activities, leading to a variety of cellular responses. Finally, Gα hydrolyzes the bound GTP to GDP and returns to the resting state by re-associating with Gβγ. The G proteins are classified with four major families based on the amino acid sequences of Gα: i/o, s, q/11, and 12/13. Here, we established the backbone resonance assignments of human Gαi3, a member of the i/o family with a molecular weight of 41 K, in complex with GDP. The chemical shifts were compared with those of Gα(i3) in complex with a GTP-analogue, GTPγS, which we recently reported, indicating that the residues with significant chemical shift differences are mostly consistent with the regions with the structural differences between the GDP- and GTPγS-bound states, as indicated in the crystal structures. The assignments of Gα(i3)·GDP would be useful for the analyses of the dynamics of Gα(i3) and its interactions with various target molecules.

CONSERVATION. Genetic assignment of large seizures of elephant ivory reveals Africa's major poaching hotspots.

Science.gov (United States)

Wasser, S K; Brown, L; Mailand, C; Mondol, S; Clark, W; Laurie, C; Weir, B S

2015-07-03

Poaching of elephants is now occurring at rates that threaten African populations with extinction. Identifying the number and location of Africa's major poaching hotspots may assist efforts to end poaching and facilitate recovery of elephant populations. We genetically assign origin to 28 large ivory seizures (≥0.5 metric tons) made between 1996 and 2014, also testing assignment accuracy. Results suggest that the major poaching hotspots in Africa may be currently concentrated in as few as two areas. Increasing law enforcement in these two hotspots could help curtail future elephant losses across Africa and disrupt this organized transnational crime. Copyright © 2015, American Association for the Advancement of Science.

CONNJUR R: an annotation strategy for fostering reproducibility in bio-NMR—protein spectral assignment

Energy Technology Data Exchange (ETDEWEB)

Fenwick, Matthew; Hoch, Jeffrey C. [UConn Health, Department of Molecular Biology and Biophysics (United States); Ulrich, Eldon [University of Wisconsin-Madison, Department of Biochemistry (United States); Gryk, Michael R., E-mail: gryk@uchc.edu [UConn Health, Department of Molecular Biology and Biophysics (United States)

2015-10-15

Reproducibility is a cornerstone of the scientific method, essential for validation of results by independent laboratories and the sine qua non of scientific progress. A key step toward reproducibility of biomolecular NMR studies was the establishment of public data repositories (PDB and BMRB). Nevertheless, bio-NMR studies routinely fall short of the requirement for reproducibility that all the data needed to reproduce the results are published. A key limitation is that considerable metadata goes unpublished, notably manual interventions that are typically applied during the assignment of multidimensional NMR spectra. A general solution to this problem has been elusive, in part because of the wide range of approaches and software packages employed in the analysis of protein NMR spectra. Here we describe an approach for capturing missing metadata during the assignment of protein NMR spectra that can be generalized to arbitrary workflows, different software packages, other biomolecules, or other stages of data analysis in bio-NMR. We also present extensions to the NMR-STAR data dictionary that enable machine archival and retrieval of the “missing” metadata.

CONNJUR R: an annotation strategy for fostering reproducibility in bio-NMR—protein spectral assignment

International Nuclear Information System (INIS)

Fenwick, Matthew; Hoch, Jeffrey C.; Ulrich, Eldon; Gryk, Michael R.

2015-01-01

Reproducibility is a cornerstone of the scientific method, essential for validation of results by independent laboratories and the sine qua non of scientific progress. A key step toward reproducibility of biomolecular NMR studies was the establishment of public data repositories (PDB and BMRB). Nevertheless, bio-NMR studies routinely fall short of the requirement for reproducibility that all the data needed to reproduce the results are published. A key limitation is that considerable metadata goes unpublished, notably manual interventions that are typically applied during the assignment of multidimensional NMR spectra. A general solution to this problem has been elusive, in part because of the wide range of approaches and software packages employed in the analysis of protein NMR spectra. Here we describe an approach for capturing missing metadata during the assignment of protein NMR spectra that can be generalized to arbitrary workflows, different software packages, other biomolecules, or other stages of data analysis in bio-NMR. We also present extensions to the NMR-STAR data dictionary that enable machine archival and retrieval of the “missing” metadata

Resonance assignment of disordered protein with repetitive and overlapping sequence using combinatorial approach reveals initial structural propensities and local restrictions in the denatured state

Energy Technology Data Exchange (ETDEWEB)

Malik, Nikita; Kumar, Ashutosh, E-mail: askutoshk@iitb.ac.in [Indian Institute of Technology Bombay, Department of Bioscience and Bioengineering (India)

2016-09-15

NMR resonance assignment of intrinsically disordered proteins poses a challenge because of the limited dispersion of amide proton chemical shifts. This becomes even more complex with the increase in the size of the system. Residue specific selective labeling/unlabeling experiments have been used to resolve the overlap, but require multiple sample preparations. Here, we demonstrate an assignment strategy requiring only a single sample of uniformly labeled {sup 13}C,{sup 15}N-protein. We have used a combinatorial approach, involving 3D-HNN, CC(CO)NH and 2D-MUSIC, which allowed us to assign a denatured centromeric protein Cse4 of 229 residues. Further, we show that even the less sensitive experiments, when used in an efficient manner can lead to the complete assignment of a complex system without the use of specialized probes in a relatively short time frame. The assignment of the amino acids discloses the presence of local structural propensities even in the denatured state accompanied by restricted motion in certain regions that provides insights into the early folding events of the protein.

Resonance assignment of disordered protein with repetitive and overlapping sequence using combinatorial approach reveals initial structural propensities and local restrictions in the denatured state

International Nuclear Information System (INIS)

Malik, Nikita; Kumar, Ashutosh

2016-01-01

NMR resonance assignment of intrinsically disordered proteins poses a challenge because of the limited dispersion of amide proton chemical shifts. This becomes even more complex with the increase in the size of the system. Residue specific selective labeling/unlabeling experiments have been used to resolve the overlap, but require multiple sample preparations. Here, we demonstrate an assignment strategy requiring only a single sample of uniformly labeled "1"3C,"1"5N-protein. We have used a combinatorial approach, involving 3D-HNN, CC(CO)NH and 2D-MUSIC, which allowed us to assign a denatured centromeric protein Cse4 of 229 residues. Further, we show that even the less sensitive experiments, when used in an efficient manner can lead to the complete assignment of a complex system without the use of specialized probes in a relatively short time frame. The assignment of the amino acids discloses the presence of local structural propensities even in the denatured state accompanied by restricted motion in certain regions that provides insights into the early folding events of the protein.

Assigning Significance in Label-Free Quantitative Proteomics to Include Single-Peptide-Hit Proteins with Low Replicates

OpenAIRE

Li, Qingbo

2010-01-01

When sample replicates are limited in a label-free proteomics experiment, selecting differentially regulated proteins with an assignment of statistical significance remains difficult for proteins with a single-peptide hit or a small fold-change. This paper aims to address this issue. An important component of the approach employed here is to utilize the rule of Minimum number of Permuted Significant Pairings (MPSP) to reduce false positives. The MPSP rule generates permuted sample pairings fr...

Assignment of protein backbone resonances using connectivity, torsion angles and 13Cα chemical shifts

International Nuclear Information System (INIS)

Morris, Laura C.; Valafar, Homayoun; Prestegard, James H.

2004-01-01

A program is presented which will return the most probable sequence location for a short connected set of residues in a protein given just 13 C α chemical shifts (δ( 13 C α )) and data restricting the φ and ψ backbone angles. Data taken from both the BioMagResBank and the Protein Data Bank were used to create a probability density function (PDF) using a multivariate normal distribution in δ( 13 C α ), φ, and ψ space for each amino acid residue. Extracting and combining probabilities for particular amino acid residues in a short proposed sequence yields a score indicative of the correctness of the proposed assignment. The program is illustrated using several proteins for which structure and 13 C α chemical shift data are available

Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets

International Nuclear Information System (INIS)

Bellstedt, Peter; Seiboth, Thomas; Häfner, Sabine; Kutscha, Henriette; Ramachandran, Ramadurai; Görlach, Matthias

2013-01-01

NMR-based structure determination of a protein requires the assignment of resonances as indispensable first step. Even though heteronuclear through-bond correlation methods are available for that purpose, challenging situations arise in cases where the protein in question only yields samples of limited concentration and/or stability. Here we present a strategy based upon specific individual unlabeling of all 20 standard amino acids to complement standard NMR experiments and to achieve unambiguous backbone assignments for the fast precipitating 23 kDa catalytic domain of human aprataxin of which only incomplete standard NMR data sets could be obtained. Together with the validation of this approach utilizing the protein GB1 as a model, a comprehensive insight into metabolic interconversion ('scrambling”) of NH and CO groups in a standard Escherichia coli expression host is provided

Spectral editing at ultra-fast magic-angle-spinning in solid-state NMR: facilitating protein sequential signal assignment by HIGHLIGHT approach

Energy Technology Data Exchange (ETDEWEB)

Wang, Songlin; Matsuda, Isamu; Long, Fei; Ishii, Yoshitaka, E-mail: yishii@uic.edu [University of Illinois at Chicago, Department of Chemistry (United States)

2016-02-15

This study demonstrates a novel spectral editing technique for protein solid-state NMR (SSNMR) to simplify the spectrum drastically and to reduce the ambiguity for protein main-chain signal assignments in fast magic-angle-spinning (MAS) conditions at a wide frequency range of 40–80 kHz. The approach termed HIGHLIGHT (Wang et al., in Chem Comm 51:15055–15058, 2015) combines the reverse {sup 13}C, {sup 15}N-isotope labeling strategy and selective signal quenching using the frequency-selective REDOR pulse sequence under fast MAS. The scheme allows one to selectively observe the signals of “highlighted” labeled amino-acid residues that precede or follow unlabeled residues through selectively quenching {sup 13}CO or {sup 15}N signals for a pair of consecutively labeled residues by recoupling {sup 13}CO–{sup 15}N dipolar couplings. Our numerical simulation results showed that the scheme yielded only ∼15 % loss of signals for the highlighted residues while quenching as much as ∼90 % of signals for non-highlighted residues. For lysine-reverse-labeled micro-crystalline GB1 protein, the 2D {sup 15}N/{sup 13}C{sub α} correlation and 2D {sup 13}C{sub α}/{sup 13}CO correlation SSNMR spectra by the HIGHLIGHT approach yielded signals only for six residues following and preceding the unlabeled lysine residues, respectively. The experimental dephasing curves agreed reasonably well with the corresponding simulation results for highlighted and quenched residues at spinning speeds of 40 and 60 kHz. The compatibility of the HIGHLIGHT approach with fast MAS allows for sensitivity enhancement by paramagnetic assisted data collection (PACC) and {sup 1}H detection. We also discuss how the HIGHLIGHT approach facilitates signal assignments using {sup 13}C-detected 3D SSNMR by demonstrating full sequential assignments of lysine-reverse-labeled micro-crystalline GB1 protein (∼300 nmol), for which data collection required only 11 h. The HIGHLIGHT approach offers valuable

Solid state NMR sequential resonance assignments and conformational analysis of the 2x10.4 kDa dimeric form of the Bacillus subtilis protein Crh

Energy Technology Data Exchange (ETDEWEB)

Boeckmann, Anja [Institut de Biologie et Chimie des Proteines, C.N.R.S UMR 5086 (France)], E-mail: a.bockmann@ibcp.fr; Lange, Adam [Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR (Germany); Galinier, Anne [Institut de Biologie Structurale et Microbiologie, C.N.R.S UPR 9043 (France); Luca, Sorin [Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR (Germany); Giraud, Nicolas; Juy, Michel [Institut de Biologie et Chimie des Proteines, C.N.R.S UMR 5086 (France); Heise, Henrike [Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR (Germany); Montserret, Roland; Penin, Francois [Institut de Biologie et Chimie des Proteines, C.N.R.S UMR 5086 (France); Baldus, Marc [Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR (Germany)], E-mail: maba@mpibpc.mpg.de

2003-12-15

Solid state NMR sample preparation and resonance assignments of the U-[{sup 13}C,{sup 15}N] 2x10.4 kDa dimeric form of the regulatory protein Crh in microcrystalline, PEG precipitated form are presented. Intra- and interresidue correlations using dipolar polarization transfer methods led to nearly complete sequential assignments of the protein, and to 88% of all {sup 15}N, {sup 13}C chemical shifts. For several residues, the resonance assignments differ significantly from those reported for the monomeric form analyzed by solution state NMR. Dihedral angles obtained from a TALOS-based statistical analysis suggest that the microcrystalline arrangement of Crh must be similar to the domain-swapped dimeric structure of a single crystal form recently solved using X-ray crystallography. For a limited number of protein residues, a remarkable doubling of the observed NMR resonances is observed indicative of local static or dynamic conformational disorder. Our study reports resonance assignments for the largest protein investigated by solid state NMR so far and describes the conformational dimeric variant of Crh with previously unknown chemical shifts.

Nano-mole scale sequential signal assignment by 1 H-detected protein solid-state NMR

KAUST Repository

Wang, Songlin; Parthasarathy, Sudhakar; Xiao, Yiling; Nishiyama, Yusuke; Long, Fei; Matsuda, Isamu; Endo, Yuki; Nemoto, Takahiro; Yamauchi, Kazuo; Asakura, Tetsuo; Takeda, Mitsuhiro; Terauchi, Tsutomu; Kainosho, Masatsune; Ishii, Yoshitaka

2015-01-01

We present a 3D 1H-detected solid-state NMR (SSNMR) approach for main-chain signal assignments of 10-100 nmol of fully protonated proteins using ultra-fast magic-angle spinning (MAS) at ∼80 kHz by a novel spectral-editing method, which permits drastic spectral simplification. The approach offers ∼110 fold time saving over a traditional 3D 13C-detected SSNMR approach. This journal is © The Royal Society of Chemistry 2015.

Assignment methodology for larger RNA oligonucleotides: Application to an ATP-binding RNA aptamer

International Nuclear Information System (INIS)

Dieckmann, Thorsten; Feigon, Juli

1997-01-01

The use of uniform 13C, 15N labeling in the NMR spectroscopic study of RNA structures has greatly facilitated the assignment process in small RNA oligonucleotides. For ribose spinsystem assignments, exploitation of these labels has followed previously developed methods for the study of proteins. However, for sequential assignment of the exchangeable and nonexchangeable protons of the nucleotides, it has been necessary to develop a variety of new NMR experiments. Even these are of limited utility in the unambiguous assignment of larger RNAs due to the short carbon relaxation times and extensive spectral overlap for all nuclei.These problems can largely be overcome by the additional use of base-type selectively 13C, 15N-labeled RNA in combination with a judicious use of related RNAs with base substitutions. We report the application of this approach to a 36-nucleotide ATP-binding RNA aptamer in complex with AMP. Complete sequential 1H assignments, as well as the majority of 13C and 15N assignments, were obtained

13C, 15N Resonance Assignment of Parts of the HET-s Prion Protein in its Amyloid Form

International Nuclear Information System (INIS)

Siemer, Ansgar B.; Ritter, Christiane; Steinmetz, Michel O.; Ernst, Matthias; Riek, Roland; Meier, Beat H.

2006-01-01

The partial 15 N and 13 C solid-state NMR resonance assignment of the HET-s prion protein fragment 218-289 in its amyloid form is presented. It is based on experiments measured at MAS frequencies in the range of 20-40 kHz using exclusively adiabatic polarization-transfer schemes. The resonance assignment within each residue is based on two-dimensional 13 C-- 13 C correlation spectra utilizing the DREAM mixing scheme. The sequential linking of the assigned residues used a set of two- and three-dimensional 15 N-- 13 C correlation experiments. Almost all cross peaks visible in the spectra are assigned, but only resonances from 43 of the 78 amino-acid residues could be detected. The missing residues are thought to be highly disordered and/or highly dynamic giving rise to broad resonance lines that escaped detection in the experiments applied. The line widths of the observed resonances are narrow and comparable to line widths observed in micro-crystalline samples. The 43 assigned residues are located in two fragments of about 20 residues

Sequence-specific assignments in the 1H NMR spectrum of the human inflammatory protein C5a

International Nuclear Information System (INIS)

Zuiderweg, E.R.P.; Mollison, K.W.; Henkin, J.; Carter, G.W.

1988-01-01

Full sequence-specific assignments for the 1 H NMR lines of the backbone protons of the human complement factor C5a are described and documented. The results were obtained by largely following the methodology developed by Wuethrich et al. Assignments for the majority of the amino acid side chain protons were obtained by using a comparison of double- and triple-quantum-filtered two-dimensional correlated experiments together with the analysis of relayed coherence transfer spectra. The assignments provide the basis for the determination of the thus far unknown three-dimensional structure of C5a from nuclear Overhauser enhancement distance constraints

A ‘just-in-time’ HN(CA)CO experiment for the backbone assignment of large proteins with high sensitivity

Science.gov (United States)

Werner-Allen, Jon W.; Jiang, Ling; Zhou, Pei

2006-07-01

Among the suite of commonly used backbone experiments, HNCACO presents an unresolved sensitivity limitation due to fast 13CO transverse relaxation and passive 13Cα-13Cβ coupling. Here, we present a high-sensitivity 'just-in-time' (JIT) HN(CA)CO pulse sequence that uniformly refocuses 13Cα-13Cβ coupling while collecting 13CO shifts in real time. Sensitivity comparisons of the 3-D JIT HN(CA)CO, a CT-HMQC-based control, and a HSQC-based control with selective 13Cα inversion pulses were performed using a 2H/13C/15N labeled sample of the 29 kDa HCA II protein at 15 °C. The JIT experiment shows a 42% signal enhancement over the CT-HMQC-based experiment. Compared to the HSQC-based experiment, the JIT experiment is 16% less sensitive for residues experiencing proper 13Cα refocusing and 13Cα-13Cβ decoupling. However, for the remaining residues, the JIT spectrum shows a 106% average sensitivity gain over the HSQC-based experiment. The high-sensitivity JIT HNCACO experiment should be particularly beneficial for studies of large proteins to provide 13CO resonance information regardless of residue type.

Toward efficient task assignment and motion planning for large-scale underwater missions

Directory of Open Access Journals (Sweden)

Somaiyeh MahmoudZadeh

2016-10-01

Full Text Available An autonomous underwater vehicle needs to possess a certain degree of autonomy for any particular underwater mission to fulfil the mission objectives successfully and ensure its safety in all stages of the mission in a large-scale operating field. In this article, a novel combinatorial conflict-free task assignment strategy, consisting of an interactive engagement of a local path planner and an adaptive global route planner, is introduced. The method takes advantage of the heuristic search potency of the particle swarm optimization algorithm to address the discrete nature of routing-task assignment approach and the complexity of nondeterministic polynomial-time-hard path planning problem. The proposed hybrid method is highly efficient as a consequence of its reactive guidance framework that guarantees successful completion of missions particularly in cluttered environments. To examine the performance of the method in a context of mission productivity, mission time management, and vehicle safety, a series of simulation studies are undertaken. The results of simulations declare that the proposed method is reliable and robust, particularly in dealing with uncertainties, and it can significantly enhance the level of a vehicle’s autonomy by relying on its reactive nature and capability of providing fast feasible solutions.

Multidimensional oriented solid-state NMR experiments enable the sequential assignment of uniformly 15N labeled integral membrane proteins in magnetically aligned lipid bilayers

International Nuclear Information System (INIS)

Mote, Kaustubh R.; Gopinath, T.; Traaseth, Nathaniel J.; Kitchen, Jason; Gor’kov, Peter L.; Brey, William W.; Veglia, Gianluigi

2011-01-01

Oriented solid-state NMR is the most direct methodology to obtain the orientation of membrane proteins with respect to the lipid bilayer. The method consists of measuring 1 H- 15 N dipolar couplings (DC) and 15 N anisotropic chemical shifts (CSA) for membrane proteins that are uniformly aligned with respect to the membrane bilayer. A significant advantage of this approach is that tilt and azimuthal (rotational) angles of the protein domains can be directly derived from analytical expression of DC and CSA values, or, alternatively, obtained by refining protein structures using these values as harmonic restraints in simulated annealing calculations. The Achilles’ heel of this approach is the lack of suitable experiments for sequential assignment of the amide resonances. In this Article, we present a new pulse sequence that integrates proton driven spin diffusion (PDSD) with sensitivity-enhanced PISEMA in a 3D experiment ([ 1 H, 15 N]-SE-PISEMA-PDSD). The incorporation of 2D 15 N/ 15 N spin diffusion experiments into this new 3D experiment leads to the complete and unambiguous assignment of the 15 N resonances. The feasibility of this approach is demonstrated for the membrane protein sarcolipin reconstituted in magnetically aligned lipid bicelles. Taken with low electric field probe technology, this approach will propel the determination of sequential assignment as well as structure and topology of larger integral membrane proteins in aligned lipid bilayers.

Protein complex prediction in large ontology attributed protein-protein interaction networks.

Science.gov (United States)

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng; Xu, Bo

2013-01-01

Protein complexes are important for unraveling the secrets of cellular organization and function. Many computational approaches have been developed to predict protein complexes in protein-protein interaction (PPI) networks. However, most existing approaches focus mainly on the topological structure of PPI networks, and largely ignore the gene ontology (GO) annotation information. In this paper, we constructed ontology attributed PPI networks with PPI data and GO resource. After constructing ontology attributed networks, we proposed a novel approach called CSO (clustering based on network structure and ontology attribute similarity). Structural information and GO attribute information are complementary in ontology attributed networks. CSO can effectively take advantage of the correlation between frequent GO annotation sets and the dense subgraph for protein complex prediction. Our proposed CSO approach was applied to four different yeast PPI data sets and predicted many well-known protein complexes. The experimental results showed that CSO was valuable in predicting protein complexes and achieved state-of-the-art performance.

Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15N-NOESY

KAUST Repository

Jang, Richard

2011-01-01

Chemical shift mapping is an important technique in NMRbased drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically. However, automated methods are necessary for high-throughput drug screening. We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C- labeling, to resolve the ambiguities for a one-toone mapping. On the three proteins, it achieves an average accuracy of 94% or better. Copyright © 2011 ACM.

Protein resonance assignment at MAS frequencies approaching 100 kHz: a quantitative comparison of J-coupling and dipolar-coupling-based transfer methods

Energy Technology Data Exchange (ETDEWEB)

Penzel, Susanne; Smith, Albert A.; Agarwal, Vipin; Hunkeler, Andreas [ETH Zürich, Physical Chemistry (Switzerland); Org, Mai-Liis; Samoson, Ago, E-mail: ago.samoson@ttu.ee [Tallinn University of Technology, NMR Instituut, Tartu Teadus, Tehnomeedikum (Estonia); Böckmann, Anja, E-mail: a.bockmann@ibcp.fr [UMR 5086 CNRS/Université de Lyon 1, Institut de Biologie et Chimie des Protéines (France); Ernst, Matthias, E-mail: maer@ethz.ch; Meier, Beat H., E-mail: beme@ethz.ch [ETH Zürich, Physical Chemistry (Switzerland)

2015-10-15

We discuss the optimum experimental conditions to obtain assignment spectra for solid proteins at magic-angle spinning (MAS) frequencies around 100 kHz. We present a systematic examination of the MAS dependence of the amide proton T{sub 2}′ times and a site-specific comparison of T{sub 2}′ at 93 kHz versus 60 kHz MAS frequency. A quantitative analysis of transfer efficiencies of building blocks, as they are used for typical 3D experiments, was performed. To do this, we compared dipolar-coupling and J-coupling based transfer steps. The building blocks were then combined into 3D experiments for sequential resonance assignment, where we evaluated signal-to-noise ratio and information content of the different 3D spectra in order to identify the best assignment strategy. Based on this comparison, six experiments were selected to optimally assign the model protein ubiquitin, solely using spectra acquired at 93 kHz MAS. Within 3 days of instrument time, the required spectra were recorded from which the backbone resonances have been assigned to over 96 %.

Multidimensional oriented solid-state NMR experiments enable the sequential assignment of uniformly 15N labeled integral membrane proteins in magnetically aligned lipid bilayers.

Science.gov (United States)

Mote, Kaustubh R; Gopinath, T; Traaseth, Nathaniel J; Kitchen, Jason; Gor'kov, Peter L; Brey, William W; Veglia, Gianluigi

2011-11-01

Oriented solid-state NMR is the most direct methodology to obtain the orientation of membrane proteins with respect to the lipid bilayer. The method consists of measuring (1)H-(15)N dipolar couplings (DC) and (15)N anisotropic chemical shifts (CSA) for membrane proteins that are uniformly aligned with respect to the membrane bilayer. A significant advantage of this approach is that tilt and azimuthal (rotational) angles of the protein domains can be directly derived from analytical expression of DC and CSA values, or, alternatively, obtained by refining protein structures using these values as harmonic restraints in simulated annealing calculations. The Achilles' heel of this approach is the lack of suitable experiments for sequential assignment of the amide resonances. In this Article, we present a new pulse sequence that integrates proton driven spin diffusion (PDSD) with sensitivity-enhanced PISEMA in a 3D experiment ([(1)H,(15)N]-SE-PISEMA-PDSD). The incorporation of 2D (15)N/(15)N spin diffusion experiments into this new 3D experiment leads to the complete and unambiguous assignment of the (15)N resonances. The feasibility of this approach is demonstrated for the membrane protein sarcolipin reconstituted in magnetically aligned lipid bicelles. Taken with low electric field probe technology, this approach will propel the determination of sequential assignment as well as structure and topology of larger integral membrane proteins in aligned lipid bilayers. © Springer Science+Business Media B.V. 2011

Contact replacement for NMR resonance assignment.

Science.gov (United States)

Xiong, Fei; Pandurangan, Gopal; Bailey-Kellogg, Chris

2008-07-01

Complementing its traditional role in structural studies of proteins, nuclear magnetic resonance (NMR) spectroscopy is playing an increasingly important role in functional studies. NMR dynamics experiments characterize motions involved in target recognition, ligand binding, etc., while NMR chemical shift perturbation experiments identify and localize protein-protein and protein-ligand interactions. The key bottleneck in these studies is to determine the backbone resonance assignment, which allows spectral peaks to be mapped to specific atoms. This article develops a novel approach to address that bottleneck, exploiting an available X-ray structure or homology model to assign the entire backbone from a set of relatively fast and cheap NMR experiments. We formulate contact replacement for resonance assignment as the problem of computing correspondences between a contact graph representing the structure and an NMR graph representing the data; the NMR graph is a significantly corrupted, ambiguous version of the contact graph. We first show that by combining connectivity and amino acid type information, and exploiting the random structure of the noise, one can provably determine unique correspondences in polynomial time with high probability, even in the presence of significant noise (a constant number of noisy edges per vertex). We then detail an efficient randomized algorithm and show that, over a variety of experimental and synthetic datasets, it is robust to typical levels of structural variation (1-2 AA), noise (250-600%) and missings (10-40%). Our algorithm achieves very good overall assignment accuracy, above 80% in alpha-helices, 70% in beta-sheets and 60% in loop regions. Our contact replacement algorithm is implemented in platform-independent Python code. The software can be freely obtained for academic use by request from the authors.

Functional assignment to JEV proteins using SVM.

Science.gov (United States)

Sahoo, Ganesh Chandra; Dikhit, Manas Ranjan; Das, Pradeep

2008-01-01

Identification of different protein functions facilitates a mechanistic understanding of Japanese encephalitis virus (JEV) infection and opens novel means for drug development. Support vector machines (SVM), useful for predicting the functional class of distantly related proteins, is employed to ascribe a possible functional class to Japanese encephalitis virus protein. Our study from SVMProt and available JE virus sequences suggests that structural and nonstructural proteins of JEV genome possibly belong to diverse protein functions, are expected to occur in the life cycle of JE virus. Protein functions common to both structural and non-structural proteins are iron-binding, metal-binding, lipid-binding, copper-binding, transmembrane, outer membrane, channels/Pores - Pore-forming toxins (proteins and peptides) group of proteins. Non-structural proteins perform functions like actin binding, zinc-binding, calcium-binding, hydrolases, Carbon-Oxygen Lyases, P-type ATPase, proteins belonging to major facilitator family (MFS), secreting main terminal branch (MTB) family, phosphotransfer-driven group translocators and ATP-binding cassette (ABC) family group of proteins. Whereas structural proteins besides belonging to same structural group of proteins (capsid, structural, envelope), they also perform functions like nuclear receptor, antibiotic resistance, RNA-binding, DNA-binding, magnesium-binding, isomerase (intra-molecular), oxidoreductase and participate in type II (general) secretory pathway (IISP).

Resonance assignments of the myristoylated Y28F/Y67F mutant of the Mason-Pfizer monkey virus matrix protein

Czech Academy of Sciences Publication Activity Database

Doležal, Michal; Hrabal, R.; Ruml, T.; Rumlová, Michaela

2015-01-01

Roč. 9, č. 2 (2015), s. 229-233 ISSN 1874-2718 Institutional support: RVO:61388963 Keywords : isotopic labeling * matrix protein * M-PMV * myristoylation * resonance assignment * reverse labeling Subject RIV: CE - Biochemistry Impact factor: 0.687, year: 2015

{sup 13}C, {sup 15}N Resonance Assignment of Parts of the HET-s Prion Protein in its Amyloid Form

Energy Technology Data Exchange (ETDEWEB)

Siemer, Ansgar B. [Physical Chemistry (Switzerland); Ritter, Christiane [Salk Institute, Structural Biology Laboratory (United States); Steinmetz, Michel O. [Paul Scherrer Institut, Biomolecular Research, Structural Biology (Switzerland); Ernst, Matthias [Physical Chemistry (Switzerland); Riek, Roland [Salk Institute, Structural Biology Laboratory (United States); Meier, Beat H. [Physical Chemistry (Switzerland)

2006-02-15

The partial {sup 15}N and {sup 13}C solid-state NMR resonance assignment of the HET-s prion protein fragment 218-289 in its amyloid form is presented. It is based on experiments measured at MAS frequencies in the range of 20-40 kHz using exclusively adiabatic polarization-transfer schemes. The resonance assignment within each residue is based on two-dimensional {sup 13}C--{sup 13}C correlation spectra utilizing the DREAM mixing scheme. The sequential linking of the assigned residues used a set of two- and three-dimensional {sup 15}N--{sup 13}C correlation experiments. Almost all cross peaks visible in the spectra are assigned, but only resonances from 43 of the 78 amino-acid residues could be detected. The missing residues are thought to be highly disordered and/or highly dynamic giving rise to broad resonance lines that escaped detection in the experiments applied. The line widths of the observed resonances are narrow and comparable to line widths observed in micro-crystalline samples. The 43 assigned residues are located in two fragments of about 20 residues.

High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins

Energy Technology Data Exchange (ETDEWEB)

Zawadzka-Kazimierczuk, Anna; Kozminski, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry (Poland); Sanderova, Hana; Krasny, Libor [Institute of Microbiology, Academy of Sciences of the Czech Republic, Laboratory of Molecular Genetics of Bacteria, Department of Bacteriology (Czech Republic)

2012-04-15

Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using {delta} subunit (20 kDa) of Bacillus subtilis RNA polymerase that has an 81-amino acid disordered part containing various repetitive sequences.

Sequence-specific {sup 1}H, {sup 13}C, and {sup 15}N resonance assignments for intestinal fatty-acid-binding protein complexed with palmitate (15.4 kDA)

Energy Technology Data Exchange (ETDEWEB)

Hodsdon, M.E.; Toner, J.J.; Cistola, D.P. [Washington Univ. School of Medicine, St. Louis, MO (United States)

1994-12-01

Intestinal fatty-acid-binding protein (I-FABP) belongs to a family of soluble, cytoplasmic proteins that are thought to function in the intracellular transport and trafficking of polar lipids. Individual members of this protein family have distinct specificities and affinities for fatty acids, cholesterol, bile salts, and retinoids. We are comparing several retinol- and fatty-acid-binding proteins from intestine in order to define the factors that control molecular recognition in this family of proteins. We have established sequential resonance assignments for uniformly {sup 13}C/{sup 15}N-enriched I-FABP complexed with perdeuterated palmitate at pH7.2 and 37{degrees}C. The assignment strategy was similar to that introduced for calmodulin. We employed seven three-dimensional NMR experiments to establish scalar couplings between backbone and sidechain atoms. Backbone atoms were correlated using triple-resonance HNCO, HNCA, TOCSY-HMQC, HCACO, and HCA(CO)N experiments. Sidechain atoms were correlated using CC-TOCSY, HCCH-TOCSY, and TOCSY-HMQC. The correlations of peaks between three-dimensional spectra were established in a computer-assisted manner using NMR COMPASS (Molecular Simulations, Inc.) Using this approach, {sup 1}H, {sup 13}C, and {sup 15}N resonance assignments have been established for 120 of the 131 residues of I-FABP. For 18 residues, amide {sup 1}H and {sup 15}N resonances were unobservable, apparently because of the rapid exchange of amide protons with bulk water at pH 7.2. The missing amide protons correspond to distinct amino acid patterns in the protein sequence, which will be discussed. During the assignment process, several sources of ambiguity in spin correlations were observed. To overcome this ambiguity, the additional inter-residue correlations often observed in the HNCA experiment were used as cross-checks for the sequential backbone assignments.

1H, 15N, and 13C resonance assignments of the third domain from the S. aureus innate immune evasion protein Eap.

Science.gov (United States)

Herrera, Alvaro I; Ploscariu, Nicoleta T; Geisbrecht, Brian V; Prakash, Om

2018-04-01

Staphylococcus aureus is a widespread and persistent pathogen of humans and livestock. The bacterium expresses a wide variety of virulence proteins, many of which serve to disrupt the host's innate immune system from recognizing and clearing bacteria with optimal efficiency. The extracellular adherence protein (Eap) is a multidomain protein that participates in various protein-protein interactions that inhibit the innate immune response, including both the complement system (Woehl et al in J Immunol 193:6161-6171, 2014) and Neutrophil Serine Proteases (NSPs) (Stapels et al in Proc Natl Acad Sci USA 111:13187-13192, 2014). The third domain of Eap, Eap3, is an ~ 11 kDa protein that was recently shown to bind complement component C4b (Woehl et al in Protein Sci 26:1595-1608, 2017) and therefore play an essential role in inhibiting the classical and lectin pathways of complement (Woehl et al in J Immunol 193:6161-6171, 2014). Since structural characterization of Eap3 is still incomplete, we acquired a series of 2D and 3D NMR spectra of Eap3 in solution. Here we report the backbone and side-chain 1 H, 15 N, and 13 C resonance assignments of Eap3 and its predicted secondary structure via the TALOS-N server. The assignment data have been deposited in the BMRB data bank under accession number 27087.

Prediction and Assignment of Function for a Divergent N-succinyl Amino Acid Racemase

Energy Technology Data Exchange (ETDEWEB)

Song,L.; Kalyanaraman, C.; Fedorov, A.; Fedorov, E.; Glasner, M.; Brown, S.; Imker, H.; Babbitt, P.; Almo, S.; et al.

2007-01-01

The protein databases contain many proteins with unknown function. A computational approach for predicting ligand specificity that requires only the sequence of the unknown protein would be valuable for directing experiment-based assignment of function. We focused on a family of unknown proteins in the mechanistically diverse enolase superfamily and used two approaches to assign function: (i) enzymatic assays using libraries of potential substrates, and (ii) in silico docking of the same libraries using a homology model based on the most similar (35% sequence identity) characterized protein. The results matched closely; an experimentally determined structure confirmed the predicted structure of the substrate-liganded complex. We assigned the N-succinyl arginine/lysine racemase function to the family, correcting the annotation (L-Ala-D/L-Glu epimerase) based on the function of the most similar characterized homolog. These studies establish that ligand docking to a homology model can facilitate functional assignment of unknown proteins by restricting the identities of the possible substrates that must be experimentally tested.

Insights into Hox protein function from a large scale combinatorial analysis of protein domains.

Directory of Open Access Journals (Sweden)

Samir Merabet

2011-10-01

Full Text Available Protein function is encoded within protein sequence and protein domains. However, how protein domains cooperate within a protein to modulate overall activity and how this impacts functional diversification at the molecular and organism levels remains largely unaddressed. Focusing on three domains of the central class Drosophila Hox transcription factor AbdominalA (AbdA, we used combinatorial domain mutations and most known AbdA developmental functions as biological readouts to investigate how protein domains collectively shape protein activity. The results uncover redundancy, interactivity, and multifunctionality of protein domains as salient features underlying overall AbdA protein activity, providing means to apprehend functional diversity and accounting for the robustness of Hox-controlled developmental programs. Importantly, the results highlight context-dependency in protein domain usage and interaction, allowing major modifications in domains to be tolerated without general functional loss. The non-pleoitropic effect of domain mutation suggests that protein modification may contribute more broadly to molecular changes underlying morphological diversification during evolution, so far thought to rely largely on modification in gene cis-regulatory sequences.

Nano-Mole Scale Side-Chain Signal Assignment by 1H-Detected Protein Solid-State NMR by Ultra-Fast Magic-Angle Spinning and Stereo-Array Isotope Labeling

KAUST Repository

Wang, Songlin; Parthasarathy, Sudhakar; Nishiyama, Yusuke; Endo, Yuki; Nemoto, Takahiro; Yamauchi, Kazuo; Asakura, Tetsuo; Takeda, Mitsuhiro; Terauchi, Tsutomu; Kainosho, Masatsune; Ishii, Yoshitaka

2015-01-01

We present a general approach in 1H-detected 13C solid-state NMR (SSNMR) for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS) at ~80 kHz, and stereo-array-isotope-labeled (SAIL) proteins [Kainosho M. et al., Nature 440, 52–57, 2006]. First, we demonstrate that 1H indirect detection improves the sensitivity and resolution of 13C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. 1H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg) that was SAIL-labeled at seven isoleucine (Ile) residues. Sensitivity was dramatically improved by 1H-detected 2D 1H/13C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over 13C-detected 2D 1H/13C SSNMR and 1D 13C CPMAS, demonstrating that 2D 1H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D 13C detection for the first time. High 1H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A 1H-detected 3D 13C/13C/1H experiment on SAIL-ubiquitin provided nearly complete 1H and 13C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems.

Nano-Mole Scale Side-Chain Signal Assignment by 1H-Detected Protein Solid-State NMR by Ultra-Fast Magic-Angle Spinning and Stereo-Array Isotope Labeling

KAUST Repository

Wang, Songlin

2015-04-09

We present a general approach in 1H-detected 13C solid-state NMR (SSNMR) for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS) at ~80 kHz, and stereo-array-isotope-labeled (SAIL) proteins [Kainosho M. et al., Nature 440, 52–57, 2006]. First, we demonstrate that 1H indirect detection improves the sensitivity and resolution of 13C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. 1H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg) that was SAIL-labeled at seven isoleucine (Ile) residues. Sensitivity was dramatically improved by 1H-detected 2D 1H/13C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over 13C-detected 2D 1H/13C SSNMR and 1D 13C CPMAS, demonstrating that 2D 1H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D 13C detection for the first time. High 1H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A 1H-detected 3D 13C/13C/1H experiment on SAIL-ubiquitin provided nearly complete 1H and 13C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems.

AUTOBA: automation of backbone assignment from HN(C)N suite of experiments.

Science.gov (United States)

Borkar, Aditi; Kumar, Dinesh; Hosur, Ramakrishna V

2011-07-01

Development of efficient strategies and automation represent important milestones of progress in rapid structure determination efforts in proteomics research. In this context, we present here an efficient algorithm named as AUTOBA (Automatic Backbone Assignment) designed to automate the assignment protocol based on HN(C)N suite of experiments. Depending upon the spectral dispersion, the user can record 2D or 3D versions of the experiments for assignment. The algorithm uses as inputs: (i) protein primary sequence and (ii) peak-lists from user defined HN(C)N suite of experiments. In the end, one gets H(N), (15)N, C(α) and C' assignments (in common BMRB format) for the individual residues along the polypeptide chain. The success of the algorithm has been demonstrated, not only with experimental spectra recorded on two small globular proteins: ubiquitin (76 aa) and M-crystallin (85 aa), but also with simulated spectra of 27 other proteins using assignment data from the BMRB.

Filtering high-throughput protein-protein interaction data using a combination of genomic features

Directory of Open Access Journals (Sweden)

Patil Ashwini

2005-04-01

Full Text Available Abstract Background Protein-protein interaction data used in the creation or prediction of molecular networks is usually obtained from large scale or high-throughput experiments. This experimental data is liable to contain a large number of spurious interactions. Hence, there is a need to validate the interactions and filter out the incorrect data before using them in prediction studies. Results In this study, we use a combination of 3 genomic features – structurally known interacting Pfam domains, Gene Ontology annotations and sequence homology – as a means to assign reliability to the protein-protein interactions in Saccharomyces cerevisiae determined by high-throughput experiments. Using Bayesian network approaches, we show that protein-protein interactions from high-throughput data supported by one or more genomic features have a higher likelihood ratio and hence are more likely to be real interactions. Our method has a high sensitivity (90% and good specificity (63%. We show that 56% of the interactions from high-throughput experiments in Saccharomyces cerevisiae have high reliability. We use the method to estimate the number of true interactions in the high-throughput protein-protein interaction data sets in Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens to be 27%, 18% and 68% respectively. Our results are available for searching and downloading at http://helix.protein.osaka-u.ac.jp/htp/. Conclusion A combination of genomic features that include sequence, structure and annotation information is a good predictor of true interactions in large and noisy high-throughput data sets. The method has a very high sensitivity and good specificity and can be used to assign a likelihood ratio, corresponding to the reliability, to each interaction.

Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone 15N or 13C′ chemical shifts of multiple contiguous residues in highly resolved 3D spectra

International Nuclear Information System (INIS)

Yoshimura, Yuichi; Kulminskaya, Natalia V.; Mulder, Frans A. A.

2015-01-01

Sequential resonance assignment strategies are typically based on matching one or two chemical shifts of adjacent residues. However, resonance overlap often leads to ambiguity in resonance assignments in particular for intrinsically disordered proteins. We investigated the potential of establishing connectivity through the three-bond couplings between sequentially adjoining backbone carbonyl carbon nuclei, combined with semi-constant time chemical shift evolution, for resonance assignments of small folded and larger unfolded proteins. Extended sequential connectivity strongly lifts chemical shift degeneracy of the backbone nuclei in disordered proteins. We show here that 3D (H)N(COCO)NH and (HN)CO(CO)NH experiments with relaxation-optimized multiple pulse mixing correlate up to seven adjacent backbone amide nitrogen or carbonyl carbon nuclei, respectively, and connections across proline residues are also obtained straightforwardly. Multiple, recurrent long-range correlations with ultra-high resolution allow backbone 1 H N , 15 N H , and 13 C′ resonance assignments to be completed from a single pair of 3D experiments

BioPlex Display: An Interactive Suite for Large-Scale AP-MS Protein-Protein Interaction Data.

Science.gov (United States)

Schweppe, Devin K; Huttlin, Edward L; Harper, J Wade; Gygi, Steven P

2018-01-05

The development of large-scale data sets requires a new means to display and disseminate research studies to large audiences. Knowledge of protein-protein interaction (PPI) networks has become a principle interest of many groups within the field of proteomics. At the confluence of technologies, such as cross-linking mass spectrometry, yeast two-hybrid, protein cofractionation, and affinity purification mass spectrometry (AP-MS), detection of PPIs can uncover novel biological inferences at a high-throughput. Thus new platforms to provide community access to large data sets are necessary. To this end, we have developed a web application that enables exploration and dissemination of the growing BioPlex interaction network. BioPlex is a large-scale interactome data set based on AP-MS of baits from the human ORFeome. The latest BioPlex data set release (BioPlex 2.0) contains 56 553 interactions from 5891 AP-MS experiments. To improve community access to this vast compendium of interactions, we developed BioPlex Display, which integrates individual protein querying, access to empirical data, and on-the-fly annotation of networks within an easy-to-use and mobile web application. BioPlex Display enables rapid acquisition of data from BioPlex and development of hypotheses based on protein interactions.

Isothermal chemical denaturation of large proteins: Path-dependence and irreversibility.

Science.gov (United States)

Wafer, Lucas; Kloczewiak, Marek; Polleck, Sharon M; Luo, Yin

2017-12-15

State functions (e.g., ΔG) are path independent and quantitatively describe the equilibrium states of a thermodynamic system. Isothermal chemical denaturation (ICD) is often used to extrapolate state function parameters for protein unfolding in native buffer conditions. The approach is prudent when the unfolding/refolding processes are path independent and reversible, but may lead to erroneous results if the processes are not reversible. The reversibility was demonstrated in several early studies for smaller proteins, but was assumed in some reports for large proteins with complex structures. In this work, the unfolding/refolding of several proteins were systematically studied using an automated ICD instrument. It is shown that: (i) the apparent unfolding mechanism and conformational stability of large proteins can be denaturant-dependent, (ii) equilibration times for large proteins are non-trivial and may introduce significant error into calculations of ΔG, (iii) fluorescence emission spectroscopy may not correspond to other methods, such as circular dichroism, when used to measure protein unfolding, and (iv) irreversible unfolding and hysteresis can occur in the absence of aggregation. These results suggest that thorough confirmation of the state functions by, for example, performing refolding experiments or using additional denaturants, is needed when quantitatively studying the thermodynamics of protein unfolding using ICD. Copyright © 2017 Elsevier Inc. All rights reserved.

1H and 15N resonance assignments of oxidized flavodoxin from Anacystis nidulans with 3D NMR

International Nuclear Information System (INIS)

Clubb, R.T.; Thanabal, V.; Wagner, G.; Osborne, C.

1991-01-01

Proton and nitrogen-15 sequence-specific nuclear magnetic resonance assignments have been determined for recombinant oxidized flavodoxin from Anacystis nidulans. Assignments were obtained by using 15 N- 1 H heteronuclear three-dimensional (3D) NMR spectroscopy on a uniformly nitrogen-15 enriched sample of the protein, pH 6.6, at 30C. For 165 residues, the backbone and a large fraction of the side-chain proton resonances have been assigned. Medium- and long-range NOE's have been used to characterize the secondary structure. In solution, flavodoxin consists of a five-stranded parallel β sheet involving residues 3-9, 31-37, 49-56, 81-89, 114-117, and 141-144. Medium-range NOE's indicate that presence of several helices. Several 15 N and 1 H resonances of the flavin mononucleotide (FMN) prosthetic group have been assigned. The FMN-binding site has been investigated by using polypeptide-FMN NOE's

Two-dimensional NMR and photo-CIDNP studies of the insulin monomer: Assignment of aromatic resonances with application to protein folding, structure, and dynamics

International Nuclear Information System (INIS)

Weiss, M.A.; Shoelson, S.E.; Nguyen, D.T.; O'Shea, E.; Karplus, M.; Khait, I.; Neuringer, L.J.; Inouye, K.; Frank, B.H.; Beckage, M.

1989-01-01

The aromatic 1 H NMR resonances of the insulin monomer are assigned at 500 MHz by comparative studies of chemically modified and genetically altered variants, including a mutant insulin (PheB25 → Leu) associated with diabetes mellitus. The two histidines, three phenylalanines, and four tyrosines are observed to be in distinct local environments; their assignment provides sensitive markers for studies of tertiary structure, protein dynamics, and protein folding. The environments of the tyrosine residues have also been investigated by photochemically induced dynamic nuclear polarization (photo-CIDNP) and analyzed in relation to packing constrains in the crystal structures of insulin. Dimerization involving specific B-chain interactions is observed with increasing protein concentration and is shown to depend on temperature, pH, and solvent composition. The differences between proinsulin and mini-proinsulin suggest a structural mechanism for the observation that the fully reduced B29-A1 analogue folds more efficiently than proinsulin to form the correct pattern of disulfide bonds. These results are discussed in relation to molecular mechanics calculations of insulin based on the available crystal structures

Large-scale analysis of phosphorylation site occupancy in eukaryotic proteins

DEFF Research Database (Denmark)

Rao, R Shyama Prasad; Møller, Ian Max

2012-01-01

in proteins is currently lacking. We have therefore analyzed the occurrence and occupancy of phosphorylated sites (~ 100,281) in a large set of eukaryotic proteins (~ 22,995). Phosphorylation probability was found to be much higher in both the  termini of protein sequences and this is much pronounced...... maximum randomness. An analysis of phosphorylation motifs indicated that just 40 motifs and a much lower number of associated kinases might account for nearly 50% of the known phosphorylations in eukaryotic proteins. Our results provide a broad picture of the phosphorylation sites in eukaryotic proteins.......Many recent high throughput technologies have enabled large-scale discoveries of new phosphorylation sites and phosphoproteins. Although they have provided a number of insights into protein phosphorylation and the related processes, an inclusive analysis on the nature of phosphorylated sites...

Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY

KAUST Repository

Jang, Richard; Gao, Xin; Li, Ming

2012-01-01

Background: Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule's introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening.Results: We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better.Conclusions: Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. 2012 Jang et al.; licensee BioMed Central Ltd.

Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY

KAUST Repository

Jang, Richard

2012-03-21

Background: Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening.Results: We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better.Conclusions: Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. 2012 Jang et al.; licensee BioMed Central Ltd.

Large-scale biophysical evaluation of protein PEGylation effects

DEFF Research Database (Denmark)

Vernet, Erik; Popa, Gina; Pozdnyakova, Irina

2016-01-01

PEGylation is the most widely used method to chemically modify protein biopharmaceuticals, but surprisingly limited public data is available on the biophysical effects of protein PEGylation. Here we report the first large-scale study, with site-specific mono-PEGylation of 15 different proteins...... of PEGylation on the thermal stability of a protein based on data generated by circular dichroism (CD), differential scanning calorimetry (DSC), or differential scanning fluorimetry (DSF). In addition, DSF was validated as a fast and inexpensive screening method for thermal unfolding studies of PEGylated...... proteins. Multivariate data analysis revealed clear trends in biophysical properties upon PEGylation for a subset of proteins, although no universal trends were found. Taken together, these findings are important in the consideration of biophysical methods and evaluation of second...

Stereospecific assignment of the NH2 resonances from the primary amides of asparagine and glutamine side chains in isotopically labeled proteins

International Nuclear Information System (INIS)

McIntosh, Lawrence P.; Brun, Emmanuel; Kay, Lewis E.

1997-01-01

An HMQC-based pulse scheme is presented for the stereospecific assignment of asparagine and glutamine side-chain amide protons. The approach makes use of the recently developed quantitative-J correlation spectroscopy [Bax, A. et al. (1994) Methods Enzymol., 239,79-105] to distinguish the E and Z primary amide protons and, as such, eliminates the need for assignments derived from more time-consuming and potentially ambiguous NOE methods. An application of this method to a uniformly 15N,13C-labeled cellulose-binding domain is presented. When used in combination with a NOESY-HSQC experiment, the predominant χ2 dihedral angles of two asparagine side chains in this protein can also be defined

Large-scale protein-protein interaction analysis in Arabidopsis mesophyll protoplasts by split firefly luciferase complementation.

Science.gov (United States)

Li, Jian-Feng; Bush, Jenifer; Xiong, Yan; Li, Lei; McCormack, Matthew

2011-01-01

Protein-protein interactions (PPIs) constitute the regulatory network that coordinates diverse cellular functions. There are growing needs in plant research for creating protein interaction maps behind complex cellular processes and at a systems biology level. However, only a few approaches have been successfully used for large-scale surveys of PPIs in plants, each having advantages and disadvantages. Here we present split firefly luciferase complementation (SFLC) as a highly sensitive and noninvasive technique for in planta PPI investigation. In this assay, the separate halves of a firefly luciferase can come into close proximity and transiently restore its catalytic activity only when their fusion partners, namely the two proteins of interest, interact with each other. This assay was conferred with quantitativeness and high throughput potential when the Arabidopsis mesophyll protoplast system and a microplate luminometer were employed for protein expression and luciferase measurement, respectively. Using the SFLC assay, we could monitor the dynamics of rapamycin-induced and ascomycin-disrupted interaction between Arabidopsis FRB and human FKBP proteins in a near real-time manner. As a proof of concept for large-scale PPI survey, we further applied the SFLC assay to testing 132 binary PPIs among 8 auxin response factors (ARFs) and 12 Aux/IAA proteins from Arabidopsis. Our results demonstrated that the SFLC assay is ideal for in vivo quantitative PPI analysis in plant cells and is particularly powerful for large-scale binary PPI screens.

Large-scale protein-protein interaction analysis in Arabidopsis mesophyll protoplasts by split firefly luciferase complementation.

Directory of Open Access Journals (Sweden)

Jian-Feng Li

Full Text Available Protein-protein interactions (PPIs constitute the regulatory network that coordinates diverse cellular functions. There are growing needs in plant research for creating protein interaction maps behind complex cellular processes and at a systems biology level. However, only a few approaches have been successfully used for large-scale surveys of PPIs in plants, each having advantages and disadvantages. Here we present split firefly luciferase complementation (SFLC as a highly sensitive and noninvasive technique for in planta PPI investigation. In this assay, the separate halves of a firefly luciferase can come into close proximity and transiently restore its catalytic activity only when their fusion partners, namely the two proteins of interest, interact with each other. This assay was conferred with quantitativeness and high throughput potential when the Arabidopsis mesophyll protoplast system and a microplate luminometer were employed for protein expression and luciferase measurement, respectively. Using the SFLC assay, we could monitor the dynamics of rapamycin-induced and ascomycin-disrupted interaction between Arabidopsis FRB and human FKBP proteins in a near real-time manner. As a proof of concept for large-scale PPI survey, we further applied the SFLC assay to testing 132 binary PPIs among 8 auxin response factors (ARFs and 12 Aux/IAA proteins from Arabidopsis. Our results demonstrated that the SFLC assay is ideal for in vivo quantitative PPI analysis in plant cells and is particularly powerful for large-scale binary PPI screens.

Calibrated peer review assignments for the earth sciences

Science.gov (United States)

Rudd, J.A.; Wang, V.Z.; Cervato, C.; Ridky, R.W.

2009-01-01

Calibrated Peer Review ??? (CPR), a web-based instructional tool developed as part of the National Science Foundation reform initiatives in undergraduate science education, allows instructors to incorporate multiple writing assignments in large courses without overwhelming the instructor. This study reports successful implementation of CPR in a large, introductory geology course and student learning of geoscience content. For each CPR assignment in this study, students studied web-based and paper resources, wrote an essay, and reviewed seven essays (three from the instructor, three from peers, and their own) on the topic. Although many students expressed negative attitudes and concerns, particularly about the peer review process of this innovative instructional approach, they also recognized the learning potential of completing CPR assignments. Comparing instruction on earthquakes and plate boundaries using a CPR assignment vs. an instructional video lecture and homework essay with extensive instructor feedback, students mastered more content via CPR instruction.

Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO)

Energy Technology Data Exchange (ETDEWEB)

Eghbalnia, Hamid R., E-mail: eghbalni@nmrfam.wisc.edu; Bahrami, Arash; Wang, Liya [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States); Assadi, Amir [University of Wisconsin-Madison, Mathematics Department (United States); Markley, John L [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)

2005-07-15

We present a novel automated strategy (PISTACHIO) for the probabilistic assignment of backbone and sidechain chemical shifts in proteins. The algorithm uses peak lists derived from various NMR experiments as input and provides as output ranked lists of assignments for all signals recognized in the input data as constituting spin systems. PISTACHIO was evaluated by comparing its performance with raw peak-picked data from 15 proteins ranging from 54 to 300 residues; the results were compared with those achieved by experts analyzing the same datasets by hand. As scored against the best available independent assignments for these proteins, the first-ranked PISTACHIO assignments were 80-100% correct for backbone signals and 75-95% correct for sidechain signals. The independent assignments benefited, in a number of cases, from structural data (e.g. from NOESY spectra) that were unavailable to PISTACHIO. Any number of datasets in any combination can serve as input. Thus PISTACHIO can be used as datasets are collected to ascertain the current extent of secure assignments, to identify residues with low assignment probability, and to suggest the types of additional data needed to remove ambiguities. The current implementation of PISTACHIO, which is available from a server on the Internet, supports input data from 15 standard double- and triple-resonance experiments. The software can readily accommodate additional types of experiments, including data from selectively labeled samples. The assignment probabilities can be carried forward and refined in subsequent steps leading to a structure. The performance of PISTACHIO showed no direct dependence on protein size, but correlated instead with data quality (completeness and signal-to-noise). PISTACHIO represents one component of a comprehensive probabilistic approach we are developing for the collection and analysis of protein NMR data.

Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO)

International Nuclear Information System (INIS)

Eghbalnia, Hamid R.; Bahrami, Arash; Wang, Liya; Assadi, Amir; Markley, John L.

2005-01-01

We present a novel automated strategy (PISTACHIO) for the probabilistic assignment of backbone and sidechain chemical shifts in proteins. The algorithm uses peak lists derived from various NMR experiments as input and provides as output ranked lists of assignments for all signals recognized in the input data as constituting spin systems. PISTACHIO was evaluated by comparing its performance with raw peak-picked data from 15 proteins ranging from 54 to 300 residues; the results were compared with those achieved by experts analyzing the same datasets by hand. As scored against the best available independent assignments for these proteins, the first-ranked PISTACHIO assignments were 80-100% correct for backbone signals and 75-95% correct for sidechain signals. The independent assignments benefited, in a number of cases, from structural data (e.g. from NOESY spectra) that were unavailable to PISTACHIO. Any number of datasets in any combination can serve as input. Thus PISTACHIO can be used as datasets are collected to ascertain the current extent of secure assignments, to identify residues with low assignment probability, and to suggest the types of additional data needed to remove ambiguities. The current implementation of PISTACHIO, which is available from a server on the Internet, supports input data from 15 standard double- and triple-resonance experiments. The software can readily accommodate additional types of experiments, including data from selectively labeled samples. The assignment probabilities can be carried forward and refined in subsequent steps leading to a structure. The performance of PISTACHIO showed no direct dependence on protein size, but correlated instead with data quality (completeness and signal-to-noise). PISTACHIO represents one component of a comprehensive probabilistic approach we are developing for the collection and analysis of protein NMR data

Approach for growth of high-quality and large protein crystals

Energy Technology Data Exchange (ETDEWEB)

Matsumura, Hiroyoshi, E-mail: matsumura@chem.eng.osaka-u.ac.jp [Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871 (Japan); JST (Japan); SOSHO Inc., Osaka 541-0053 (Japan); Sugiyama, Shigeru; Hirose, Mika; Kakinouchi, Keisuke; Maruyama, Mihoko; Murai, Ryota [Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871 (Japan); JST (Japan); Adachi, Hiroaki; Takano, Kazufumi [Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871 (Japan); JST (Japan); SOSHO Inc., Osaka 541-0053 (Japan); Murakami, Satoshi [JST (Japan); SOSHO Inc., Osaka 541-0053 (Japan); Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501 (Japan); Mori, Yusuke; Inoue, Tsuyoshi [Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871 (Japan); JST (Japan); SOSHO Inc., Osaka 541-0053 (Japan)

2011-01-01

Three crystallization methods, including crystallization in the presence of a semi-solid agarose gel, top-seeded solution growth (TSSG) and a large-scale hanging-drop method, have previously been presented. In this study, crystallization has been further evaluated in the presence of a semi-solid agarose gel by crystallizing additional proteins. A novel crystallization method combining TSSG and the large-scale hanging-drop method has also been developed. Three crystallization methods for growing large high-quality protein crystals, i.e. crystallization in the presence of a semi-solid agarose gel, top-seeded solution growth (TSSG) and a large-scale hanging-drop method, have previously been presented. In this study the effectiveness of crystallization in the presence of a semi-solid agarose gel has been further evaluated by crystallizing additional proteins in the presence of 2.0% (w/v) agarose gel, resulting in complete gelification with high mechanical strength. In TSSG the seed crystals are hung by a seed holder protruding from the top of the growth vessel to prevent polycrystallization. In the large-scale hanging-drop method, a cut pipette tip was used to maintain large-scale droplets consisting of protein–precipitant solution. Here a novel crystallization method that combines TSSG and the large-scale hanging-drop method is reported. A large and single crystal of lysozyme was obtained by this method.

Dissecting water binding sites at protein-protein interfaces: a lesson from the atomic structures in the Protein Data Bank.

Science.gov (United States)

Mukherjee, Sunandan; Nithin, Chandran; Divakaruni, Yasaswi; Bahadur, Ranjit Prasad

2018-04-04

We dissect the protein-protein interfaces into water preservation (WP), water hydration (WH) and water dehydration (WD) sites by comparing the water-mediated hydrogen bonds (H-bond) in the bound and unbound states of the interacting subunits. Upon subunit complexation, if a H-bond between an interface water and a protein polar group is retained, we assign it as WP site; if it is lost, we assign it as WD site and if a new H-bond is created, we assign it as WH site. We find that the density of WD sites is highest followed by WH and WP sites except in antigen and (or) antibody complexes, where the density of WH sites is highest followed by WD and WP sites. Furthermore, we find that WP sites are the most conserved followed by WD and WH sites in all class of complexes except in antigen and (or) antibody complexes, where WD sites are the most conserved followed by WH and WP sites. A significant number of WP and WH sites are involved in water bridges that stabilize the subunit interactions. At WH sites, the residues involved in water bridges are significantly better conserved than the other residues. However, no such difference is observed at WP sites. Interestingly, WD sites are generally replaced with direct H-bonds upon subunit complexation. Significantly, we observe many water-mediated H-bonds remain preserved in spite of large conformational changes upon subunit complexation. These findings have implications in predicting and engineering water binding sites at protein-protein interfaces.

Evolution favors protein mutational robustness in sufficiently large populations

Directory of Open Access Journals (Sweden)

Venturelli Ophelia S

2007-07-01

Full Text Available Abstract Background An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar proteins can differ substantially in their robustness to mutations and capacity to evolve new functions, but it has remained unclear whether any of these differences might be due to evolutionary selection for these properties. Results Here we use laboratory experiments to demonstrate that evolution favors protein mutational robustness if the evolving population is sufficiently large. We neutrally evolve cytochrome P450 proteins under identical selection pressures and mutation rates in populations of different sizes, and show that proteins from the larger and thus more polymorphic population tend towards higher mutational robustness. Proteins from the larger population also evolve greater stability, a biophysical property that is known to enhance both mutational robustness and evolvability. The excess mutational robustness and stability is well described by mathematical theory, and can be quantitatively related to the way that the proteins occupy their neutral network. Conclusion Our work is the first experimental demonstration of the general tendency of evolution to favor mutational robustness and protein stability in highly polymorphic populations. We suggest that this phenomenon could contribute to the mutational robustness and evolvability of viruses and bacteria that exist in large populations.

Optimisation of timetable-based, stochastic transit assignment models based on MSA

DEFF Research Database (Denmark)

Nielsen, Otto Anker; Frederiksen, Rasmus Dyhr

2006-01-01

(CRM), such a large-scale transit assignment model was developed and estimated. The Stochastic User Equilibrium problem was solved by the Method of Successive Averages (MSA). However, the model suffered from very large calculation times. The paper focuses on how to optimise transit assignment models...

Pythoscape: A framework for generation of large protein similarity networks

OpenAIRE

Babbitt, Patricia; Barber, AE; Babbitt, PC

2012-01-01

Pythoscape is a framework implemented in Python for processing large protein similarity networks for visualization in other software packages. Protein similarity networks are graphical representations of sequence, structural and other similarities among pr

Direct methods and residue type specific isotope labeling in NMR structure determination and model-driven sequential assignment

International Nuclear Information System (INIS)

Schedlbauer, Andreas; Auer, Renate; Ledolter, Karin; Tollinger, Martin; Kloiber, Karin; Lichtenecker, Roman; Ruedisser, Simon; Hommel, Ulrich; Schmid, Walther; Konrat, Robert; Kontaxis, Georg

2008-01-01

Direct methods in NMR based structure determination start from an unassigned ensemble of unconnected gaseous hydrogen atoms. Under favorable conditions they can produce low resolution structures of proteins. Usually a prohibitively large number of NOEs is required, to solve a protein structure ab-initio, but even with a much smaller set of distance restraints low resolution models can be obtained which resemble a protein fold. One problem is that at such low resolution and in the absence of a force field it is impossible to distinguish the correct protein fold from its mirror image. In a hybrid approach these ambiguous models have the potential to aid in the process of sequential backbone chemical shift assignment when 13 C β and 13 C' shifts are not available for sensitivity reasons. Regardless of the overall fold they enhance the information content of the NOE spectra. These, combined with residue specific labeling and minimal triple-resonance data using 13 C α connectivity can provide almost complete sequential assignment. Strategies for residue type specific labeling with customized isotope labeling patterns are of great advantage in this context. Furthermore, this approach is to some extent error-tolerant with respect to data incompleteness, limited precision of the peak picking, and structural errors caused by misassignment of NOEs

Scaffolding Assignments and Activities for Undergraduate Research Methods

Science.gov (United States)

Fisher, Sarah; Justwan, Florian

2018-01-01

This article details assignments and lessons created for and tested in research methods courses at two different universities, a large state school and a small liberal arts college. Each assignment or activity utilized scaffolding. Students were asked to push beyond their comfort zone while utilizing concrete and/or creative examples,…

A general assignment method for oriented sample (OS) solid-state NMR of proteins based on the correlation of resonances through heteronuclear dipolar couplings in samples aligned parallel and perpendicular to the magnetic field.

Science.gov (United States)

Lu, George J; Son, Woo Sung; Opella, Stanley J

2011-04-01

A general method for assigning oriented sample (OS) solid-state NMR spectra of proteins is demonstrated. In principle, this method requires only a single sample of a uniformly ¹⁵N-labeled membrane protein in magnetically aligned bilayers, and a previously assigned isotropic chemical shift spectrum obtained either from solution NMR on micelle or isotropic bicelle samples or from magic angle spinning (MAS) solid-state NMR on unoriented proteoliposomes. The sequential isotropic resonance assignments are transferred to the OS solid-state NMR spectra of aligned samples by correlating signals from the same residue observed in protein-containing bilayers aligned with their normals parallel and perpendicular to the magnetic field. The underlying principle is that the resonances from the same residue have heteronuclear dipolar couplings that differ by exactly a factor of two between parallel and perpendicular alignments. The method is demonstrated on the membrane-bound form of Pf1 coat protein in phospholipid bilayers, whose assignments have been previously made using an earlier generation of methods that relied on the preparation of many selectively labeled (by residue type) samples. The new method provides the correct resonance assignments using only a single uniformly ¹⁵N-labeled sample, two solid-state NMR spectra, and a previously assigned isotropic spectrum. Significantly, this approach is equally applicable to residues in alpha helices, beta sheets, loops, and any other elements of tertiary structure. Moreover, the strategy bridges between OS solid-state NMR of aligned samples and solution NMR or MAS solid-state NMR of unoriented samples. In combination with the development of complementary experimental methods, it provides a step towards unifying these apparently different NMR approaches. Copyright © 2011 Elsevier Inc. All rights reserved.

Solving Classification Problems for Large Sets of Protein Sequences with the Example of Hox and ParaHox Proteins

Directory of Open Access Journals (Sweden)

Stefanie D. Hueber

2016-02-01

Full Text Available Phylogenetic methods are key to providing models for how a given protein family evolved. However, these methods run into difficulties when sequence divergence is either too low or too high. Here, we provide a case study of Hox and ParaHox proteins so that additional insights can be gained using a new computational approach to help solve old classification problems. For two (Gsx and Cdx out of three ParaHox proteins the assignments differ between the currently most established view and four alternative scenarios. We use a non-phylogenetic, pairwise-sequence-similarity-based method to assess which of the previous predictions, if any, are best supported by the sequence-similarity relationships between Hox and ParaHox proteins. The overall sequence-similarities show Gsx to be most similar to Hox2–3, and Cdx to be most similar to Hox4–8. The results indicate that a purely pairwise-sequence-similarity-based approach can provide additional information not only when phylogenetic inference methods have insufficient information to provide reliable classifications (as was shown previously for central Hox proteins, but also when the sequence variation is so high that the resulting phylogenetic reconstructions are likely plagued by long-branch-attraction artifacts.

A systematic analysis of backbone amide assignments achieved via combinatorial selective labelling of amino acids

Energy Technology Data Exchange (ETDEWEB)

Jeremy Craven, C. [University of Sheffield, Department of Biotechnology and Molecular Biology (United Kingdom); Al-Owais, Moza; Parker, Martin J. [University of Leeds, Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology (United Kingdom)], E-mail: m.j.parker@leeds.ac.uk

2007-06-15

With the advent of high-yield cell-free expressions systems, many researchers are exploiting selective isotope labelling of amino acids to increase the efficiency and accuracy of the NMR assignment process. We developed recently a combinatorial selective labelling (CSL) method capable of yielding large numbers of residue-type and sequence-specific backbone amide assignments, which involves comparing cross-peak intensities in {sup 1}H-{sup 15}N HSQC and 2D {sup 1}H-{sup 15}N HNCO spectra collected for five samples containing different combinations of {sup 13}C- and {sup 15}N-labelled amino acids [Parker MJ, Aulton-Jones M, Hounslow A, Craven C J (2004) J Am Chem Soc 126:5020-5021]. In this paper we develop a robust method for establishing the reliability of these assignments. We have performed a detailed statistical analysis of the CSL data collected for a model system (the B1 domain of protein G from Streptococcus), developing a scoring method which allows the confidence in assignments to be assessed, and which enables the effects of overlap on assignment fidelity to be predicted. To further test the scoring method and also to assess the performance of CSL in relation to sample quality, we have applied the method to the CSL data collected for GFP in our previous study.

A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences

Energy Technology Data Exchange (ETDEWEB)

Wang Jun; Liu Haiyan [University of Science and Technology of China, Hefei National Laboratory for Physical Sciences at the Microscale, and Key Laboratory of Structural Biology, School of Life Sciences (China)], E-mail: hyliu@ustc.edu.cn

2007-01-15

Chemical shifts contain substantial information about protein local conformations. We present a method to assign individual protein backbone dihedral angles into specific regions on the Ramachandran map based on the amino acid sequences and the chemical shifts of backbone atoms of tripeptide segments. The method uses a scoring function derived from the Bayesian probability for the central residue of a query tripeptide segment to have a particular conformation. The Ramachandran map is partitioned into representative regions at two levels of resolution. The lower resolution partitioning is equivalent to the conventional definitions of different secondary structure regions on the map. At the higher resolution level, the {alpha} and {beta} regions are further divided into subregions. Predictions are attempted at both levels of resolution. We compared our method with TALOS using the original TALOS database, and obtained comparable results. Although TALOS may produce the best results with currently available databases which are much enlarged, the Bayesian-probability-based approach can provide a quantitative measure for the reliability of predictions.

1H, 13C, and 15N resonance assignment of the N-terminal domainof Mason-Pfizer monkey virus capsid protein, CA 1-140

Czech Academy of Sciences Publication Activity Database

Macek, Pavel; Žídek, L.; Rumlová, Michaela; Pichová, Iva; Sklenář, V.

2008-01-01

Roč. 2, č. 1 (2008), s. 43-45 ISSN 1874-2718 R&D Projects: GA MŠk LC545; GA MŠk(CZ) LC06030; GA MŠk 1M0508 Institutional research plan: CEZ:AV0Z50200510; CEZ:AV0Z40550506 Keywords : nmr * assignment * capsid protein Subject RIV: EE - Microbiology, Virology Impact factor: 0.015, year: 2008

Assignment of 1H, 13C, and 15N resonances of WT matrix protein and its R55F mutant from Mason-Pfizer monkey virus

Czech Academy of Sciences Publication Activity Database

Vlach, J.; Lipov, J.; Veverka, V.; Rumlová, Michaela; Ruml, T.; Hrabal, R.

2005-01-01

Roč. 31, - (2005), s. 381-382 ISSN 0925-2738 R&D Projects: GA ČR GA203/03/0490 Institutional research plan: CEZ:AV0Z4055905 Keywords : Mason-Pfizer monkey virus * NMR resonance assignment * matrix protein Subject RIV: CE - Biochemistry Impact factor: 2.180, year: 2005

Combination of Bcl-2 and MYC protein expression improves high-risk stratification in diffuse large B-cell lymphoma

Directory of Open Access Journals (Sweden)

Wang J

2015-09-01

Full Text Available Jing Wang,* Min Zhou,* Jing-Yan Xu,* Bing Chen, Jian OuyangDepartment of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, People’s Republic of China*These authors contributed equally to this work and should be considered as cofirst authorsPurpose: To evaluate whether the addition of two biological markers (MYC and BCL-2 protein overexpression improves the stratification of high-risk patients with diffuse large B-cell lymphoma (DLBCL.Method: Seven risk factors were identified at diagnosis, and a maximum of 7 points were assigned to each patient. The patients were classified according to four risk groups: low (0–1, low-intermediate (2–3, high-intermediate (4, and high (5–7. Only high-risk patients with DLBCL were included in this analysis. We retrospectively examined 20 cases from 2008 to 2013 at the Nanjing Drum Tower Hospital.Results: The median expression of MYC protein was 60%, and 17 of 20 (65% evaluable cases overexpressed MYC. The median expression of BCL-2 protein was also 60%. Eighteen of 20 (90% evaluable cases showed BCL-2 overexpression. Additionally, 12 out of 20 cases (60% demonstrated coexpression of MYC and BCL-2 proteins. The percentages of overall survival and progression-free survival at the median follow-up time (36 months were 33.3%±16.1% and 16.9%±13.5%, respectively. By comparison, nine, four, and 20 patients were classified as high risk based on the International Prognostic Index (IPI, National Comprehensive Cancer Network(NCCN-IPI, and revised IPI criteria, respectively. According to the IPI and NCCN-IPI stratification, the risk groups demonstrated closely overlapping survival curves. In addition, four out of 20 cases were identified as low-intermediate risk according to the NCCN-IPI criteria.Conclusion: The addition of MYC and BCL-2 protein expression to the IPI could identify a subset of DLBCL patients with high-risk clinicopathological characteristics and

Development and Application of ANN Model for Worker Assignment into Virtual Cells of Large Sized Configurations

International Nuclear Information System (INIS)

Murali, R. V.; Fathi, Khalid; Puri, A. B.

2010-01-01

This paper presents an extended version of study already undertaken on development of an artificial neural networks (ANNs) model for assigning workforce into virtual cells under virtual cellular manufacturing systems (VCMS) environments. Previously, the same authors have introduced this concept and applied it to virtual cells of two-cell configuration and the results demonstrated that ANNs could be a worth applying tool for carrying out workforce assignments. In this attempt, three-cell configurations problems are considered for worker assignment task. Virtual cells are formed under dual resource constraint (DRC) context in which the number of available workers is less than the total number of machines available. Since worker assignment tasks are quite non-linear and highly dynamic in nature under varying inputs and conditions and, in parallel, ANNs have the ability to model complex relationships between inputs and outputs and find similar patterns effectively, an attempt was earlier made to employ ANNs into the above task. In this paper, the multilayered perceptron with feed forward (MLP-FF) neural network model has been reused for worker assignment tasks of three-cell configurations under DRC context and its performance at different time periods has been analyzed. The previously proposed worker assignment model has been reconfigured and cell formation solutions available for three-cell configuration in the literature are used in combination to generate datasets for training ANNs framework. Finally, results of the study have been presented and discussed.

Toxicological relationships between proteins obtained from protein target predictions of large toxicity databases

International Nuclear Information System (INIS)

Nigsch, Florian; Mitchell, John B.O.

2008-01-01

The combination of models for protein target prediction with large databases containing toxicological information for individual molecules allows the derivation of 'toxiclogical' profiles, i.e., to what extent are molecules of known toxicity predicted to interact with a set of protein targets. To predict protein targets of drug-like and toxic molecules, we built a computational multiclass model using the Winnow algorithm based on a dataset of protein targets derived from the MDL Drug Data Report. A 15-fold Monte Carlo cross-validation using 50% of each class for training, and the remaining 50% for testing, provided an assessment of the accuracy of that model. We retained the 3 top-ranking predictions and found that in 82% of all cases the correct target was predicted within these three predictions. The first prediction was the correct one in almost 70% of cases. A model built on the whole protein target dataset was then used to predict the protein targets for 150 000 molecules from the MDL Toxicity Database. We analysed the frequency of the predictions across the panel of protein targets for experimentally determined toxicity classes of all molecules. This allowed us to identify clusters of proteins related by their toxicological profiles, as well as toxicities that are related. Literature-based evidence is provided for some specific clusters to show the relevance of the relationships identified

Protein homology model refinement by large-scale energy optimization.

Science.gov (United States)

Park, Hahnbeom; Ovchinnikov, Sergey; Kim, David E; DiMaio, Frank; Baker, David

2018-03-20

Proteins fold to their lowest free-energy structures, and hence the most straightforward way to increase the accuracy of a partially incorrect protein structure model is to search for the lowest-energy nearby structure. This direct approach has met with little success for two reasons: first, energy function inaccuracies can lead to false energy minima, resulting in model degradation rather than improvement; and second, even with an accurate energy function, the search problem is formidable because the energy only drops considerably in the immediate vicinity of the global minimum, and there are a very large number of degrees of freedom. Here we describe a large-scale energy optimization-based refinement method that incorporates advances in both search and energy function accuracy that can substantially improve the accuracy of low-resolution homology models. The method refined low-resolution homology models into correct folds for 50 of 84 diverse protein families and generated improved models in recent blind structure prediction experiments. Analyses of the basis for these improvements reveal contributions from both the improvements in conformational sampling techniques and the energy function.

Capacity constrained assignment in spatial databases

DEFF Research Database (Denmark)

U, Leong Hou; Yiu, Man Lung; Mouratidis, Kyriakos

2008-01-01

large to fit in main memory. Motivated by this fact, we propose efficient algorithms for optimal assignment that employ novel edge-pruning strategies, based on the spatial properties of the problem. Additionally, we develop approximate (i.e., suboptimal) CCA solutions that provide a trade-off between...

rRNA maturation in yeast cells depleted of large ribosomal subunit proteins.

Directory of Open Access Journals (Sweden)

Gisela Pöll

Full Text Available The structural constituents of the large eukaryotic ribosomal subunit are 3 ribosomal RNAs, namely the 25S, 5.8S and 5S rRNA and about 46 ribosomal proteins (r-proteins. They assemble and mature in a highly dynamic process that involves more than 150 proteins and 70 small RNAs. Ribosome biogenesis starts in the nucleolus, continues in the nucleoplasm and is completed after nucleo-cytoplasmic translocation of the subunits in the cytoplasm. In this work we created 26 yeast strains, each of which conditionally expresses one of the large ribosomal subunit (LSU proteins. In vivo depletion of the analysed LSU r-proteins was lethal and led to destabilisation and degradation of the LSU and/or its precursors. Detailed steady state and metabolic pulse labelling analyses of rRNA precursors in these mutant strains showed that LSU r-proteins can be grouped according to their requirement for efficient progression of different steps of large ribosomal subunit maturation. Comparative analyses of the observed phenotypes and the nature of r-protein-rRNA interactions as predicted by current atomic LSU structure models led us to discuss working hypotheses on i how individual r-proteins control the productive processing of the major 5' end of 5.8S rRNA precursors by exonucleases Rat1p and Xrn1p, and ii the nature of structural characteristics of nascent LSUs that are required for cytoplasmic accumulation of nascent subunits but are nonessential for most of the nuclear LSU pre-rRNA processing events.

Traffic assignment models in large-scale applications

DEFF Research Database (Denmark)

Rasmussen, Thomas Kjær

the potential of the method proposed and the possibility to use individual-based GPS units for travel surveys in real-life large-scale multi-modal networks. Congestion is known to highly influence the way we act in the transportation network (and organise our lives), because of longer travel times...... of observations of actual behaviour to obtain estimates of the (monetary) value of different travel time components, thereby increasing the behavioural realism of largescale models. vii The generation of choice sets is a vital component in route choice models. This is, however, not a straight-forward task in real......, but the reliability of the travel time also has a large impact on our travel choices. Consequently, in order to improve the realism of transport models, correct understanding and representation of two values that are related to the value of time (VoT) are essential: (i) the value of congestion (VoC), as the Vo...

Pythoscape: a framework for generation of large protein similarity networks.

Science.gov (United States)

Barber, Alan E; Babbitt, Patricia C

2012-11-01

Pythoscape is a framework implemented in Python for processing large protein similarity networks for visualization in other software packages. Protein similarity networks are graphical representations of sequence, structural and other similarities among proteins for which pairwise all-by-all similarity connections have been calculated. Mapping of biological and other information to network nodes or edges enables hypothesis creation about sequence-structure-function relationships across sets of related proteins. Pythoscape provides several options to calculate pairwise similarities for input sequences or structures, applies filters to network edges and defines sets of similar nodes and their associated data as single nodes (termed representative nodes) for compression of network information and output data or formatted files for visualization.

Privacy-Preserving Task Assignment in Spatial Crowdsourcing

KAUST Repository

Liu, An

2017-09-20

With the progress of mobile devices and wireless networks, spatial crowdsourcing (SC) is emerging as a promising approach for problem solving. In SC, spatial tasks are assigned to and performed by a set of human workers. To enable effective task assignment, however, both workers and task requesters are required to disclose their locations to untrusted SC systems. In this paper, we study the problem of assigning workers to tasks in a way that location privacy for both workers and task requesters is preserved. We first combine the Paillier cryptosystem with Yao’s garbled circuits to construct a secure protocol that assigns the nearest worker to a task. Considering that this protocol cannot scale to a large number of workers, we then make use of Geohash, a hierarchical spatial index to design a more efficient protocol that can securely find approximate nearest workers. We theoretically show that these two protocols are secure against semi-honest adversaries. Through extensive experiments on two real-world datasets, we demonstrate the efficiency and effectiveness of our protocols.

An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database

International Nuclear Information System (INIS)

Kobayashi, Naohiro; Harano, Yoko; Tochio, Naoya; Nakatani, Eiichi; Kigawa, Takanori; Yokoyama, Shigeyuki; Mading, Steve; Ulrich, Eldon L.; Markley, John L.; Akutsu, Hideo; Fujiwara, Toshimichi

2012-01-01

Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including 1 H, 13 C and 15 N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001–2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies.

Detecting differential protein expression in large-scale population proteomics

Energy Technology Data Exchange (ETDEWEB)

Ryu, Soyoung; Qian, Weijun; Camp, David G.; Smith, Richard D.; Tompkins, Ronald G.; Davis, Ronald W.; Xiao, Wenzhong

2014-06-17

Mass spectrometry-based high-throughput quantitative proteomics shows great potential in clinical biomarker studies, identifying and quantifying thousands of proteins in biological samples. However, methods are needed to appropriately handle issues/challenges unique to mass spectrometry data in order to detect as many biomarker proteins as possible. One issue is that different mass spectrometry experiments generate quite different total numbers of quantified peptides, which can result in more missing peptide abundances in an experiment with a smaller total number of quantified peptides. Another issue is that the quantification of peptides is sometimes absent, especially for less abundant peptides and such missing values contain the information about the peptide abundance. Here, we propose a Significance Analysis for Large-scale Proteomics Studies (SALPS) that handles missing peptide intensity values caused by the two mechanisms mentioned above. Our model has a robust performance in both simulated data and proteomics data from a large clinical study. Because varying patients’ sample qualities and deviating instrument performances are not avoidable for clinical studies performed over the course of several years, we believe that our approach will be useful to analyze large-scale clinical proteomics data.

METHODOLOGY AND CALCULATIONS FOR THE ASSIGNMENT OF WASTE GROUPS FOR THE LARGE UNDERGROUND WASTE STORAGE TANKS AT THE HANFORD SITE

Energy Technology Data Exchange (ETDEWEB)

WEBER RA

2009-01-16

The Hanford Site contains 177 large underground radioactive waste storage tanks (28 double-shell tanks and 149 single-shell tanks). These tanks are categorized into one of three waste groups (A, B, and C) based on their waste and tank characteristics. These waste group assignments reflect a tank's propensity to retain a significant volume of flammable gases and the potential of the waste to release retained gas by a buoyant displacement gas release event. Assignments of waste groups to the 177 double-shell tanks and single-shell tanks, as reported in this document, are based on a Monte Carlo analysis of three criteria. The first criterion is the headspace flammable gas concentration following release of retained gas. This criterion determines whether the tank contains sufficient retained gas such that the well-mixed headspace flammable gas concentration would reach 100% of the lower flammability limit if the entire tank's retained gas were released. If the volume of retained gas is not sufficient to reach 100% of the lower flammability limit, then flammable conditions cannot be reached and the tank is classified as a waste group C tank independent of the method the gas is released. The second criterion is the energy ratio and considers whether there is sufficient supernatant on top of the saturated solids such that gas-bearing solids have the potential energy required to break up the material and release gas. Tanks that are not waste group C tanks and that have an energy ratio < 3.0 do not have sufficient potential energy to break up material and release gas and are assigned to waste group B. These tanks are considered to represent a potential induced flammable gas release hazard, but no spontaneous buoyant displacement flammable gas release hazard. Tanks that are not waste group C tanks and have an energy ratio {ge} 3.0, but that pass the third criterion (buoyancy ratio < 1.0, see below) are also assigned to waste group B. Even though the designation as

METHODOLOGY AND CALCULATIONS FOR THE ASSIGNMENT OF WASTE GROUPS FOR THE LARGE UNDERGROUND WASTE STORAGE TANKS AT THE HANFORD SITE

Energy Technology Data Exchange (ETDEWEB)

FOWLER KD

2007-12-27

This document categorizes each of the large waste storage tanks into one of several categories based on each tank's waste characteristics. These waste group assignments reflect a tank's propensity to retain a significant volume of flammable gases and the potential of the waste to release retained gas by a buoyant displacement event. Revision 7 is the annual update of the calculations of the flammable gas Waste Groups for DSTs and SSTs. The Hanford Site contains 177 large underground radioactive waste storage tanks (28 double-shell tanks and 149 single-shell tanks). These tanks are categorized into one of three waste groups (A, B, and C) based on their waste and tank characteristics. These waste group assignments reflect a tank's propensity to retain a significant volume of flammable gases and the potential of the waste to release retained gas by a buoyant displacement gas release event. Assignments of waste groups to the 177 double-shell tanks and single-shell tanks, as reported in this document, are based on a Monte Carlo analysis of three criteria. The first criterion is the headspace flammable gas concentration following release of retained gas. This criterion determines whether the tank contains sufficient retained gas such that the well-mixed headspace flammable gas concentration would reach 100% of the lower flammability limit if the entire tank's retained gas were released. If the volume of retained gas is not sufficient to reach 100% of the lower flammability limit, then flammable conditions cannot be reached and the tank is classified as a waste group C tank independent of the method the gas is released. The second criterion is the energy ratio and considers whether there is sufficient supernatant on top of the saturated solids such that gas-bearing solids have the potential energy required to break up the material and release gas. Tanks that are not waste group C tanks and that have an energy ratio < 3.0 do not have sufficient

Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament

Science.gov (United States)

Yu, Garmay; A, Shvetsov; D, Karelov; D, Lebedev; A, Radulescu; M, Petukhov; V, Isaev-Ivanov

2012-02-01

Based on X-ray crystallographic data available at Protein Data Bank, we have built molecular dynamics (MD) models of homologous recombinases RecA from E. coli and D. radiodurans. Functional form of RecA enzyme, which is known to be a long helical filament, was approximated by a trimer, simulated in periodic water box. The MD trajectories were analyzed in terms of large-scale conformational motions that could be detectable by neutron and X-ray scattering techniques. The analysis revealed that large-scale RecA monomer dynamics can be described in terms of relative motions of 7 subdomains. Motion of C-terminal domain was the major contributor to the overall dynamics of protein. Principal component analysis (PCA) of the MD trajectories in the atom coordinate space showed that rotation of C-domain is correlated with the conformational changes in the central domain and N-terminal domain, that forms the monomer-monomer interface. Thus, even though C-terminal domain is relatively far from the interface, its orientation is correlated with large-scale filament conformation. PCA of the trajectories in the main chain dihedral angle coordinate space implicates a co-existence of a several different large-scale conformations of the modeled trimer. In order to clarify the relationship of independent domain orientation with large-scale filament conformation, we have performed analysis of independent domain motion and its implications on the filament geometry.

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

Science.gov (United States)

Tang, Qingling; Fenton, Aron W

2017-09-01

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

Accelerating large-scale protein structure alignments with graphics processing units

Directory of Open Access Journals (Sweden)

Pang Bin

2012-02-01

Full Text Available Abstract Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs. As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU.

Incentivized optimal advert assignment via utility decomposition

NARCIS (Netherlands)

Kelly, F.; Key, P.; Walton, N.

2014-01-01

We consider a large-scale Ad-auction where adverts are assigned over a potentially infinite number of searches. We capture the intrinsic asymmetries in information between advertisers, the advert platform and the space of searches: advertisers know and can optimize the average performance of their

An efficient randomized algorithm for contact-based NMR backbone resonance assignment.

Science.gov (United States)

Kamisetty, Hetunandan; Bailey-Kellogg, Chris; Pandurangan, Gopal

2006-01-15

Backbone resonance assignment is a critical bottleneck in studies of protein structure, dynamics and interactions by nuclear magnetic resonance (NMR) spectroscopy. A minimalist approach to assignment, which we call 'contact-based', seeks to dramatically reduce experimental time and expense by replacing the standard suite of through-bond experiments with the through-space (nuclear Overhauser enhancement spectroscopy, NOESY) experiment. In the contact-based approach, spectral data are represented in a graph with vertices for putative residues (of unknown relation to the primary sequence) and edges for hypothesized NOESY interactions, such that observed spectral peaks could be explained if the residues were 'close enough'. Due to experimental ambiguity, several incorrect edges can be hypothesized for each spectral peak. An assignment is derived by identifying consistent patterns of edges (e.g. for alpha-helices and beta-sheets) within a graph and by mapping the vertices to the primary sequence. The key algorithmic challenge is to be able to uncover these patterns even when they are obscured by significant noise. This paper develops, analyzes and applies a novel algorithm for the identification of polytopes representing consistent patterns of edges in a corrupted NOESY graph. Our randomized algorithm aggregates simplices into polytopes and fixes inconsistencies with simple local modifications, called rotations, that maintain most of the structure already uncovered. In characterizing the effects of experimental noise, we employ an NMR-specific random graph model in proving that our algorithm gives optimal performance in expected polynomial time, even when the input graph is significantly corrupted. We confirm this analysis in simulation studies with graphs corrupted by up to 500% noise. Finally, we demonstrate the practical application of the algorithm on several experimental beta-sheet datasets. Our approach is able to eliminate a large majority of noise edges and to

Solid-state NMR analysis of membrane proteins and protein aggregates by proton detected spectroscopy

International Nuclear Information System (INIS)

Zhou, Donghua H.; Nieuwkoop, Andrew J.; Berthold, Deborah A.; Comellas, Gemma; Sperling, Lindsay J.; Tang, Ming; Shah, Gautam J.; Brea, Elliott J.; Lemkau, Luisel R.; Rienstra, Chad M.

2012-01-01

Solid-state NMR has emerged as an important tool for structural biology and chemistry, capable of solving atomic-resolution structures for proteins in membrane-bound and aggregated states. Proton detection methods have been recently realized under fast magic-angle spinning conditions, providing large sensitivity enhancements for efficient examination of uniformly labeled proteins. The first and often most challenging step of protein structure determination by NMR is the site-specific resonance assignment. Here we demonstrate resonance assignments based on high-sensitivity proton-detected three-dimensional experiments for samples of different physical states, including a fully-protonated small protein (GB1, 6 kDa), a deuterated microcrystalline protein (DsbA, 21 kDa), a membrane protein (DsbB, 20 kDa) prepared in a lipid environment, and the extended core of a fibrillar protein (α-synuclein, 14 kDa). In our implementation of these experiments, including CONH, CO(CA)NH, CANH, CA(CO)NH, CBCANH, and CBCA(CO)NH, dipolar-based polarization transfer methods have been chosen for optimal efficiency for relatively high protonation levels (full protonation or 100 % amide proton), fast magic-angle spinning conditions (40 kHz) and moderate proton decoupling power levels. Each H–N pair correlates exclusively to either intra- or inter-residue carbons, but not both, to maximize spectral resolution. Experiment time can be reduced by at least a factor of 10 by using proton detection in comparison to carbon detection. These high-sensitivity experiments are especially important for membrane proteins, which often have rather low expression yield. Proton-detection based experiments are expected to play an important role in accelerating protein structure elucidation by solid-state NMR with the improved sensitivity and resolution.

BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures

Science.gov (United States)

Sarti, E.; Zamuner, S.; Cossio, P.; Laio, A.; Seno, F.; Trovato, A.

2013-12-01

In protein structure prediction it is of crucial importance, especially at the refinement stage, to score efficiently large sets of models by selecting the ones that are closest to the native state. We here present a new computational tool, BACHSCORE, that allows its users to rank different structural models of the same protein according to their quality, evaluated by using the BACH++ (Bayesian Analysis Conformation Hunt) scoring function. The original BACH statistical potential was already shown to discriminate with very good reliability the protein native state in large sets of misfolded models of the same protein. BACH++ features a novel upgrade in the solvation potential of the scoring function, now computed by adapting the LCPO (Linear Combination of Pairwise Orbitals) algorithm. This change further enhances the already good performance of the scoring function. BACHSCORE can be accessed directly through the web server: bachserver.pd.infn.it. Catalogue identifier: AEQD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQD_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 130159 No. of bytes in distributed program, including test data, etc.: 24 687 455 Distribution format: tar.gz Programming language: C++. Computer: Any computer capable of running an executable produced by a g++ compiler (4.6.3 version). Operating system: Linux, Unix OS-es. RAM: 1 073 741 824 bytes Classification: 3. Nature of problem: Evaluate the quality of a protein structural model, taking into account the possible “a priori” knowledge of a reference primary sequence that may be different from the amino-acid sequence of the model; the native protein structure should be recognized as the best model. Solution method: The contact potential scores the occurrence of any given type of residue pair in 5 possible

Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions.

Science.gov (United States)

Delaforge, Elise; Milles, Sigrid; Huang, Jie-Rong; Bouvier, Denis; Jensen, Malene Ringkjøbing; Sattler, Michael; Hart, Darren J; Blackledge, Martin

2016-01-01

Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales.

Luminescent conjugated oligothiophenes for sensitive fluorescent assignment of protein inclusion bodies.

Science.gov (United States)

Klingstedt, Therése; Blechschmidt, Cristiane; Nogalska, Anna; Prokop, Stefan; Häggqvist, Bo; Danielsson, Olof; Engel, W King; Askanas, Valerie; Heppner, Frank L; Nilsson, K Peter R

2013-03-18

Small hydrophobic ligands identifying intracellular protein deposits are of great interest, as protein inclusion bodies are the pathological hallmark of several degenerative diseases. Here we report that fluorescent amyloid ligands, termed luminescent conjugated oligothiophenes (LCOs), rapidly and with high sensitivity detect protein inclusion bodies in skeletal muscle tissue from patients with sporadic inclusion body myositis (s-IBM). LCOs having a conjugated backbone of at least five thiophene units emitted strong fluorescence upon binding, and showed co-localization with proteins reported to accumulate in s-IBM protein inclusion bodies. Compared with conventional amyloid ligands, LCOs identified a larger fraction of immunopositive inclusion bodies. When the conjugated thiophene backbone was extended with terminal carboxyl groups, the LCO revealed striking spectral differences between distinct protein inclusion bodies. We conclude that 1) LCOs are sensitive, rapid and powerful tools for identifying protein inclusion bodies and 2) LCOs identify a wider range of protein inclusion bodies than conventional amyloid ligands. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

Science.gov (United States)

Pritišanac, Iva; Degiacomi, Matteo T; Alderson, T Reid; Carneiro, Marta G; Ab, Eiso; Siegal, Gregg; Baldwin, Andrew J

2017-07-19

Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity. MAGMA gives 100% accuracy in confident assignments when tested against both synthetic data, and 9 cross-validated examples using both solution- and solid-state NMR data. We show that this remarkable accuracy enables a user to distinguish between alternative protein structures. In a drug discovery application on HSP90, we show the method can rapidly and efficiently distinguish between possible ligand binding modes. By providing an exact and robust solution to methyl resonance assignment, MAGMA can facilitate significantly accelerated studies of supramolecular machines using methyl-based NMR spectroscopy.

Effortless assignment with 4D covariance sequential correlation maps.

Science.gov (United States)

Harden, Bradley J; Mishra, Subrata H; Frueh, Dominique P

2015-11-01

Traditional Nuclear Magnetic Resonance (NMR) assignment procedures for proteins rely on preliminary peak-picking to identify and label NMR signals. However, such an approach has severe limitations when signals are erroneously labeled or completely neglected. The consequences are especially grave for proteins with substantial peak overlap, and mistakes can often thwart entire projects. To overcome these limitations, we previously introduced an assignment technique that bypasses traditional pick peaking altogether. Covariance Sequential Correlation Maps (COSCOMs) transform the indirect connectivity information provided by multiple 3D backbone spectra into direct (H, N) to (H, N) correlations. Here, we present an updated method that utilizes a single four-dimensional spectrum rather than a suite of three-dimensional spectra. We demonstrate the advantages of 4D-COSCOMs relative to their 3D counterparts. We introduce improvements accelerating their calculation. We discuss practical considerations affecting their quality. And finally we showcase their utility in the context of a 52 kDa cyclization domain from a non-ribosomal peptide synthetase. Copyright © 2015 Elsevier Inc. All rights reserved.

Light-fuelled transport of large dendrimers and proteins.

Science.gov (United States)

Koskela, Jenni E; Liljeström, Ville; Lim, Jongdoo; Simanek, Eric E; Ras, Robin H A; Priimagi, Arri; Kostiainen, Mauri A

2014-05-14

This work presents a facile water-based supramolecular approach for light-induced surface patterning. The method is based upon azobenzene-functionalized high-molecular weight triazine dendrimers up to generation 9, demonstrating that even very large globular supramolecular complexes can be made to move in response to light. We also demonstrate light-fuelled macroscopic movements in native biomolecules, showing that complexes of apoferritin protein and azobenzene can effectively form light-induced surface patterns. Fundamentally, the results establish that thin films comprising both flexible and rigid globular particles of large diameter can be moved with light, whereas the presented material concepts offer new possibilities for the yet marginally explored biological applications of azobenzene surface patterning.

Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex.

Science.gov (United States)

Tuttle, Lisa M; Pacheco, Derek; Warfield, Linda; Luo, Jie; Ranish, Jeff; Hahn, Steven; Klevit, Rachel E

2018-03-20

Transcription activation domains (ADs) are inherently disordered proteins that often target multiple coactivator complexes, but the specificity of these interactions is not understood. Efficient transcription activation by yeast Gcn4 requires its tandem ADs and four activator-binding domains (ABDs) on its target, the Mediator subunit Med15. Multiple ABDs are a common feature of coactivator complexes. We find that the large Gcn4-Med15 complex is heterogeneous and contains nearly all possible AD-ABD interactions. Gcn4-Med15 forms via a dynamic fuzzy protein-protein interface, where ADs bind the ABDs in multiple orientations via hydrophobic regions that gain helicity. This combinatorial mechanism allows individual low-affinity and specificity interactions to generate a biologically functional, specific, and higher affinity complex despite lacking a defined protein-protein interface. This binding strategy is likely representative of many activators that target multiple coactivators, as it allows great flexibility in combinations of activators that can cooperate to regulate genes with variable coactivator requirements. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions

Directory of Open Access Journals (Sweden)

Elise Delaforge

2016-09-01

Full Text Available Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales.

Effects of NMR spectral resolution on protein structure calculation.

Directory of Open Access Journals (Sweden)

Suhas Tikole

Full Text Available Adequate digital resolution and signal sensitivity are two critical factors for protein structure determinations by solution NMR spectroscopy. The prime objective for obtaining high digital resolution is to resolve peak overlap, especially in NOESY spectra with thousands of signals where the signal analysis needs to be performed on a large scale. Achieving maximum digital resolution is usually limited by the practically available measurement time. We developed a method utilizing non-uniform sampling for balancing digital resolution and signal sensitivity, and performed a large-scale analysis of the effect of the digital resolution on the accuracy of the resulting protein structures. Structure calculations were performed as a function of digital resolution for about 400 proteins with molecular sizes ranging between 5 and 33 kDa. The structural accuracy was assessed by atomic coordinate RMSD values from the reference structures of the proteins. In addition, we monitored also the number of assigned NOESY cross peaks, the average signal sensitivity, and the chemical shift spectral overlap. We show that high resolution is equally important for proteins of every molecular size. The chemical shift spectral overlap depends strongly on the corresponding spectral digital resolution. Thus, knowing the extent of overlap can be a predictor of the resulting structural accuracy. Our results show that for every molecular size a minimal digital resolution, corresponding to the natural linewidth, needs to be achieved for obtaining the highest accuracy possible for the given protein size using state-of-the-art automated NOESY assignment and structure calculation methods.

Privacy-Preserving Task Assignment in Spatial Crowdsourcing

KAUST Repository

Liu, An; Li, Zhi-Xu; Liu, Guan-Feng; Zheng, Kai; Zhang, Min; Li, Qing; Zhang, Xiangliang

2017-01-01

untrusted SC systems. In this paper, we study the problem of assigning workers to tasks in a way that location privacy for both workers and task requesters is preserved. We first combine the Paillier cryptosystem with Yao’s garbled circuits to construct a secure protocol that assigns the nearest worker to a task. Considering that this protocol cannot scale to a large number of workers, we then make use of Geohash, a hierarchical spatial index to design a more efficient protocol that can securely find approximate nearest workers. We theoretically show that these two protocols are secure against semi-honest adversaries. Through extensive experiments on two real-world datasets, we demonstrate the efficiency and effectiveness of our protocols.

Designing Internet research assignments: building a framework for instructor collaboration

Directory of Open Access Journals (Sweden)

David Ward

2000-01-01

Full Text Available Internet knowledge is increasing steadily among instructors in the academic world. As courses incorporate more instructional technology, traditional undergraduate research assignments are adapting to reflect the changing world of information and information access. New library assignments reflect this shift as well, with term papers and research projects asking students to use Web sites as an information resource, in addition to the standard literature of periodicals and monographs. But the many pitfalls the library profession has learned in its own metamorphosis during the past decade are often repeated in these newer course assignments. The authors in this paper present a framework for librarians to interact with instructors to incorporate Internet resources into traditional term paper and research assignments. They suggest a framework for creating sample assignments librarians can take to campus instructional units, to show the teaching community at large what the library profession has learned from first-hand experience.

Solving Large Quadratic|Assignment Problems in Parallel

DEFF Research Database (Denmark)

Clausen, Jens; Perregaard, Michael

1997-01-01

and recalculation of bounds between branchings when used in a parallel Branch-and-Bound algorithm. The algorithm has been implemented on a 16-processor MEIKO Computing Surface with Intel i860 processors. Computational results from the solution of a number of large QAPs, including the classical Nugent 20...... processors, and have hence not been ideally suited for computations essentially involving non-vectorizable computations on integers.In this paper we investigate the combination of one of the best bound functions for a Branch-and-Bound algorithm (the Gilmore-Lawler bound) and various testing, variable binding...

Large protein as a potential target for use in rabies diagnostics.

Science.gov (United States)

Santos Katz, I S; Dias, M H; Lima, I F; Chaves, L B; Ribeiro, O G; Scheffer, K C; Iwai, L K

Rabies is a zoonotic viral disease that remains a serious threat to public health worldwide. The rabies lyssavirus (RABV) genome encodes five structural proteins, multifunctional and significant for pathogenicity. The large protein (L) presents well-conserved genomic regions, which may be a good alternative to generate informative datasets for development of new methods for rabies diagnosis. This paper describes the development of a technique for the identification of L protein in several RABV strains from different hosts, demonstrating that MS-based proteomics is a potential method for antigen identification and a good alternative for rabies diagnosis.

Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a

International Nuclear Information System (INIS)

Zuiderweg, E.R.P.; Fesik, S.W.

1989-01-01

The utility of three-dimensional heteronuclear NMR spectroscopy for the assignment of 1 H and 15 N resonances of the inflammatory protein C5a (MW 8500), uniformly labeled with 15 N, is demonstrated at a protein concentration of 0.7 mM. It is shown that dramatic simplification of the 2D nuclear Overhauser effect spectrum (NOESY) is obtained by editing with respect to the frequency of the 15 N heteronucleus in a third dimension. The improved resolution in the 3D experiment largely facilitates the assignment of protein NMR spectra and allows for the determination of distance constraints from otherwise overlapping NOE cross peaks for purposes of 3D structure determination. The results show that 15 N heteronuclear 3D NMR can facilitate the structure determination of small proteins and promises to be a useful tool for the study of larger systems that cannot be studied by conventional 2D NMR techniques

Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a

Energy Technology Data Exchange (ETDEWEB)

Zuiderweg, E.R.P.; Fesik, S.W. (Abbott Laboratories, Abbott Park, IL (USA))

1989-03-21

The utility of three-dimensional heteronuclear NMR spectroscopy for the assignment of {sup 1}H and {sup 15}N resonances of the inflammatory protein C5a (MW 8500), uniformly labeled with {sup 15}N, is demonstrated at a protein concentration of 0.7 mM. It is shown that dramatic simplification of the 2D nuclear Overhauser effect spectrum (NOESY) is obtained by editing with respect to the frequency of the {sup 15}N heteronucleus in a third dimension. The improved resolution in the 3D experiment largely facilitates the assignment of protein NMR spectra and allows for the determination of distance constraints from otherwise overlapping NOE cross peaks for purposes of 3D structure determination. The results show that {sup 15}N heteronuclear 3D NMR can facilitate the structure determination of small proteins and promises to be a useful tool for the study of larger systems that cannot be studied by conventional 2D NMR techniques.

TROSY of side-chain amides in large proteins

Science.gov (United States)

Liu, Aizhuo; Yao, Lishan; Li, Yue; Yan, Honggao

2012-01-01

By using the mixed solvent of 50% H2O/50% D2O and employing deuterium decoupling, TROSY experiments exclusively detect NMR signals from semideuterated isotopomers of carboxamide groups with high sensitivities for proteins with molecular weights up to 80 kDa. This isotopomer-selective strategy extends TROSY experiments from exclusively detecting backbone to both backbone and side-chain amides, particularly in large proteins. Because of differences in both TROSY effect and dynamics between 15N–HE{DZ} and 15N–HZ{DE} isotopomers of the same carboxamide, the 15N transverse magnetization of the latter relaxes significantly faster than that of the former, which provides a direct and reliable stereospecific distinction between the two configurations. The TROSY effects on the 15N–HE{DZ} isotopomers of side-chain amides are as significant as on backbone amides. PMID:17347000

Grouping puts figure-ground assignment in context by constraining propagation of edge assignment.

Science.gov (United States)

Brooks, Joseph L; Brook, Joseph L; Driver, Jon

2010-05-01

Figure-ground organization involves the assignment of edges to a figural shape on one or the other side of each dividing edge. Established visual cues for edge assignment primarily concern relatively local rather than contextual factors. In the present article, we show that an assignment for a locally unbiased edge can be affected by an assignment of a remote contextual edge that has its own locally biased assignment. We find that such propagation of edge assignment from the biased remote context occurs only when the biased and unbiased edges are grouped. This new principle, whereby grouping constrains the propagation of figural edge assignment, emerges from both subjective reports and an objective short-term edge-matching task. It generalizes from moving displays involving grouping by common fate and collinearity, to static displays with grouping by similarity of edge-contrast polarity, or apparent occlusion. Our results identify a new contextual influence on edge assignment. They also identify a new mechanistic relation between grouping and figure-ground processes, whereby grouping between remote elements can constrain the propagation of edge assignment between those elements. Supplemental materials for this article may be downloaded from http://app.psychonomic-journals.org/content/supplemental.

FLEET ASSIGNMENT MODELLING

Directory of Open Access Journals (Sweden)

2016-01-01

Full Text Available The article is devoted to the airline scheduling process and methods of its modeling. This article describes the main stages of airline scheduling process (scheduling, fleet assignment, revenue management, operations, their features and interactions. The main part of scheduling process is fleet assignment. The optimal solution of the fleet assignment problem enables airlines to increase their incomes up to 3 % due to quality improving of connections and execution of the planned number of flights operated by less number of aircraft than usual or planned earlier. Fleet assignment of scheduling process is examined and Conventional Leg-Based Fleet Assignment Model is analyzed. Finally strong and weak aspects of the model (SWOT are released and applied. The article gives a critical analysis of FAM model, with the purpose of identi- fying possible options and constraints of its use (for example, in cases of short-term and long-term planning, changing the schedule or replacing the aircraft, as well as possible ways to improve the model.

Sequence-specific assignment of methyl groups from the neuronal SNARE complex using lanthanide-induced pseudocontact shifts

International Nuclear Information System (INIS)

Pan, Yun-Zu; Quade, Bradley; Brewer, Kyle D.; Szabo, Monika; Swarbrick, James D.; Graham, Bim; Rizo, Josep

2016-01-01

Neurotransmitter release depends critically on the neuronal SNARE complex formed by syntaxin-1, SNAP-25 and synaptobrevin, as well as on other proteins such as Munc18-1, Munc13-1 and synaptotagmin-1. Although three-dimensional structures are available for these components, it is still unclear how they are assembled between the synaptic vesicle and plasma membranes to trigger fast, Ca 2+ -dependent membrane fusion. Methyl TROSY NMR experiments provide a powerful tool to study complexes between these proteins, but assignment of the methyl groups of the SNARE complex is hindered by its limited solubility. Here we report the assignment of the isoleucine, leucine, methionine and valine methyl groups of the four SNARE motifs of syntaxin-1, SNAP-25 and synaptobrevin within the SNARE complex based solely on measurements of lanthanide-induced pseudocontact shifts. Our results illustrate the power of this approach to assign protein resonances without the need of triple resonance experiments and provide an invaluable tool for future structural studies of how the SNARE complex binds to other components of the release machinery.

Sequence-specific assignment of methyl groups from the neuronal SNARE complex using lanthanide-induced pseudocontact shifts

Energy Technology Data Exchange (ETDEWEB)

Pan, Yun-Zu; Quade, Bradley; Brewer, Kyle D. [University of Texas Southwestern Medical Center, Department of Biophysics (United States); Szabo, Monika; Swarbrick, James D.; Graham, Bim [Monash Institute of Pharmaceutical Sciences, Monash University (Australia); Rizo, Josep, E-mail: Jose.Rizo-Rey@UTSouthwestern.edu [University of Texas Southwestern Medical Center, Department of Biophysics (United States)

2016-12-15

Neurotransmitter release depends critically on the neuronal SNARE complex formed by syntaxin-1, SNAP-25 and synaptobrevin, as well as on other proteins such as Munc18-1, Munc13-1 and synaptotagmin-1. Although three-dimensional structures are available for these components, it is still unclear how they are assembled between the synaptic vesicle and plasma membranes to trigger fast, Ca{sup 2+}-dependent membrane fusion. Methyl TROSY NMR experiments provide a powerful tool to study complexes between these proteins, but assignment of the methyl groups of the SNARE complex is hindered by its limited solubility. Here we report the assignment of the isoleucine, leucine, methionine and valine methyl groups of the four SNARE motifs of syntaxin-1, SNAP-25 and synaptobrevin within the SNARE complex based solely on measurements of lanthanide-induced pseudocontact shifts. Our results illustrate the power of this approach to assign protein resonances without the need of triple resonance experiments and provide an invaluable tool for future structural studies of how the SNARE complex binds to other components of the release machinery.

Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex

Directory of Open Access Journals (Sweden)

Lisa M. Tuttle

2018-03-01

Full Text Available Summary: Transcription activation domains (ADs are inherently disordered proteins that often target multiple coactivator complexes, but the specificity of these interactions is not understood. Efficient transcription activation by yeast Gcn4 requires its tandem ADs and four activator-binding domains (ABDs on its target, the Mediator subunit Med15. Multiple ABDs are a common feature of coactivator complexes. We find that the large Gcn4-Med15 complex is heterogeneous and contains nearly all possible AD-ABD interactions. Gcn4-Med15 forms via a dynamic fuzzy protein-protein interface, where ADs bind the ABDs in multiple orientations via hydrophobic regions that gain helicity. This combinatorial mechanism allows individual low-affinity and specificity interactions to generate a biologically functional, specific, and higher affinity complex despite lacking a defined protein-protein interface. This binding strategy is likely representative of many activators that target multiple coactivators, as it allows great flexibility in combinations of activators that can cooperate to regulate genes with variable coactivator requirements. : Tuttle et al. report a “fuzzy free-for-all” interaction mechanism that explains how seemingly unrelated transcription activators converge on a limited number of coactivator targets. The mechanism provides a rationale for the observation that individually weak and low-specificity interactions can combine to produce biologically critical function without requiring highly ordered structure. Keywords: transcription activation, intrinsically disordered proteins, fuzzy binding

Incorporating breeding abundance into spatial assignments on continuous surfaces.

Science.gov (United States)

Rushing, Clark S; Marra, Peter P; Studds, Colin E

2017-06-01

Determining the geographic connections between breeding and nonbreeding populations, termed migratory connectivity, is critical to advancing our understanding of the ecology and conservation of migratory species. Assignment models based on stable isotopes historically have been an important tool for studying migratory connectivity of small-bodied species, but the low resolution of these assignments has generated interest into combining isotopes with other sources in information. Abundance is one of the most appealing data sources to include in isotope-based assignments, but there are currently no statistical methods or guidelines for optimizing the contribution of stable isotopes and abundance for inferring migratory connectivity. Using known-origin stable-hydrogen isotope samples of six Neotropical migratory bird species, we rigorously assessed the performance of assignment models that differentially weight the contribution of the isotope and abundance data. For two species with adequate sample sizes, we used Pareto optimality to determine the set of models that simultaneously minimized both assignment error rate and assignment area. We then assessed the ability of the top models from these two species to improve assignments of the remaining four species compared to assignments based on isotopes alone. We show that the increased precision of models that include abundance is often offset by a large increase in assignment error. However, models that optimally weigh the abundance data relative to the isotope data can result in higher precision and, in some cases, lower error than models based on isotopes alone. The top models, however, depended on the distribution of relative breeding abundance, with patchier distributions requiring stronger downweighting of abundance, and we present general guidelines for future studies. These results confirm that breeding abundance can be an important source of information for studies investigating broad-scale movements of

Interactive visual exploration and refinement of cluster assignments.

Science.gov (United States)

Kern, Michael; Lex, Alexander; Gehlenborg, Nils; Johnson, Chris R

2017-09-12

With ever-increasing amounts of data produced in biology research, scientists are in need of efficient data analysis methods. Cluster analysis, combined with visualization of the results, is one such method that can be used to make sense of large data volumes. At the same time, cluster analysis is known to be imperfect and depends on the choice of algorithms, parameters, and distance measures. Most clustering algorithms don't properly account for ambiguity in the source data, as records are often assigned to discrete clusters, even if an assignment is unclear. While there are metrics and visualization techniques that allow analysts to compare clusterings or to judge cluster quality, there is no comprehensive method that allows analysts to evaluate, compare, and refine cluster assignments based on the source data, derived scores, and contextual data. In this paper, we introduce a method that explicitly visualizes the quality of cluster assignments, allows comparisons of clustering results and enables analysts to manually curate and refine cluster assignments. Our methods are applicable to matrix data clustered with partitional, hierarchical, and fuzzy clustering algorithms. Furthermore, we enable analysts to explore clustering results in context of other data, for example, to observe whether a clustering of genomic data results in a meaningful differentiation in phenotypes. Our methods are integrated into Caleydo StratomeX, a popular, web-based, disease subtype analysis tool. We show in a usage scenario that our approach can reveal ambiguities in cluster assignments and produce improved clusterings that better differentiate genotypes and phenotypes.

A Review on Eigenstructure Assignment Methods and Orthogonal Eigenstructure Control of Structural Vibrations

Directory of Open Access Journals (Sweden)

Mohammad Rastgaar

2009-01-01

Full Text Available This paper provides a state-of-the-art review of eigenstructure assignment methods for vibration cancellation. Eigenstructure assignment techniques have been widely used during the past three decades for vibration suppression in structures, especially in large space structures. These methods work similar to mode localization in which global vibrations are managed such that they remain localized within the structure. Such localization would help reducing vibrations more effectively than other methods of vibration cancellation, by virtue of confining the vibrations close to the source of disturbance. The common objective of different methods of eigenstructure assignment is to provide controller design freedom beyond pole placement, and define appropriate shapes for the eigenvectors of the systems. These methods; however, offer a large and complex design space of options that can often overwhelm the control designer. Recent developments in orthogonal eigenstructure control offers a significant simplification of the design task while allowing some experience-based design freedom. The majority of the papers from the past three decades in structural vibration cancellation using eigenstructure assignment methods are reviewed, along with recent studies that introduce new developments in eigenstructure assignment techniques.

Thermodynamic database for proteins: features and applications.

Science.gov (United States)

Gromiha, M Michael; Sarai, Akinori

2010-01-01

We have developed a thermodynamic database for proteins and mutants, ProTherm, which is a collection of a large number of thermodynamic data on protein stability along with the sequence and structure information, experimental methods and conditions, and literature information. This is a valuable resource for understanding/predicting the stability of proteins, and it can be accessible at http://www.gibk26.bse.kyutech.ac.jp/jouhou/Protherm/protherm.html . ProTherm has several features including various search, display, and sorting options and visualization tools. We have analyzed the data in ProTherm to examine the relationship among thermodynamics, structure, and function of proteins. We describe the progress on the development of methods for understanding/predicting protein stability, such as (i) relationship between the stability of protein mutants and amino acid properties, (ii) average assignment method, (iii) empirical energy functions, (iv) torsion, distance, and contact potentials, and (v) machine learning techniques. The list of online resources for predicting protein stability has also been provided.

Simultaneous display of two large proteins on the head and tail of bacteriophage lambda

Science.gov (United States)

2013-01-01

Background Consistent progress in the development of bacteriophage lambda display platform as an alternative to filamentous phage display system was achieved in the recent years. The lambda phage has been engineered to display efficiently multiple copies of peptides or even large protein domains providing a powerful tool for screening libraries of peptides, proteins and cDNA. Results In the present work we describe an original method for dual display of large proteins on the surface of lambda particles. An anti-CEA single-chain antibody fragment and green fluorescent protein or alkaline phosphatase were simultaneously displayed by engineering both gpD and gpV lambda proteins. Conclusions Here we show that such modified phage particles can be used for the detection of target molecules in vitro and in vivo. Dual expression of functional moieties on the surface of the lambda phage might open the way to generation of a new class of diagnostic and therapeutic targeted nanoparticles. PMID:24073829

Backbone and sidechain 1H, 13C and 15N resonance assignments of the human brain-type fatty acid binding protein (FABP7) in its apo form and the holo forms binding to DHA, oleic acid, linoleic acid and elaidic acid

DEFF Research Database (Denmark)

Oeemig, Jesper S; Jørgensen, Mathilde L; Hansen, Mikka S

2009-01-01

In this manuscript, we present the backbone and side chain assignments of human brain-type fatty acid binding protein, also known as FABP7, in its apo form and in four different holo forms, bound to DHA, oleic acid, linoleic acid and elaidic acid.......In this manuscript, we present the backbone and side chain assignments of human brain-type fatty acid binding protein, also known as FABP7, in its apo form and in four different holo forms, bound to DHA, oleic acid, linoleic acid and elaidic acid....

Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples

Energy Technology Data Exchange (ETDEWEB)

Gopinath, T. [University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics (United States); Mote, Kaustubh R. [University of Minnesota, Department of Chemistry (United States); Veglia, Gianluigi, E-mail: vegli001@umn.edu [University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics (United States)

2015-05-15

We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living {sup 15}N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through {sup 15}N–{sup 15}N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish {sup 15}N–{sup 15}N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI–HETCOR and 3D PISEMAI–HETCOR-mixing experiments.

Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples.

Science.gov (United States)

Gopinath, T; Mote, Kaustubh R; Veglia, Gianluigi

2015-05-01

We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living (15)N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through (15)N-(15)N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish (15)N-(15)N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments.

Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples

International Nuclear Information System (INIS)

Gopinath, T.; Mote, Kaustubh R.; Veglia, Gianluigi

2015-01-01

We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living 15 N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through 15 N– 15 N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish 15 N– 15 N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI–HETCOR and 3D PISEMAI–HETCOR-mixing experiments

Nitrogen-detected CAN and CON experiments as alternative experiments for main chain NMR resonance assignments

International Nuclear Information System (INIS)

Takeuchi, Koh; Heffron, Gregory; Sun, Zhen-Yu J.; Frueh, Dominique P.; Wagner, Gerhard

2010-01-01

Heteronuclear direct-detection experiments, which utilize the slower relaxation properties of low γ nuclei, such as 13 C have recently been proposed for sequence-specific assignment and structural analyses of large, unstructured, and/or paramagnetic proteins. Here we present two novel 15 N direct-detection experiments. The CAN experiment sequentially connects amide 15 N resonances using 13 C α chemical shift matching, and the CON experiment connects the preceding 13 C' nuclei. When starting from the same carbon polarization, the intensities of nitrogen signals detected in the CAN or CON experiments would be expected four times lower than those of carbon resonances observed in the corresponding 13 C-detecting experiment, NCA-DIPAP or NCO-IPAP (Bermel et al. 2006b; Takeuchi et al. 2008). However, the disadvantage due to the lower γ is counteracted by the slower 15 N transverse relaxation during detection, the possibility for more efficient decoupling in both dimensions, and relaxation optimized properties of the pulse sequences. As a result, the median S/N in the 15 N observe CAN experiment is 16% higher than in the 13 C observe NCA-DIPAP experiment. In addition, significantly higher sensitivity was observed for those residues that are hard to detect in the NCA-DIPAP experiment, such as Gly, Ser and residues with high-field C α resonances. Both CAN and CON experiments are able to detect Pro resonances that would not be observed in conventional proton-detected experiments. In addition, those experiments are free from problems of incomplete deuterium-to-proton back exchange in amide positions of perdeuterated proteins expressed in D 2 O. Thus, these features and the superior resolution of 15 N-detected experiments provide an attractive alternative for main chain assignments. The experiments are demonstrated with the small model protein GB1 at conditions simulating a 150 kDa protein, and the 52 kDa glutathione S-transferase dimer, GST.

An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming

KAUST Repository

Abbas, Ahmed

2014-04-19

Despite significant advances in automated nuclear magnetic resonance-based protein structure determination, the high numbers of false positives and false negatives among the peaks selected by fully automated methods remain a problem. These false positives and negatives impair the performance of resonance assignment methods. One of the main reasons for this problem is that the computational research community often considers peak picking and resonance assignment to be two separate problems, whereas spectroscopists use expert knowledge to pick peaks and assign their resonances at the same time. We propose a novel framework that simultaneously conducts slice picking and spin system forming, an essential step in resonance assignment. Our framework then employs a genetic algorithm, directed by both connectivity information and amino acid typing information from the spin systems, to assign the spin systems to residues. The inputs to our framework can be as few as two commonly used spectra, i.e., CBCA(CO)NH and HNCACB. Different from the existing peak picking and resonance assignment methods that treat peaks as the units, our method is based on \\'slices\\', which are one-dimensional vectors in three-dimensional spectra that correspond to certain (N, H) values. Experimental results on both benchmark simulated data sets and four real protein data sets demonstrate that our method significantly outperforms the state-of-the-art methods while using a less number of spectra than those methods. Our method is freely available at http://sfb.kaust.edu.sa/Pages/Software.aspx. © 2014 Springer Science+Business Media.

Biodegradable Magnetic Silica@Iron Oxide Nanovectors with Ultra-Large Mesopores for High Protein Loading, Magnetothermal Release, and Delivery

KAUST Repository

Omar, Haneen

2016-11-29

The delivery of large cargos of diameter above 15 nm for biomedical applications has proved challenging since it requires biocompatible, stably-loaded, and biodegradable nanomaterials. In this study, we describe the design of biodegradable silica-iron oxide hybrid nanovectors with large mesopores for large protein delivery in cancer cells. The mesopores of the nanomaterials spanned from 20 to 60 nm in diameter and post-functionalization allowed the electrostatic immobilization of large proteins (e.g. mTFP-Ferritin, ~ 534 kDa). Half of the content of the nanovectors was based with iron oxide nanophases which allowed the rapid biodegradation of the carrier in fetal bovine serum and a magnetic responsiveness. The nanovectors released large protein cargos in aqueous solution under acidic pH or magnetic stimuli. The delivery of large proteins was then autonomously achieved in cancer cells via the silica-iron oxide nanovectors, which is thus a promising for biomedical applications.

UOP LDR 300 All Assignments New

OpenAIRE

ADMIN

2018-01-01

UOP LDR 300 All Assignments New Check this A+ tutorial guideline at http://www.ldr300assignment.com/ldr-300-uop/ldr-300-all-assignments-latest For more classes visit http://www.ldr300assignment.com LDR 300 Week 1 Assignment Leadership Assessment (2 Papers) LDR 300 Week 2 Assignment Leadership Theories Matrix (2 Set) LDR 300 Week 2 Assignment Formulating Leadership Part I (2 Papers) LDR 300 Week 3 Assignment Interaction and Influence Amo...

Comprehensive large-scale assessment of intrinsic protein disorder.

Science.gov (United States)

Walsh, Ian; Giollo, Manuel; Di Domenico, Tomás; Ferrari, Carlo; Zimmermann, Olav; Tosatto, Silvio C E

2015-01-15

Intrinsically disordered regions are key for the function of numerous proteins. Due to the difficulties in experimental disorder characterization, many computational predictors have been developed with various disorder flavors. Their performance is generally measured on small sets mainly from experimentally solved structures, e.g. Protein Data Bank (PDB) chains. MobiDB has only recently started to collect disorder annotations from multiple experimental structures. MobiDB annotates disorder for UniProt sequences, allowing us to conduct the first large-scale assessment of fast disorder predictors on 25 833 different sequences with X-ray crystallographic structures. In addition to a comprehensive ranking of predictors, this analysis produced the following interesting observations. (i) The predictors cluster according to their disorder definition, with a consensus giving more confidence. (ii) Previous assessments appear over-reliant on data annotated at the PDB chain level and performance is lower on entire UniProt sequences. (iii) Long disordered regions are harder to predict. (iv) Depending on the structural and functional types of the proteins, differences in prediction performance of up to 10% are observed. The datasets are available from Web site at URL: http://mobidb.bio.unipd.it/lsd. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Fair Package Assignment

Science.gov (United States)

Lahaie, Sébastien; Parkes, David C.

We consider the problem of fair allocation in the package assignment model, where a set of indivisible items, held by single seller, must be efficiently allocated to agents with quasi-linear utilities. A fair assignment is one that is efficient and envy-free. We consider a model where bidders have superadditive valuations, meaning that items are pure complements. Our central result is that core outcomes are fair and even coalition-fair over this domain, while fair distributions may not even exist for general valuations. Of relevance to auction design, we also establish that the core is equivalent to the set of anonymous-price competitive equilibria, and that superadditive valuations are a maximal domain that guarantees the existence of anonymous-price competitive equilibrium. Our results are analogs of core equivalence results for linear prices in the standard assignment model, and for nonlinear, non-anonymous prices in the package assignment model with general valuations.

Analyses of the Sequence and Structural Properties Corresponding to Pentapeptide and Large Palindromes in Proteins.

Directory of Open Access Journals (Sweden)

Settu Sridhar

Full Text Available The analyses of 3967 representative proteins selected from the Protein Data Bank revealed the presence of 2803 pentapeptide and large palindrome sequences with known secondary structure conformation. These represent 2014 unique palindrome sequences. 60% palindromes are not associated with any regular secondary structure and 28% are in helix conformation, 11% in strand conformation and 1% in the coil conformation. The average solvent accessibility values are in the range between 0-155.28 Å2 suggesting that the palindromes in proteins can be either buried, exposed to the solvent or share an intermittent property. The number of residue neighborhood contacts defined by interactions ≤ 3.2 Ǻ is in the range between 0-29 residues. Palindromes of the same length in helix, strand and coil conformation are associated with different amino acid residue preferences at the individual positions. Nearly, 20% palindromes interact with catalytic/active site residues, ligand or metal ions in proteins and may therefore be important for function in the corresponding protein. The average hydrophobicity values for the pentapeptide and large palindromes range between -4.3 to +4.32 and the number of palindromes is almost equally distributed between the negative and positive hydrophobicity values. The palindromes represent 107 different protein families and the hydrolases, transferases, oxidoreductases and lyases contain relatively large number of palindromes.

TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra

Energy Technology Data Exchange (ETDEWEB)

Zawadzka-Kazimierczuk, Anna; Kozminski, Wiktor [University of Warsaw, Faculty of Chemistry (Poland); Billeter, Martin, E-mail: martin.billeter@chem.gu.se [University of Gothenburg, Biophysics Group, Department of Chemistry and Molecular Biology (Sweden)

2012-09-15

While NMR studies of proteins typically aim at structure, dynamics or interactions, resonance assignments represent in almost all cases the initial step of the analysis. With increasing complexity of the NMR spectra, for example due to decreasing extent of ordered structure, this task often becomes both difficult and time-consuming, and the recording of high-dimensional data with high-resolution may be essential. Random sampling of the evolution time space, combined with sparse multidimensional Fourier transform (SMFT), allows for efficient recording of very high dimensional spectra ({>=}4 dimensions) while maintaining high resolution. However, the nature of this data demands for automation of the assignment process. Here we present the program TSAR (Tool for SMFT-based Assignment of Resonances), which exploits all advantages of SMFT input. Moreover, its flexibility allows to process data from any type of experiments that provide sequential connectivities. The algorithm was tested on several protein samples, including a disordered 81-residue fragment of the {delta} subunit of RNA polymerase from Bacillus subtilis containing various repetitive sequences. For our test examples, TSAR achieves a high percentage of assigned residues without any erroneous assignments.

1H NMR studies of human lysozyme: Spectral assignment and comparison with hen lysozyme

International Nuclear Information System (INIS)

Redfield, C.; Dobson, C.M.

1990-01-01

Complete main-chain (NH and αCH) 1 H NMR assignments are reported for the 130 residues of human lysozyme, along with extensive assignments for side-chain protons. Analysis of 2-D NOESY experiments shows that the regions of secondary structure for human lysozyme in solution are essentially identical with those found previously in a similar study of hen lysozyme and are in close accord with the structure of the protein reported previously from x-ray diffraction studies in the crystalline state. Comparison of the chemical shifts, spin-spin coupling constants, and hydrogen exchange behavior are also consistent with closely similar structures for the two proteins in solution. In a number of cases specific differences in the NMR parameters between hen and human lysozymes can be correlated with specific differences observed in the crystal structures

Plagiarism-Proofing Assignments

Science.gov (United States)

Johnson, Doug

2004-01-01

Mr. Johnson has discovered that the higher the level of student engagement and creativity, the lower the probability of plagiarism. For teachers who would like to see such desirable results, he describes the characteristics of assignments that are most likely to produce them. Two scenarios of types of assignments that avoid plagiarism are…

Support Vector Machines Trained with Evolutionary Algorithms Employing Kernel Adatron for Large Scale Classification of Protein Structures.

Science.gov (United States)

Arana-Daniel, Nancy; Gallegos, Alberto A; López-Franco, Carlos; Alanís, Alma Y; Morales, Jacob; López-Franco, Adriana

2016-01-01

With the increasing power of computers, the amount of data that can be processed in small periods of time has grown exponentially, as has the importance of classifying large-scale data efficiently. Support vector machines have shown good results classifying large amounts of high-dimensional data, such as data generated by protein structure prediction, spam recognition, medical diagnosis, optical character recognition and text classification, etc. Most state of the art approaches for large-scale learning use traditional optimization methods, such as quadratic programming or gradient descent, which makes the use of evolutionary algorithms for training support vector machines an area to be explored. The present paper proposes an approach that is simple to implement based on evolutionary algorithms and Kernel-Adatron for solving large-scale classification problems, focusing on protein structure prediction. The functional properties of proteins depend upon their three-dimensional structures. Knowing the structures of proteins is crucial for biology and can lead to improvements in areas such as medicine, agriculture and biofuels.

Extensive de novo solid-state NMR assignments of the 33 kDa C-terminal domain of the Ure2 prion

International Nuclear Information System (INIS)

Habenstein, Birgit; Wasmer, Christian; Bousset, Luc; Sourigues, Yannick; Schütz, Anne; Loquet, Antoine; Meier, Beat H.; Melki, Ronald; Böckmann, Anja

2011-01-01

We present the de novo resonance assignments for the crystalline 33 kDa C-terminal domain of the Ure2 prion using an optimized set of five 3D solid-state NMR spectra. We obtained, using a single uniformly 13 C, 15 N labeled protein sample, sequential chemical-shift information for 74% of the N, Cα, Cβ triples, and for 80% of further side-chain resonances for these spin systems. We describe the procedures and protocols devised, and discuss possibilities and limitations of the assignment of this largest protein assigned today by solid-state NMR, and for which no solution-state NMR shifts were available. A comparison of the NMR chemical shifts with crystallographic data reveals that regions with high crystallographic B-factors are particularly difficult to assign. While the secondary structure elements derived from the chemical shift data correspond mainly to those present in the X-ray crystal structure, we detect an additional helical element and structural variability in the protein crystal, most probably originating from the different molecules in the asymmetric unit, with the observation of doubled resonances in several parts, including entire stretches, of the protein. Our results provide the point of departure towards an atomic-resolution structural analysis of the C-terminal Ure2p domain in the context of the full-length prion fibrils.

Extensive de novo solid-state NMR assignments of the 33 kDa C-terminal domain of the Ure2 prion

Energy Technology Data Exchange (ETDEWEB)

Habenstein, Birgit [UMR 5086 CNRS/Universite de Lyon 1, Institut de Biologie et Chimie des Proteines (France); Wasmer, Christian [Harvard Medical School (United States); Bousset, Luc; Sourigues, Yannick [UPR 3082 CNRS, Laboratoire d' Enzymologie et Biochimie Structurales (France); Schuetz, Anne [ETH Zurich, Physical Chemistry (Switzerland); Loquet, Antoine [Max Planck Institute for Biophysical Chemistry (Germany); Meier, Beat H., E-mail: beme@ethz.ch [ETH Zurich, Physical Chemistry (Switzerland); Melki, Ronald, E-mail: melki@lebs.cnrs-gif.fr [UPR 3082 CNRS, Laboratoire d' Enzymologie et Biochimie Structurales (France); Boeckmann, Anja, E-mail: a.bockmann@ibcp.fr [UMR 5086 CNRS/Universite de Lyon 1, Institut de Biologie et Chimie des Proteines (France)

2011-11-15

We present the de novo resonance assignments for the crystalline 33 kDa C-terminal domain of the Ure2 prion using an optimized set of five 3D solid-state NMR spectra. We obtained, using a single uniformly {sup 13}C, {sup 15}N labeled protein sample, sequential chemical-shift information for 74% of the N, C{alpha}, C{beta} triples, and for 80% of further side-chain resonances for these spin systems. We describe the procedures and protocols devised, and discuss possibilities and limitations of the assignment of this largest protein assigned today by solid-state NMR, and for which no solution-state NMR shifts were available. A comparison of the NMR chemical shifts with crystallographic data reveals that regions with high crystallographic B-factors are particularly difficult to assign. While the secondary structure elements derived from the chemical shift data correspond mainly to those present in the X-ray crystal structure, we detect an additional helical element and structural variability in the protein crystal, most probably originating from the different molecules in the asymmetric unit, with the observation of doubled resonances in several parts, including entire stretches, of the protein. Our results provide the point of departure towards an atomic-resolution structural analysis of the C-terminal Ure2p domain in the context of the full-length prion fibrils.

Chemical shift assignments of the first and second RRMs of Nrd1, a fission yeast MAPK-target RNA binding protein.

Science.gov (United States)

Kobayashi, Ayaho; Kanaba, Teppei; Satoh, Ryosuke; Ito, Yutaka; Sugiura, Reiko; Mishima, Masaki

2017-10-01

Negative regulator differentiation 1 (Nrd1), a fission yeast RNA binding protein, modulates cytokinesis and sexual development and contributes to stress granule formation in response to environmental stresses. Nrd1 comprises four RRM domains and binds and stabilizes Cdc4 mRNA that encodes the myosin II light chain. Nrd1 binds the Cpc2 fission-yeast RACK1 homolog, and the interaction promotes Nrd1 localization to stress granules. Interestingly, Pmk1 mitogen-activated protein kinase phosphorylates Thr40 in the unstructured N-terminal region and Thr126 in the first RRM domain of Nrd1. Phosphorylation significantly reduces RNA-binding activity and likely modulates Nrd1 function. To reveal the relationship between the structure and function of Nrd1 and how phosphorylation affects structure, we used heteronuclear NMR techniques to investigate the three-dimensional structure of Nrd1. Here we report the 1 H, 13 C, and 15 N resonance assignments of RRM1-RRM2 (residues 108-284) comprising the first and second RRMs obtained using heteronuclear NMR techniques. Secondary structures derived from the chemical shifts are reported. These data should contribute to the understanding of the three-dimensional structure of the RRM1-RRM2 region of Nrd1 and the perturbation caused by phosphorylation.

Dynamics of domain coverage of the protein sequence universe

Science.gov (United States)

2012-01-01

Background The currently known protein sequence space consists of millions of sequences in public databases and is rapidly expanding. Assigning sequences to families leads to a better understanding of protein function and the nature of the protein universe. However, a large portion of the current protein space remains unassigned and is referred to as its “dark matter”. Results Here we suggest that true size of “dark matter” is much larger than stated by current definitions. We propose an approach to reducing the size of “dark matter” by identifying and subtracting regions in protein sequences that are not likely to contain any domain. Conclusions Recent improvements in computational domain modeling result in a decrease, albeit slowly, in the relative size of “dark matter”; however, its absolute size increases substantially with the growth of sequence data. PMID:23157439

Dynamics of domain coverage of the protein sequence universe

Directory of Open Access Journals (Sweden)

Rekapalli Bhanu

2012-11-01

Full Text Available Abstract Background The currently known protein sequence space consists of millions of sequences in public databases and is rapidly expanding. Assigning sequences to families leads to a better understanding of protein function and the nature of the protein universe. However, a large portion of the current protein space remains unassigned and is referred to as its “dark matter”. Results Here we suggest that true size of “dark matter” is much larger than stated by current definitions. We propose an approach to reducing the size of “dark matter” by identifying and subtracting regions in protein sequences that are not likely to contain any domain. Conclusions Recent improvements in computational domain modeling result in a decrease, albeit slowly, in the relative size of “dark matter”; however, its absolute size increases substantially with the growth of sequence data.

Assignment of methyl NMR resonances of a 52 kDa protein with residue-specific 4D correlation maps

International Nuclear Information System (INIS)

Mishra, Subrata H.; Frueh, Dominique P.

2015-01-01

Methyl groups have become key probes for structural and functional studies by nuclear magnetic resonance. However, their NMR signals cluster in a small spectral region and assigning their resonances can be a tedious process. Here, we present a method that facilitates assignment of methyl resonances from assigned amide groups. Calculating the covariance between sensitive methyl and amide 3D spectra, each providing correlations to C α and C β separately, produces 4D correlation maps directly correlating methyl groups to amide groups. Optimal correlation maps are obtained by extracting residue-specific regions, applying derivative to the dimensions subject to covariance, and multiplying 4D maps stemming from different 3D spectra. The latter procedure rescues weak signals that may be missed in traditional assignment procedures. Using these covariance correlation maps, nearly all assigned isoleucine, leucine, and valine amide resonances of a 52 kDa nonribosomal peptide synthetase cyclization domain were paired with their corresponding methyl groups

AVID: An integrative framework for discovering functional relationships among proteins

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Keating Amy E

2005-06-01

Full Text Available Abstract Background Determining the functions of uncharacterized proteins is one of the most pressing problems in the post-genomic era. Large scale protein-protein interaction assays, global mRNA expression analyses and systematic protein localization studies provide experimental information that can be used for this purpose. The data from such experiments contain many false positives and false negatives, but can be processed using computational methods to provide reliable information about protein-protein relationships and protein function. An outstanding and important goal is to predict detailed functional annotation for all uncharacterized proteins that is reliable enough to effectively guide experiments. Results We present AVID, a computational method that uses a multi-stage learning framework to integrate experimental results with sequence information, generating networks reflecting functional similarities among proteins. We illustrate use of the networks by making predictions of detailed Gene Ontology (GO annotations in three categories: molecular function, biological process, and cellular component. Applied to the yeast Saccharomyces cerevisiae, AVID provides 37,451 pair-wise functional linkages between 4,191 proteins. These relationships are ~65–78% accurate, as assessed by cross-validation testing. Assignments of highly detailed functional descriptors to proteins, based on the networks, are estimated to be ~67% accurate for GO categories describing molecular function and cellular component and ~52% accurate for terms describing biological process. The predictions cover 1,490 proteins with no previous annotation in GO and also assign more detailed functions to many proteins annotated only with less descriptive terms. Predictions made by AVID are largely distinct from those made by other methods. Out of 37,451 predicted pair-wise relationships, the greatest number shared in common with another method is 3,413. Conclusion AVID provides

Lipid bilayer-bound conformation of an integral membrane beta barrel protein by multidimensional MAS NMR

International Nuclear Information System (INIS)

Eddy, Matthew T.; Su, Yongchao; Silvers, Robert; Andreas, Loren; Clark, Lindsay; Wagner, Gerhard; Pintacuda, Guido; Emsley, Lyndon; Griffin, Robert G.

2015-01-01

The human voltage dependent anion channel 1 (VDAC) is a 32 kDa β-barrel integral membrane protein that controls the transport of ions across the outer mitochondrial membrane. Despite the determination of VDAC solution and diffraction structures, a structural basis for the mechanism of its function is not yet fully understood. Biophysical studies suggest VDAC requires a lipid bilayer to achieve full function, motivating the need for atomic resolution structural information of VDAC in a membrane environment. Here we report an essential step toward that goal: extensive assignments of backbone and side chain resonances for VDAC in DMPC lipid bilayers via magic angle spinning nuclear magnetic resonance (MAS NMR). VDAC reconstituted into DMPC lipid bilayers spontaneously forms two-dimensional lipid crystals, showing remarkable spectral resolution (0.5–0.3 ppm for 13 C line widths and <0.5 ppm 15 N line widths at 750 MHz). In addition to the benefits of working in a lipid bilayer, several distinct advantages are observed with the lipid crystalline preparation. First, the strong signals and sharp line widths facilitated extensive NMR resonance assignments for an integral membrane β-barrel protein in lipid bilayers by MAS NMR. Second, a large number of residues in loop regions were readily observed and assigned, which can be challenging in detergent-solubilized membrane proteins where loop regions are often not detected due to line broadening from conformational exchange. Third, complete backbone and side chain chemical shift assignments could be obtained for the first 25 residues, which comprise the functionally important N-terminus. The reported assignments allow us to compare predicted torsion angles for VDAC prepared in DMPC 2D lipid crystals, DMPC liposomes, and LDAO-solubilized samples to address the possible effects of the membrane mimetic environment on the conformation of the protein. Concluding, we discuss the strengths and weaknesses of the reported

Expanded microbial genome coverage and improved protein family annotation in the COG database.

Science.gov (United States)

Galperin, Michael Y; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2015-01-01

Microbial genome sequencing projects produce numerous sequences of deduced proteins, only a small fraction of which have been or will ever be studied experimentally. This leaves sequence analysis as the only feasible way to annotate these proteins and assign to them tentative functions. The Clusters of Orthologous Groups of proteins (COGs) database (http://www.ncbi.nlm.nih.gov/COG/), first created in 1997, has been a popular tool for functional annotation. Its success was largely based on (i) its reliance on complete microbial genomes, which allowed reliable assignment of orthologs and paralogs for most genes; (ii) orthology-based approach, which used the function(s) of the characterized member(s) of the protein family (COG) to assign function(s) to the entire set of carefully identified orthologs and describe the range of potential functions when there were more than one; and (iii) careful manual curation of the annotation of the COGs, aimed at detailed prediction of the biological function(s) for each COG while avoiding annotation errors and overprediction. Here we present an update of the COGs, the first since 2003, and a comprehensive revision of the COG annotations and expansion of the genome coverage to include representative complete genomes from all bacterial and archaeal lineages down to the genus level. This re-analysis of the COGs shows that the original COG assignments had an error rate below 0.5% and allows an assessment of the progress in functional genomics in the past 12 years. During this time, functions of many previously uncharacterized COGs have been elucidated and tentative functional assignments of many COGs have been validated, either by targeted experiments or through the use of high-throughput methods. A particularly important development is the assignment of functions to several widespread, conserved proteins many of which turned out to participate in translation, in particular rRNA maturation and tRNA modification. The new version of the

Partially-deuterated samples of HET-s(218–289) fibrils: assignment and deuterium isotope effect

Energy Technology Data Exchange (ETDEWEB)

Smith, Albert A.; Ravotti, Francesco; Testori, Emilie; Cadalbert, Riccardo; Ernst, Matthias, E-mail: maer@ethz.ch [ETH Zürich, Physical Chemistry (Switzerland); Böckmann, Anja, E-mail: a.bockmann@ibcp.fr [Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon (France); Meier, Beat H., E-mail: beme@ethz.ch [ETH Zürich, Physical Chemistry (Switzerland)

2017-02-15

Fast magic-angle spinning and partial sample deuteration allows direct detection of {sup 1}H in solid-state NMR, yielding significant gains in mass sensitivity. In order to further analyze the spectra, {sup 1}H detection requires assignment of the {sup 1}H resonances. In this work, resonance assignments of backbone H{sup N} and Hα are presented for HET-s(218–289) fibrils, based on the existing assignment of Cα, Cβ, C’, and N resonances. The samples used are partially deuterated for higher spectral resolution, and the shifts in resonance frequencies of Cα and Cβ due to the deuterium isotope effect are investigated. It is shown that the deuterium isotope effect can be estimated and used for assigning resonances of deuterated samples in solid-state NMR, based on known resonances of the protonated protein.

(¹⁵N ± ¹³C') edited (4, 3)D-H(CC)CONH TOCSY and (4, 3)D-NOESY HNCO experiments for unambiguous side chain and NOE assignments of proteins with high shift degeneracy.

Science.gov (United States)

Kumar, Dinesh; Arora, Ashish

2011-11-01

Well-resolved and unambiguous through-bond correlations and NOE data are crucial for high-quality protein structure determination by NMR. In this context, we present here (4, 3)D reduced dimensionality (RD) experiments: H(CC)CONH TOCSY and NOESY HNCO--which instead of (15)N shifts exploit the linear combination of (15)N(i) and (13)C'(i-1) shifts (where i is a residue number) to resolve the through-bond (1)H-(1)H correlations and through-space (1)H-(1)H NOEs. The strategy makes use of the fact that (15)N and (13)C' chemical shifts when combined linearly provide a dispersion which is better compared to those of the individual chemical shifts. The extended dispersion thus available in these experiments will help to obtain the unambiguous side chain and accurate NOE assignments especially for medium-sized alpha-helical or partially unstructured proteins [molecular weight (MW) between 12-15 kDa] as well as higher MW (between 15-25 kDa) folded proteins where spectral overlap renders inaccurate and ambiguous NOEs. Further, these reduced dimensionality experiments in combination with routinely used (15)N and (13)C' edited TOCSY and NOESY experiments will provide an alternative way for high-quality NMR structure determination of large unstable proteins (with very high shift degeneracy), which are not at all amenable to 4D NMR. The utility of these experiments has been demonstrated here using (13)C/(15)N labeled ubiquitin (76 aa) protein. Copyright © 2011 John Wiley & Sons, Ltd.

Sequential backbone assignment based on dipolar amide-to-amide correlation experiments

Energy Technology Data Exchange (ETDEWEB)

Xiang, ShengQi; Grohe, Kristof; Rovó, Petra; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Linser, Rasmus, E-mail: rali@nmr.mpibpc.mpg.de [Max Planck Institute for Biophysical Chemistry, Department for NMR-Based Structural Biology (Germany)

2015-07-15

Proton detection in solid-state NMR has seen a tremendous increase in popularity in the last years. New experimental techniques allow to exploit protons as an additional source of information on structure, dynamics, and protein interactions with their surroundings. In addition, sensitivity is mostly improved and ambiguity in assignment experiments reduced. We show here that, in the solid state, sequential amide-to-amide correlations turn out to be an excellent, complementary way to exploit amide shifts for unambiguous backbone assignment. For a general assessment, we compare amide-to-amide experiments with the more common {sup 13}C-shift-based methods. Exploiting efficient CP magnetization transfers rather than less efficient INEPT periods, our results suggest that the approach is very feasible for solid-state NMR.

Sequential backbone assignment based on dipolar amide-to-amide correlation experiments

International Nuclear Information System (INIS)

Xiang, ShengQi; Grohe, Kristof; Rovó, Petra; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Linser, Rasmus

2015-01-01

Proton detection in solid-state NMR has seen a tremendous increase in popularity in the last years. New experimental techniques allow to exploit protons as an additional source of information on structure, dynamics, and protein interactions with their surroundings. In addition, sensitivity is mostly improved and ambiguity in assignment experiments reduced. We show here that, in the solid state, sequential amide-to-amide correlations turn out to be an excellent, complementary way to exploit amide shifts for unambiguous backbone assignment. For a general assessment, we compare amide-to-amide experiments with the more common 13 C-shift-based methods. Exploiting efficient CP magnetization transfers rather than less efficient INEPT periods, our results suggest that the approach is very feasible for solid-state NMR

EFFECTS OF PROTEIN-XANTHOPHYLL (PX CONCENTRATE OF ALFALFA ADDITIVE TO CRUDE PROTEIN-REDUCED DIETS ON NITROGEN EXCRETION, GROWTH PERFORMANCE AND MEAT QUALITY OF PIGS

Directory of Open Access Journals (Sweden)

Eugeniusz GRELA

2009-06-01

Full Text Available The infl uence of protein-xanthophyll (PX concentrate of alfalfa supplement to crude protein-reduced diets was examined in relation to nitrogen excretion, performance parameters and pig meat quality. The investigations included 60 growers (PL x PLW x Duroc crossbreeds assigned to 3 groups. The conclusion is that there is a large potential to decrease nitrogen emission to the environment by 10% lowering of dietary crude protein intake along with reduced animal growth rate and elevated mixture utilization. Inclusion of a protein-xanthophyll concentrate (PX of alfalfa to the diet is likely to diminish disadvantageous productive parameters arising from limiting of total crude protein level in relation to the requirements of pigs feeding norms [1993]. At the same time, it improves feed nitrogen utilization and reduces noxious odour emissions from a piggery. The components of a protein-xanthophyll concentrate (PX contribute to increased liver and kidney weight.

Systemic transport of Alfalfa mosaic virus can be mediated by the movement proteins of several viruses assigned to five genera of the 30K family.

Science.gov (United States)

Fajardo, Thor V M; Peiró, Ana; Pallás, Vicente; Sánchez-Navarro, Jesús

2013-03-01

We previously showed that the movement protein (MP) gene of Alfalfa mosaic virus (AMV) is functionally exchangeable for the cell-to-cell transport of the corresponding genes of Tobacco mosaic virus (TMV), Brome mosaic virus, Prunus necrotic ringspot virus, Cucumber mosaic virus and Cowpea mosaic virus. We have analysed the capacity of the heterologous MPs to systemically transport the corresponding chimeric AMV genome. All MPs were competent in systemic transport but required the fusion at their C terminus of the coat protein-interacting C-terminal 44 aa (A44) of the AMV MP. Except for the TMV MP, the presence of the hybrid virus in upper leaves correlated with the capacity to move locally. These results suggest that all the MPs assigned to the 30K superfamily should be exchangeable not only for local virus movement but also for systemic transport when the A44 fragment is present.

Dynamic Sequence Assignment.

Science.gov (United States)

1983-12-01

D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

Wildlife forensic science: A review of genetic geographic origin assignment.

Science.gov (United States)

Ogden, Rob; Linacre, Adrian

2015-09-01

Wildlife forensic science has become a key means of enforcing legislation surrounding the illegal trade in protected and endangered species. A relatively new dimension to this area of forensic science is to determine the geographic origin of a seized sample. This review focuses on DNA testing, which relies on assignment of an unknown sample to its genetic population of origin. Key examples of this are the trade in timber, fish and ivory and these are used only to illustrate the large number of species for which this type of testing is potentially available. The role of mitochondrial and nuclear DNA markers is discussed, alongside a comparison of neutral markers with those exhibiting signatures of selection, which potentially offer much higher levels of assignment power to address specific questions. A review of assignment tests is presented along with detailed methods for evaluating error rates and considerations for marker selection. The availability and quality of reference data are of paramount importance to support assignment applications and ensure reliability of any conclusions drawn. The genetic methods discussed have been developed initially as investigative tools but comment is made regarding their use in courts. The potential to compliment DNA markers with elemental assays for greater assignment power is considered and finally recommendations are made for the future of this type of testing. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Complete resonance assignment for the polypeptide backbone of interleukin 1β using three-dimensional heteronuclear NMR spectroscopy

International Nuclear Information System (INIS)

Driscoll, P.C.; Clore, G.M.; Marion, D.; Gronenborn, A.M.; Wingfield, P.T.

1990-01-01

The complete sequence-specific assignment of the 15 N and 1 H backbone resonances of the NMR spectrum of recombinant human interleukin 1β has been obtained by using primarily 15 N- 1 H heteronuclear three-dimensional (3D) NMR techniques in combination with 15 N- 1 H heteronuclear and 1 H homonuclear two-dimensional NMR. The fingerprint region of the spectrum was analyzed by using a combination of 3D heteronuclear 1 H Hartmann-Hahn 15 N- 1 H multiple quantum coherence (3D HOHAHA-HMQC) and 3D heteronuclear 1 H nuclear Overhauser 15 N- 1 H multiple quantum coherence (3D NOESY-HMQC) spectroscopies. The authors show that the problems of amide NH and C α H chemical shift degeneracy that are prevalent for proteins of the size are readily overcome by using the 3D heteronuclear NMR technique. A doubling of some peaks in the spectrum was found to be due to N-terminal heterogeneity of the 15 N-labeled protein, corresponding to a mixture of wild-type and des-Ala-1-interleukin 1β. The complete list of 15 N and 1 H assignments is given for all the amide NH and C α H resonances of all non-proline residues, as well as the 1 H assignments for some of the amino acid side chains. This first example of the sequence-specific assignment of a protein using heteronuclear 3D NMR provides a basis for further conformational and dynamic studies of interleukin 1β

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

Science.gov (United States)

The, Matthew; MacCoss, Michael J.; Noble, William S.; Käll, Lukas

2016-11-01

Percolator is a widely used software tool that increases yield in shotgun proteomics experiments and assigns reliable statistical confidence measures, such as q values and posterior error probabilities, to peptides and peptide-spectrum matches (PSMs) from such experiments. Percolator's processing speed has been sufficient for typical data sets consisting of hundreds of thousands of PSMs. With our new scalable approach, we can now also analyze millions of PSMs in a matter of minutes on a commodity computer. Furthermore, with the increasing awareness for the need for reliable statistics on the protein level, we compared several easy-to-understand protein inference methods and implemented the best-performing method—grouping proteins by their corresponding sets of theoretical peptides and then considering only the best-scoring peptide for each protein—in the Percolator package. We used Percolator 3.0 to analyze the data from a recent study of the draft human proteome containing 25 million spectra (PM:24870542). The source code and Ubuntu, Windows, MacOS, and Fedora binary packages are available from http://percolator.ms/ under an Apache 2.0 license.

Characterisation of silent and active genes for a variable large protein of Borrelia recurrentis

Directory of Open Access Journals (Sweden)

Scragg Ian G

2002-10-01

Full Text Available Abstract Background We report the characterisation of the variable large protein (vlp gene expressed by clinical isolate A1 of Borrelia recurrentis; the agent of the life-threatening disease louse-borne relapsing fever. Methods The major vlp protein of this isolate was characterised and a DNA probe created. Use of this together with standard molecular methods was used to determine the location of the vlp1B. recurrentis A1 gene in both this and other isolates. Results This isolate was found to carry silent and expressed copies of the vlp1B. recurrentis A1 gene on plasmids of 54 kbp and 24 kbp respectively, whereas a different isolate, A17, had only the silent vlp1B. recurrentis A17 on a 54 kbp plasmid. Silent and expressed vlp1 have identical mature protein coding regions but have different 5' regions, both containing different potential lipoprotein leader sequences. Only one form of vlp1 is transcribed in the A1 isolate of B. recurrentis, yet both 5' upstream sequences of this vlp1 gene possess features of bacterial promoters. Conclusion Taken together these results suggest that antigenic variation in B. recurrentis may result from recombination of variable large and small protein genes at the junction between lipoprotein leader sequence and mature protein coding region. However, this hypothetical model needs to be validated by further identification of expressed and silent variant protein genes in other B. recurrentis isolates.

Assignment of the human gene for pregnancy-associated plasma protein A (PAPPA) to 9q33.1 by fluorescence in situ hybridization to mitotic and meiotic chromosomes

DEFF Research Database (Denmark)

Silahtaroglu, A N; Tümer, Z; Kristensen, Torsten

1993-01-01

Low levels of pregnancy-associated plasma protein A (PAPPA) during the first trimester has been suggested as a biochemical indicator of pregnancies with aneuploid fetuses. Furthermore, the complete absence of PAPPA in pregnancies associated with Cornelia de Lange syndrome (CL) has suggested...... a causal connection between PAPPA and the development of CL. We have assigned the locus for PAPPA to chromosome region 9q33.1 on mitotic and meiotic chromosomes by fluorescence in situ hybridization, using a 3.7-kb partial PAPPA cDNA probe...

Clustering structures of large proteins using multifractal analyses based on a 6-letter model and hydrophobicity scale of amino acids

International Nuclear Information System (INIS)

Yang Jianyi; Yu Zuguo; Anh, Vo

2009-01-01

The Schneider and Wrede hydrophobicity scale of amino acids and the 6-letter model of protein are proposed to study the relationship between the primary structure and the secondary structural classification of proteins. Two kinds of multifractal analyses are performed on the two measures obtained from these two kinds of data on large proteins. Nine parameters from the multifractal analyses are considered to construct the parameter spaces. Each protein is represented by one point in these spaces. A procedure is proposed to separate large proteins in the α, β, α + β and α/β structural classes in these parameter spaces. Fisher's linear discriminant algorithm is used to assess our clustering accuracy on the 49 selected large proteins. Numerical results indicate that the discriminant accuracies are satisfactory. In particular, they reach 100.00% and 84.21% in separating the α proteins from the {β, α + β, α/β} proteins in a parameter space; 92.86% and 86.96% in separating the β proteins from the {α + β, α/β} proteins in another parameter space; 91.67% and 83.33% in separating the α/β proteins from the α + β proteins in the last parameter space.

A constraint logic programming approach to associate 1D and 3D structural components for large protein complexes.

Science.gov (United States)

Dal Palù, Alessandro; Pontelli, Enrico; He, Jing; Lu, Yonggang

2007-01-01

The paper describes a novel framework, constructed using Constraint Logic Programming (CLP) and parallelism, to determine the association between parts of the primary sequence of a protein and alpha-helices extracted from 3D low-resolution descriptions of large protein complexes. The association is determined by extracting constraints from the 3D information, regarding length, relative position and connectivity of helices, and solving these constraints with the guidance of a secondary structure prediction algorithm. Parallelism is employed to enhance performance on large proteins. The framework provides a fast, inexpensive alternative to determine the exact tertiary structure of unknown proteins.

"C.R.E.A.T.E."-ing Unique Primary-Source Research Paper Assignments for a Pleasure and Pain Course Teaching Neuroscientific Principles in a Large General Education Undergraduate Course.

Science.gov (United States)

Bodnar, Richard J; Rotella, Francis M; Loiacono, Ilyssa; Coke, Tricia; Olsson, Kerstin; Barrientos, Alicia; Blachorsky, Lauren; Warshaw, Deena; Buras, Agata; Sanchez, Ciara M; Azad, Raihana; Stellar, James R

2016-01-01

A large (250 registrants) General Education lecture course, Pleasure and Pain, presented basic neuroscience principles as they related to animal and human models of pleasure and pain by weaving basic findings related to food and drug addiction and analgesic states with human studies examining empathy, social neuroscience and neuroeconomics. In its first four years, the course grade was based on weighted scores from two multiple-choice exams and a five-page review of three unique peer-reviewed research articles. Although well-registered and well-received, 18% of the students received Incomplete grades, primarily due to failing to submit the paper that went largely unresolved and eventually resulted in a failing grade. To rectify this issue, a modified version of the C.R.E.A.T.E. (Consider, Read, Elucidate hypotheses, Analyze and interpret data, Think of the next Experiment) method replaced the paper with eight structured assignments focusing on an initial general-topic article, the introduction-methods, and results-discussion of each of three related peer-review neuroscience-related articles, and a final summary. Compliance in completing these assignments was very high, resulting in only 11 INC grades out of 228 students. Thus, use of the C.R.E.A.T.E. method reduced the percentage of problematic INC grades from 18% to 4.8%, a 73% decline, without changing the overall grade distribution. Other analyses suggested the students achieved a deeper understanding of the scientific process using the C.R.E.A.T.E. method relative to the original term paper assignment.

Applications of random forest feature selection for fine-scale genetic population assignment.

Science.gov (United States)

Sylvester, Emma V A; Bentzen, Paul; Bradbury, Ian R; Clément, Marie; Pearce, Jon; Horne, John; Beiko, Robert G

2018-02-01

Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine-learning algorithms (random forest, regularized random forest and guided regularized random forest) compared with F ST ranking for selection of single nucleotide polymorphisms (SNP) for fine-scale population assignment. We applied these methods to an unpublished SNP data set for Atlantic salmon ( Salmo salar ) and a published SNP data set for Alaskan Chinook salmon ( Oncorhynchus tshawytscha ). In each species, we identified the minimum panel size required to obtain a self-assignment accuracy of at least 90% using each method to create panels of 50-700 markers Panels of SNPs identified using random forest-based methods performed up to 7.8 and 11.2 percentage points better than F ST -selected panels of similar size for the Atlantic salmon and Chinook salmon data, respectively. Self-assignment accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each data set, respectively, a level of accuracy never reached for these species using F ST -selected panels. Our results demonstrate a role for machine-learning approaches in marker selection across large genomic data sets to improve assignment for management and conservation of exploited populations.

Resonance Assignments and Secondary Structure Analysis of Dynein Light Chain 8 by Magic-angle Spinning NMR Spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Sun, Shangjin; Butterworth, Andrew H.; Paramasivam, Sivakumar; Yan, Si; Lightcap, Christine M.; Williams, John C.; Polenova, Tatyana E.

2011-08-04

Dynein light chain LC8 is the smallest subunit of the dynein motor complex and has been shown to play important roles in both dynein-dependent and dynein-independent physiological functions via its interaction with a number of its binding partners. It has also been linked to pathogenesis including roles in viral infections and tumorigenesis. Structural information for LC8-target proteins is critical to understanding the underlying function of LC8 in these complexes. However, some LC8-target interactions are not amenable to structural characterization by conventional structural biology techniques owing to their large size, low solubility, and crystallization difficulties. Here, we report magic-angle spinning (MAS) NMR studies of the homodimeric apo-LC8 protein as a first effort in addressing more complex, multi-partner, LC8-based protein assemblies. We have established site-specific backbone and side-chain resonance assignments for the majority of the residues of LC8, and show TALOS+-predicted torsion angles ø and ψ in close agreement with most residues in the published LC8 crystal structure. Data obtained through these studies will provide the first step toward using MAS NMR to examine the LC8 structure, which will eventually be used to investigate protein–protein interactions in larger systems that cannot be determined by conventional structural studies.

Structure based alignment and clustering of proteins (STRALCP)

Science.gov (United States)

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

Generating functional analysis of complex formation and dissociation in large protein interaction networks

International Nuclear Information System (INIS)

Coolen, A C C; Rabello, S

2009-01-01

We analyze large systems of interacting proteins, using techniques from the non-equilibrium statistical mechanics of disordered many-particle systems. Apart from protein production and removal, the most relevant microscopic processes in the proteome are complex formation and dissociation, and the microscopic degrees of freedom are the evolving concentrations of unbound proteins (in multiple post-translational states) and of protein complexes. Here we only include dimer-complexes, for mathematical simplicity, and we draw the network that describes which proteins are reaction partners from an ensemble of random graphs with an arbitrary degree distribution. We show how generating functional analysis methods can be used successfully to derive closed equations for dynamical order parameters, representing an exact macroscopic description of the complex formation and dissociation dynamics in the infinite system limit. We end this paper with a discussion of the possible routes towards solving the nontrivial order parameter equations, either exactly (in specific limits) or approximately.

Phylogenetic profiles of all membrane transport proteins of the malaria parasite highlight new drug targets

Directory of Open Access Journals (Sweden)

January Weiner 3rd

2016-08-01

Full Text Available In order to combat the on-going malaria epidemic, discovery of new drug targets remains vital. Proteins that are essential to survival and specific to malaria parasites are key candidates. To survive within host cells, the parasites need to acquire nutrients and dispose of waste products across multiple membranes. Additionally, like all eukaryotes, they must redistribute ions and organic molecules between their various internal membrane bound compartments. Membrane transport proteins mediate all of these processes and are considered important mediators of drug resistance as well as drug targets in their own right. Recently, using advanced experimental genetic approaches and streamlined life cycle profiling, we generated a large collection of Plasmodium berghei gene deletion mutants and assigned essential gene functions, highlighting potential targets for prophylactic, therapeutic, and transmission-blocking anti-malarial drugs. Here, we present a comprehensive orthology assignment of all Plasmodium falciparum putative membrane transport proteins and provide a detailed overview of the associated essential gene functions obtained through experimental genetics studies in human and murine model parasites. Furthermore, we discuss the phylogeny of selected potential drug targets identified in our functional screen. We extensively discuss the results in the context of the functional assignments obtained using gene targeting available to date.

TRP channel proteins and signal transduction.

Science.gov (United States)

Minke, Baruch; Cook, Boaz

2002-04-01

TRP channel proteins constitute a large and diverse family of proteins that are expressed in many tissues and cell types. This family was designated TRP because of a spontaneously occurring Drosophila mutant lacking TRP that responded to a continuous light with a transient receptor potential (hence TRP). In addition to responses to light, TRPs mediate responses to nerve growth factor, pheromones, olfaction, mechanical, chemical, temperature, pH, osmolarity, vasorelaxation of blood vessels, and metabolic stress. Furthermore, mutations in several members of TRP-related channel proteins are responsible for several diseases, such as several tumors and neurodegenerative disorders. TRP-related channel proteins are found in a variety of organisms, tissues, and cell types, including nonexcitable, smooth muscle, and neuronal cells. The large functional diversity of TRPs is also reflected in their diverse permeability to ions, although, in general, they are classified as nonselective cationic channels. The molecular domains that are conserved in all members of the TRP family constitute parts of the transmembrane domains and in most members also the ankyrin-like repeats at the NH2 terminal of the protein and a "TRP domain" at the COOH terminal, which is a highly conserved 25-amino acid stretch with still unknown function. All of the above features suggest that members of the TRP family are "special assignment" channels, which are recruited to diverse signaling pathways. The channels' roles and characteristics such as gating mechanism, regulation, and permeability are determined by evolution according to the specific functional requirements.

Neandertals' large lower thorax may represent adaptation to high protein diet.

Science.gov (United States)

Ben-Dor, Miki; Gopher, Avi; Barkai, Ran

2016-07-01

Humans are limited in their capacity to convert protein into energy. We present a hypothesis that a "bell" shaped thorax and a wide pelvis evolved in Neandertals, at least in part, as an adaptation to a high protein diet. A high protein diet created a need to house an enlarged liver and urinary system in a wider lower trunk. To test the hypothesis, we applied a model developed to identify points of nutritional stress. A ratio of obligatory dietary fat to total animal fat and protein sourced calories is calculated based on various known and estimated parameters. Stress is identified when the obligatory dietary fat ratio is higher than fat content ratios in available prey. The model predicts that during glacial winters, when carbohydrates weren't available, 74%-85% of Neandertals' caloric intake would have had to come from animal fat. Large animals contain around 50% fat calories, and their fat content is diminished during winter, so a significant stressful dietary fat deficit was identified by the model. This deficit could potentially be ameliorated by an increased capability to convert protein into energy. Given that high protein consumption is associated with larger liver and kidneys in animal models, it appears likely that the enlarged inferior section of the Neandertals thorax and possibly, in part, also his wide pelvis, represented an adaptation to provide encasement for those enlarged organs. Behavioral and evolutionary implications of the hypothesis are also discussed. Am J Phys Anthropol 160:367-378, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Using HL7 in hospital staff assignments.

Science.gov (United States)

Unluturk, Mehmet S

2014-02-01

Hospital staff assignments are the instructions that allocate the hospital staff members to the hospital beds. Currently, hospital administrators make the assignments without accessing the information regarding the occupancy of the hospital beds and the acuity of the patient. As a result, administrators cannot distinguish between occupied and unoccupied beds, and may therefore assign staff to unoccupied beds. This gives rise to uneven and inefficient staff assignments. In this paper, the hospital admission-discharge-transfer (ADT) system is employed both as a data source and an assignment device to create staff assignments. When the patient data is newly added or modified, the ADT system updates the assignment software client with the relevant data. Based on the relevant data, the assignment software client is able to construct staff assignments in a more efficient way. © 2013 Elsevier Ltd. All rights reserved.

Sensitivity enhancement for membrane proteins reconstituted in parallel and perpendicular oriented bicelles obtained by using repetitive cross-polarization and membrane-incorporated free radicals

Energy Technology Data Exchange (ETDEWEB)

Koroloff, Sophie N. [North Carolina State University, Department of Chemistry (United States); Tesch, Deanna M. [Shaw University (United States); Awosanya, Emmanuel O.; Nevzorov, Alexander A., E-mail: alex-nevzorov@ncsu.edu [North Carolina State University, Department of Chemistry (United States)

2017-02-15

Multidimensional separated local-field and spin-exchange experiments employed by oriented-sample solid-state NMR are essential for structure determination and spectroscopic assignment of membrane proteins reconstituted in macroscopically aligned lipid bilayers. However, these experiments typically require a large number of scans in order to establish interspin correlations. Here we have shown that a combination of optimized repetitive cross polarization (REP-CP) and membrane-embedded free radicals allows one to enhance the signal-to-noise ratio by factors 2.4-3.0 in the case of Pf1 coat protein reconstituted in magnetically aligned bicelles with their normals being either parallel or perpendicular to the main magnetic field. Notably, spectral resolution is not affected at the 2:1 radical-to-protein ratio. Spectroscopic assignment of Pf1 coat protein in the parallel bicelles has been established as an illustration of the method. The proposed methodology will advance applications of oriented-sample NMR technique when applied to samples containing smaller quantities of proteins and three-dimensional experiments.

Automated assignment and 3D structure calculations using combinations of 2D homonuclear and 3D heteronuclear NOESY spectra

International Nuclear Information System (INIS)

Oezguen, Numan; Adamian, Larisa; Xu Yuan; Rajarathnam, Krishna; Braun, Werner

2002-01-01

The NOAH/DIAMOD suite uses feedback filtering and self-correcting distance geometry to generate 3D structures from unassigned NOESY spectra. In this study we determined the minimum set of experiments needed to generate a high quality structure bundle. Different combinations of 3D 15 N-edited, 13 C-edited HSQC-NOESY and 2D homonuclear 1 H- 1 H NOESY spectra of the 77 amino acid protein, myeloid progenitor inhibitory factor-1 (MPIF-1) were used as input for NOAH/DIAMOD calculations. The quality of the assignments of NOESY cross peaks and the accuracy of the automatically generated 3D structures were compared to those obtained with a conventional manual procedure. Combining data from two types of experiments synergistically increased the number of peaks assigned unambiguously in both individual spectra. As a general trend for the accuracy of the structures we observed structural variations in the backbone fold of the final structures of about 2 A for single spectral data, of 1 A to 1.5 A for double spectral data, and of 0.6 A for triple spectral data sets. The quality of the assignments and 3D structures from the optimal data using all three spectra were similar to those obtained from traditional assignment methods with structural variations within the bundle of 0.6 A and 1.3 A for backbone and heavy atoms, respectively. Almost all constraints (97%) of the automatic NOESY cross peak assignments were cross compatible with the structures from the conventional manual assignment procedure, and an even larger proportion (99%) of the manually derived constraints were compatible with the automatically determined 3D structures. The two mean structures determined by both methods differed only by 1.3 A rmsd for the backbone atoms in the well-defined regions of the protein. Thus NOAD/DIAMOD analysis of spectra from labeled proteins provides a reliable method for high throughput analysis of genomic targets

Predicting Protein Function via Semantic Integration of Multiple Networks.

Science.gov (United States)

Yu, Guoxian; Fu, Guangyuan; Wang, Jun; Zhu, Hailong

2016-01-01

Determining the biological functions of proteins is one of the key challenges in the post-genomic era. The rapidly accumulated large volumes of proteomic and genomic data drives to develop computational models for automatically predicting protein function in large scale. Recent approaches focus on integrating multiple heterogeneous data sources and they often get better results than methods that use single data source alone. In this paper, we investigate how to integrate multiple biological data sources with the biological knowledge, i.e., Gene Ontology (GO), for protein function prediction. We propose a method, called SimNet, to Semantically integrate multiple functional association Networks derived from heterogenous data sources. SimNet firstly utilizes GO annotations of proteins to capture the semantic similarity between proteins and introduces a semantic kernel based on the similarity. Next, SimNet constructs a composite network, obtained as a weighted summation of individual networks, and aligns the network with the kernel to get the weights assigned to individual networks. Then, it applies a network-based classifier on the composite network to predict protein function. Experiment results on heterogenous proteomic data sources of Yeast, Human, Mouse, and Fly show that, SimNet not only achieves better (or comparable) results than other related competitive approaches, but also takes much less time. The Matlab codes of SimNet are available at https://sites.google.com/site/guoxian85/simnet.

¹H, ¹³C, and ¹⁵N backbone and side-chain chemical shift assignment of the toxin Doc in the unbound state.

Science.gov (United States)

De Gieter, Steven; Loris, Remy; van Nuland, Nico A J; Garcia-Pino, Abel

2014-04-01

Toxin-antitoxin (TA) modules in bacteria are involved in pathogenesis, antibiotic stress response, persister formation and programmed cell death. The toxin Doc, from the phd/doc module, blocks protein synthesis by targeting the translation machinery. Despite a large wealth of biophysical and biochemical data on the regulatory aspects of the operon transcription and role of Doc co-activator and co-repressor, little is still know on the molecular basis of Doc toxicity. Structural information about this toxin is only available for its inhibited state bound to the antitoxin Phd. Here we report the (1)H, (15)N and (13)C backbone and side chain chemical shift assignments of the toxin Doc from of bacteriophage P1 (the model protein from this family of TA modules) in its free state. The BMRB accession number is 18899.

Sequence-specific 1H NMR resonance assignments of Bacillus subtilis HPr: Use of spectra obtained from mutants to resolve spectral overlap

International Nuclear Information System (INIS)

Wittekind, M.; Klevit, R.E.; Reizer, J.

1990-01-01

On the basis of an analysis of two-dimensional 1 H NMR spectra, the complete sequence-specific 1 H NMR assignments are presented for the phosphocarrier protein HPr from the Gram-positive bacterium Bacillus subtilis. During the assignment procedure, extensive use was made of spectra obtained from point mutants of HPr in order to resolve spectral overlap and to provide verification of assignments. Regions of regular secondary structure were identified by characteristic patterns of sequential backbone proton NOEs and slowly exchanging amide protons. B subtilis HPr contains four β-strands that form a single antiparallel β-sheet and two well-defined α-helices. There are two stretches of extended backbone structure, one of which contains the active site His 15 . The overall fold of the protein is very similar to that of Escherichia coli HPr determined by NMR studies

Value assignment of nutrient concentrations in five standard reference materials and six reference materials.

Science.gov (United States)

Sharpless, K E; Gill, L M

2000-01-01

A number of food-matrix reference materials (RMs) are available from the National Institute of Standards and Technology (NIST) and from Agriculture Canada through NIST. Most of these materials were originally value-assigned for their elemental composition (major, minor, and trace elements), but no additional nutritional information was provided. Two of the materials were certified for selected organic constituents. Ten of these materials (Standard Reference Material [SRM] 1,563 Cholesterol and Fat-Soluble Vitamins in Coconut Oil [Natural and Fortified], SRM 1,566b Oyster Tissue, SRM 1,570a Spinach Leaves, SRM 1,974a Organics in Mussel Tissue (Mytilus edulis), RM 8,415 Whole Egg Powder, RM 8,418 Wheat Gluten, RM 8,432 Corn Starch, RM 8,433 Corn Bran, RM 8,435 Whole Milk Powder, and RM 8,436 Durum Wheat Flour) were recently distributed by NIST to 4 laboratories with expertise in food analysis for the measurement of proximates (solids, fat, protein, etc.), calories, and total dietary fiber, as appropriate. SRM 1846 Infant Formula was distributed as a quality control sample for the proximates and for analysis for individual fatty acids. Two of the materials (Whole Egg Powder and Whole Milk Powder) were distributed in an earlier interlaboratory comparison exercise in which they were analyzed for several vitamins. Value assignment of analyte concentrations in these 11 SRMs and RMs, based on analyses by the collaborating laboratories, is described in this paper. These materials are intended primarily for validation of analytical methods for the measurement of nutrients in foods of similar composition (based on AOAC INTERNATIONAL's fat-protein-carbohydrate triangle). They may also be used as "primary control materials" in the value assignment of in-house control materials of similar composition. The addition of proximate information for 10 existing reference materials means that RMs are now available from NIST with assigned values for proximates in 6 of the 9 sectors of

Chemical shift assignments of the partially deuterated Fyn SH2-SH3 domain.

Science.gov (United States)

Kieken, Fabien; Loth, Karine; van Nuland, Nico; Tompa, Peter; Lenaerts, Tom

2018-04-01

Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the SH2 and the SH3 domain with intra-molecular regions, leading to a closed structure incompetent with substrate modification. Here, we report the 1 H, 15 N and 13 C backbone- and side-chain chemical shift assignments of the partially deuterated Fyn SH3-SH2 domain and structural differences between tandem and single domains. The BMRB accession number is 27165.

Experiments and strategies for the assignment of fully13 C/15N-labelled polypeptides by solid state NMR

International Nuclear Information System (INIS)

Straus, Suzana K.; Bremi, Tobias; Ernst, Richard R.

1998-01-01

High-resolution heteronuclear NMR correlation experiments and strategies are proposed for the assignment of fully 13 C/ 15 N-labelled polypeptides in the solid state. By the combination of intra-residue and inter-residue 13 C- 15 N correlation experiments with 13 C- 13 C spin-diffusion studies, it becomes feasible to partially assign backbone and side-chain resonances in solid proteins. The performance of sequences using 15 N instead of 13 C detection is evaluated regarding sensitivity and resolution for a labelled dipeptide (L-Val-L-Phe). The techniques are used for a partial assignment of the 15 N and 13 C resonances in human ubiquitin

A note on ranking assignments using reoptimization

DEFF Research Database (Denmark)

Pedersen, Christian Roed; Nielsen, L.R.; Andersen, K.A.

2005-01-01

We consider the problem of ranking assignments according to cost in the classical linear assignment problem. An algorithm partitioning the set of possible assignments, as suggested by Murty, is presented where, for each partition, the optimal assignment is calculated using a new reoptimization...

Competitive Traffic Assignment in Road Networks

Directory of Open Access Journals (Sweden)

Krylatov Alexander Y.

2016-09-01

Full Text Available Recently in-vehicle route guidance and information systems are rapidly developing. Such systems are expected to reduce congestion in an urban traffic area. This social benefit is believed to be reached by imposing the route choices on the network users that lead to the system optimum traffic assignment. However, guidance service could be offered by different competitive business companies. Then route choices of different mutually independent groups of users may reject traffic assignment from the system optimum state. In this paper, a game theoretic approach is shown to be very efficient to formalize competitive traffic assignment problem with various groups of users in the form of non-cooperative network game with the Nash equilibrium search. The relationships between the Wardrop’s system optimum associated with the traffic assignment problem and the Nash equilibrium associated with the competitive traffic assignment problem are investigated. Moreover, some related aspects of the Nash equilibrium and the Wardrop’s user equilibrium assignments are also discussed.

Backbone resonance assignments of the outer membrane lipoprotein FrpD from Neisseria meningitidis

Czech Academy of Sciences Publication Activity Database

Bumba, Ladislav; Sviridova, E.; Kutá-Smatanová, Ivana; Řezáčová, Pavlína; Veverka, Václav

2014-01-01

Roč. 8, č. 1 (2014), s. 53-55 ISSN 1874-2718 R&D Projects: GA ČR(CZ) GAP207/11/0717; GA MŠk(CZ) LK11205 Institutional support: RVO:61388963 ; RVO:61388971 ; RVO:67179843 Keywords : Neisseria meningitidis * FrpC * FrpD * backbone assignments * NMR * iron-regulated protein Subject RIV: CE - Biochemistry Impact factor: 0.760, year: 2014

FISCAL DECENTRALIZATION IN THE DRC: EVIDENCE OFREVENUE ASSIGNMENT

Directory of Open Access Journals (Sweden)

Angelita Kithatu-Kiwekete

2017-07-01

Full Text Available The rationalefor central government to devolve resources for service provisionhas been debated in decentralization literature. Decentralization enhancesdemocracy,encouragesparticipation in local development initiativesandpromotes local political accountability.This discourse has been complemented bythe implementation of fiscal decentralization to increase the ability of sub-nationalgovernment in financing municipal service delivery. Fiscal decentralization hasoften been adopted by African statessince the onset ofthe New PublicManagement erain an effortto improvethe standard ofgovernance. The concernis that African states have taken minimal steps to adopt fiscal devolution thatpromotes revenue assignment which in turn limits sub-nationalgovernments’ability to generate own source revenues.This article examines the revenue assignment function of fiscal decentralization inthe Democratic Republic of Congo(DRCinthelight of decentralizationconcerns that have been raised by civil society, as the country charts its course todemocracy. The article is a desktop study that will consider documents andpoliciesin theDRCon thenational, provincialand locallevel as far asstaterevenue sourcesare concerned. Revenue assignment should enable DRC’sprovinces and local authoritiestogeneratesignificantrevenueindependently.However, post-conflict reconstruction and development efforts in the Great Lakesregion and in the DRC have largely isolated decentralization which wouldotherwise entrench local fiscalautonomy infinancing for local services anddevelopment. The article concludes that revenue generation for local authoritiesandtheprovinces in the DRC is still very centralised by the national government.Thearticleproposes policy recommendations that will be useful for the country toensurethatdecentralization effortsinclude fiscal devolution toenhance thefinancing for local development initiatives.

Real life working shift assignment problem

Science.gov (United States)

Sze, San-Nah; Kwek, Yeek-Ling; Tiong, Wei-King; Chiew, Kang-Leng

2017-07-01

This study concerns about the working shift assignment in an outlet of Supermarket X in Eastern Mall, Kuching. The working shift assignment needs to be solved at least once in every month. Current approval process of working shifts is too troublesome and time-consuming. Furthermore, the management staff cannot have an overview of manpower and working shift schedule. Thus, the aim of this study is to develop working shift assignment simulation and propose a working shift assignment solution. The main objective for this study is to fulfill manpower demand at minimum operation cost. Besides, the day off and meal break policy should be fulfilled accordingly. Demand based heuristic is proposed to assign working shift and the quality of the solution is evaluated by using the real data.

Raman spectroscopy of adsorbed water in clays: first attempt at band assignment

Energy Technology Data Exchange (ETDEWEB)

Ligny, Dominique de; Guillaud, Emmanuel [Institut Lumiere Matiere, CNRS, Universite Lyon 1, 12 rue Ada Byron, 69622 Villeurbanne (France); Gailhanou, Helene; Blanc, Philippe [BRGM, Service D3E, 3 avenue Claude Guillemin, 45000 Orleans (France)

2013-07-01

Raman spectroscopy can be a useful tool to determine water content within clays, or even in highly saturated solutions. The following assignment is proposed for the OH region of SAz-2: the two large bands at 3260 and 3475 cm{sup -1} are assigned to water in pores, the first one to water molecules coordinated to the interlayer cations, and the second one to structural Al-OH groups The band at 3600 cm{sup -1} is therefore more likely related to adsorbed water on the clay surface. Simple intensity ratios of these different bands give good estimates of water content. (authors)

24 CFR 221.770 - Assignment option.

Science.gov (United States)

2010-04-01

... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Assignment option. 221.770 Section... § 221.770 Assignment option. A mortgagee holding a conditional or firm commitment issued on or before... mortgagee's approved underwriter on or before November 30, 1983) has the option to assign, transfer and...

Job Assignments under Moral Hazard

DEFF Research Database (Denmark)

Koch, Alexander; Nafziger, Julia

Inefficient job assignments are usually explained with incomplete information about employees' abilities or contractual imperfections. We show that inefficient assignments arise even without uncertainty about the employee's ability and with complete contracts. Building on this result we provide...

24 CFR 221.255 - Assignment option.

Science.gov (United States)

2010-04-01

... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Assignment option. 221.255 Section... Assignment option. (a) A mortgagee holding a mortgage insured pursuant to a conditional or firm commitment issued on or before November 30, 1983 has the option to assign, transfer and deliver to the Commissioner...

“C.R.E.A.T.E.”-ing Unique Primary-Source Research Paper Assignments for a Pleasure and Pain Course Teaching Neuroscientific Principles in a Large General Education Undergraduate Course

Science.gov (United States)

Bodnar, Richard J.; Rotella, Francis M.; Loiacono, Ilyssa; Coke, Tricia; Olsson, Kerstin; Barrientos, Alicia; Blachorsky, Lauren; Warshaw, Deena; Buras, Agata; Sanchez, Ciara M.; Azad, Raihana; Stellar, James R.

2016-01-01

A large (250 registrants) General Education lecture course, Pleasure and Pain, presented basic neuroscience principles as they related to animal and human models of pleasure and pain by weaving basic findings related to food and drug addiction and analgesic states with human studies examining empathy, social neuroscience and neuroeconomics. In its first four years, the course grade was based on weighted scores from two multiple-choice exams and a five-page review of three unique peer-reviewed research articles. Although well-registered and well-received, 18% of the students received Incomplete grades, primarily due to failing to submit the paper that went largely unresolved and eventually resulted in a failing grade. To rectify this issue, a modified version of the C.R.E.A.T.E. (Consider, Read, Elucidate hypotheses, Analyze and interpret data, Think of the next Experiment) method replaced the paper with eight structured assignments focusing on an initial general-topic article, the introduction-methods, and results-discussion of each of three related peer-review neuroscience-related articles, and a final summary. Compliance in completing these assignments was very high, resulting in only 11 INC grades out of 228 students. Thus, use of the C.R.E.A.T.E. method reduced the percentage of problematic INC grades from 18% to 4.8%, a 73% decline, without changing the overall grade distribution. Other analyses suggested the students achieved a deeper understanding of the scientific process using the C.R.E.A.T.E. method relative to the original term paper assignment. PMID:27385918

Large-scale identification of odorant-binding proteins and chemosensory proteins from expressed sequence tags in insects

Science.gov (United States)

2009-01-01

Background Insect odorant binding proteins (OBPs) and chemosensory proteins (CSPs) play an important role in chemical communication of insects. Gene discovery of these proteins is a time-consuming task. In recent years, expressed sequence tags (ESTs) of many insect species have accumulated, thus providing a useful resource for gene discovery. Results We have developed a computational pipeline to identify OBP and CSP genes from insect ESTs. In total, 752,841 insect ESTs were examined from 54 species covering eight Orders of Insecta. From these ESTs, 142 OBPs and 177 CSPs were identified, of which 117 OBPs and 129 CSPs are new. The complete open reading frames (ORFs) of 88 OBPs and 123 CSPs were obtained by electronic elongation. We randomly chose 26 OBPs from eight species of insects, and 21 CSPs from four species for RT-PCR validation. Twenty two OBPs and 16 CSPs were confirmed by RT-PCR, proving the efficiency and reliability of the algorithm. Together with all family members obtained from the NCBI (OBPs) or the UniProtKB (CSPs), 850 OBPs and 237 CSPs were analyzed for their structural characteristics and evolutionary relationship. Conclusions A large number of new OBPs and CSPs were found, providing the basis for deeper understanding of these proteins. In addition, the conserved motif and evolutionary analysis provide some new insights into the evolution of insect OBPs and CSPs. Motif pattern fine-tune the functions of OBPs and CSPs, leading to the minor difference in binding sex pheromone or plant volatiles in different insect Orders. PMID:20034407

Exploring the composition of protein-ligand binding sites on a large scale.

Directory of Open Access Journals (Sweden)

Nickolay A Khazanov

Full Text Available The residue composition of a ligand binding site determines the interactions available for diffusion-mediated ligand binding, and understanding general composition of these sites is of great importance if we are to gain insight into the functional diversity of the proteome. Many structure-based drug design methods utilize such heuristic information for improving prediction or characterization of ligand-binding sites in proteins of unknown function. The Binding MOAD database if one of the largest curated sets of protein-ligand complexes, and provides a source of diverse, high-quality data for establishing general trends of residue composition from currently available protein structures. We present an analysis of 3,295 non-redundant proteins with 9,114 non-redundant binding sites to identify residues over-represented in binding regions versus the rest of the protein surface. The Binding MOAD database delineates biologically-relevant "valid" ligands from "invalid" small-molecule ligands bound to the protein. Invalids are present in the crystallization medium and serve no known biological function. Contacts are found to differ between these classes of ligands, indicating that residue composition of biologically relevant binding sites is distinct not only from the rest of the protein surface, but also from surface regions capable of opportunistic binding of non-functional small molecules. To confirm these trends, we perform a rigorous analysis of the variation of residue propensity with respect to the size of the dataset and the content bias inherent in structure sets obtained from a large protein structure database. The optimal size of the dataset for establishing general trends of residue propensities, as well as strategies for assessing the significance of such trends, are suggested for future studies of binding-site composition.

Large-scale proteomic identification of S100 proteins in breast cancer tissues

International Nuclear Information System (INIS)

Cancemi, Patrizia; Di Cara, Gianluca; Albanese, Nadia Ninfa; Costantini, Francesca; Marabeti, Maria Rita; Musso, Rosa; Lupo, Carmelo; Roz, Elena; Pucci-Minafra, Ida

2010-01-01

Attempts to reduce morbidity and mortality in breast cancer is based on efforts to identify novel biomarkers to support prognosis and therapeutic choices. The present study has focussed on S100 proteins as a potentially promising group of markers in cancer development and progression. One reason of interest in this family of proteins is because the majority of the S100 genes are clustered on a region of human chromosome 1q21 that is prone to genomic rearrangements. Moreover, there is increasing evidence that S100 proteins are often up-regulated in many cancers, including breast, and this is frequently associated with tumour progression. Samples of breast cancer tissues were obtained during surgical intervention, according to the bioethical recommendations, and cryo-preserved until used. Tissue extracts were submitted to proteomic preparations for 2D-IPG. Protein identification was performed by N-terminal sequencing and/or peptide mass finger printing. The majority of the detected S100 proteins were absent, or present at very low levels, in the non-tumoral tissues adjacent to the primary tumor. This finding strengthens the role of S100 proteins as putative biomarkers. The proteomic screening of 100 cryo-preserved breast cancer tissues showed that some proteins were ubiquitously expressed in almost all patients while others appeared more sporadic. Most, if not all, of the detected S100 members appeared reciprocally correlated. Finally, from the perspective of biomarkers establishment, a promising finding was the observation that patients which developed distant metastases after a three year follow-up showed a general tendency of higher S100 protein expression, compared to the disease-free group. This article reports for the first time the comparative proteomic screening of several S100 protein members among a large group of breast cancer patients. The results obtained strongly support the hypothesis that a significant deregulation of multiple S100 protein members is

An algorithm for ranking assignments using reoptimization

DEFF Research Database (Denmark)

Pedersen, Christian Roed; Nielsen, Lars Relund; Andersen, Kim Allan

2008-01-01

We consider the problem of ranking assignments according to cost in the classical linear assignment problem. An algorithm partitioning the set of possible assignments, as suggested by Murty, is presented where, for each partition, the optimal assignment is calculated using a new reoptimization...... technique. Computational results for the new algorithm are presented...

48 CFR 42.602 - Assignment and location.

Science.gov (United States)

2010-10-01

... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Assignment and location... Assignment and location. (a) A CACO may be assigned only when (1) the contractor has at least two locations..., or a full-time CACO may be assigned. In determining the location of the CACO, the responsible agency...

Using interviews to understand the assignment mechanism in a nonexperimental study: the case of eighth grade algebra.

Science.gov (United States)

Rickles, Jordan H

2011-10-01

Many inquiries regarding the causal effects of policies or programs are based on research designs where the treatment assignment process is unknown, and thus valid inferences depend on tenuous assumptions about the assignment mechanism. This article draws attention to the importance of understanding the assignment mechanism in policy and program evaluation studies, and illustrates how information collected through interviews can develop a richer understanding of the assignment mechanism. Focusing on the issue of student assignment to algebra in 8th grade, I show how a preliminary data collection effort aimed at understanding the assignment mechanism is particularly beneficial in multisite observational studies in education. The findings, based on ten interviews and administrative data from a large school district, draw attention to the often ignored heterogeneity in the assignment mechanism across schools. These findings likely extend beyond the current research project in question to related educational policy issues such as ability grouping, tracking, differential course taking, and curricular intensity, as well as other social programs in which the assignment mechanism can differ across sites.

Geographical assignment of hospitalists in an urban teaching hospital: feasibility and impact on efficiency and provider satisfaction.

Science.gov (United States)

Bryson, Christine; Boynton, Greta; Stepczynski, Anna; Garb, Jane; Kleppel, Reva; Irani, Farzan; Natanasabapathy, Siva; Stefan, Mihaela S

2017-10-01

To evaluate whether implementation of a geographic model of assigning hospitalists is feasible and sustainable in a large hospitalist program and assess its impact on provider satisfaction, perceived efficiency and patient outcomes. Pre (3 months) - post (12 months) intervention study conducted from June 2014 through September 2015 at a tertiary care medical center with a large hospitalist program caring for patients scattered in 4 buildings and 16 floors. Hospitalists were assigned to a particular nursing unit (geographic assignment) with a goal of having over 80% of their assigned patients located on their assigned unit. Satisfaction and perceived efficiency were assessed through a survey administered before and after the intervention. Geographic assignment percentage increased from an average of 60% in the pre-intervention period to 93% post-intervention. The number of hospitalists covering a 32 bed unit decreased from 8-10 pre to 2-3 post-intervention. A majority of physicians (87%) thought that geography had a positive impact on the overall quality of care. Respondents reported that they felt that geography increased time spent with patient/caregivers to discuss plan of care (p < 0.001); improved communication with nurses (p = 0.0009); and increased sense of teamwork with nurses/case managers (p < 0.001). Mean length of stay (4.54 vs 4.62 days), 30-day readmission rates (16.0% vs 16.6%) and patient satisfaction (79.9 vs 77.3) did not change significantly between the pre- and post-implementation period. The discharge before noon rate improved slightly (47.5% - 54.1%). Implementation of a unit-based model in a large hospitalist program is feasible and sustainable with appropriate planning and support. The geographical model of care increased provider satisfaction and perceived efficiency; it also facilitated the implementation of other key interventions such as interdisciplinary rounds.

Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks.

Directory of Open Access Journals (Sweden)

Sumeet Agarwal

2010-06-01

Full Text Available The idea of "date" and "party" hubs has been influential in the study of protein-protein interaction networks. Date hubs display low co-expression with their partners, whilst party hubs have high co-expression. It was proposed that party hubs are local coordinators whereas date hubs are global connectors. Here, we show that the reported importance of date hubs to network connectivity can in fact be attributed to a tiny subset of them. Crucially, these few, extremely central, hubs do not display particularly low expression correlation, undermining the idea of a link between this quantity and hub function. The date/party distinction was originally motivated by an approximately bimodal distribution of hub co-expression; we show that this feature is not always robust to methodological changes. Additionally, topological properties of hubs do not in general correlate with co-expression. However, we find significant correlations between interaction centrality and the functional similarity of the interacting proteins. We suggest that thinking in terms of a date/party dichotomy for hubs in protein interaction networks is not meaningful, and it might be more useful to conceive of roles for protein-protein interactions rather than for individual proteins.

Predicting protein complexes from weighted protein-protein interaction graphs with a novel unsupervised methodology: Evolutionary enhanced Markov clustering.

Science.gov (United States)

Theofilatos, Konstantinos; Pavlopoulou, Niki; Papasavvas, Christoforos; Likothanassis, Spiros; Dimitrakopoulos, Christos; Georgopoulos, Efstratios; Moschopoulos, Charalampos; Mavroudi, Seferina

2015-03-01

Proteins are considered to be the most important individual components of biological systems and they combine to form physical protein complexes which are responsible for certain molecular functions. Despite the large availability of protein-protein interaction (PPI) information, not much information is available about protein complexes. Experimental methods are limited in terms of time, efficiency, cost and performance constraints. Existing computational methods have provided encouraging preliminary results, but they phase certain disadvantages as they require parameter tuning, some of them cannot handle weighted PPI data and others do not allow a protein to participate in more than one protein complex. In the present paper, we propose a new fully unsupervised methodology for predicting protein complexes from weighted PPI graphs. The proposed methodology is called evolutionary enhanced Markov clustering (EE-MC) and it is a hybrid combination of an adaptive evolutionary algorithm and a state-of-the-art clustering algorithm named enhanced Markov clustering. EE-MC was compared with state-of-the-art methodologies when applied to datasets from the human and the yeast Saccharomyces cerevisiae organisms. Using public available datasets, EE-MC outperformed existing methodologies (in some datasets the separation metric was increased by 10-20%). Moreover, when applied to new human datasets its performance was encouraging in the prediction of protein complexes which consist of proteins with high functional similarity. In specific, 5737 protein complexes were predicted and 72.58% of them are enriched for at least one gene ontology (GO) function term. EE-MC is by design able to overcome intrinsic limitations of existing methodologies such as their inability to handle weighted PPI networks, their constraint to assign every protein in exactly one cluster and the difficulties they face concerning the parameter tuning. This fact was experimentally validated and moreover, new

Using codon optimization, chaperone co-expression, and rational mutagenesis for production and NMR assignments of human eIF2α

International Nuclear Information System (INIS)

Ito, Takuhiro; Wagner, Gerhard

2004-01-01

Producing a well behaved sample at high concentration is one of the main hurdles when starting a new project on an interesting protein. Especially when one attempts to overexpress a eukaryotic protein in bacteria, some difficulties are encountered, such as low expression level, low solubility, or even lack of folded structure. Overexpression in prokaryotic systems is highly desirable for cost-effective production of different isotope-labeled samples needed for NMR studies. Here we describe generally applicable methods for obtaining highly concentrated protein samples efficiently. This approach was developed as we tried to produce a NMR-suitable sample of the 35 kDa human translation initiation factor eIF2α, a protein that expresses poorly in E. coli and has very low solubility. First, an E. coli codon-optimized gene was synthesized on a thermal cycler, which increased the expression level by a factor of two. Second, we used co-expression of bacterial chaperone proteins, which largely increased the fraction of correctly folded protein found in the soluble phase. Third, we used rational mutagenesis guided by both the sequence alignment among homologues and the homology of one domain to a known fold for improving solubility and stability of the target protein by tenfold. Combining all these methods made it possible to produce from a one-liter preparation a 0.5 mM sample of human eIF2α that showed well-resolved NMR spectra and enabled nearly complete assignment of the protein. These methods may be generally useful for studies of other eukaryotic proteins that are otherwise difficult to express and exhibit poor solubility

On-demand high-capacity ride-sharing via dynamic trip-vehicle assignment.

Science.gov (United States)

Alonso-Mora, Javier; Samaranayake, Samitha; Wallar, Alex; Frazzoli, Emilio; Rus, Daniela

2017-01-17

Ride-sharing services are transforming urban mobility by providing timely and convenient transportation to anybody, anywhere, and anytime. These services present enormous potential for positive societal impacts with respect to pollution, energy consumption, congestion, etc. Current mathematical models, however, do not fully address the potential of ride-sharing. Recently, a large-scale study highlighted some of the benefits of car pooling but was limited to static routes with two riders per vehicle (optimally) or three (with heuristics). We present a more general mathematical model for real-time high-capacity ride-sharing that (i) scales to large numbers of passengers and trips and (ii) dynamically generates optimal routes with respect to online demand and vehicle locations. The algorithm starts from a greedy assignment and improves it through a constrained optimization, quickly returning solutions of good quality and converging to the optimal assignment over time. We quantify experimentally the tradeoff between fleet size, capacity, waiting time, travel delay, and operational costs for low- to medium-capacity vehicles, such as taxis and van shuttles. The algorithm is validated with ∼3 million rides extracted from the New York City taxicab public dataset. Our experimental study considers ride-sharing with rider capacity of up to 10 simultaneous passengers per vehicle. The algorithm applies to fleets of autonomous vehicles and also incorporates rebalancing of idling vehicles to areas of high demand. This framework is general and can be used for many real-time multivehicle, multitask assignment problems.

Expansion of protein domain repeats.

Directory of Open Access Journals (Sweden)

Asa K Björklund

2006-08-01

Full Text Available Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mechanisms behind these tandem duplications are not well-understood. Here, we have studied the evolution, function, protein structure, gene structure, and phylogenetic distribution of domain repeats. For this purpose we have assigned Pfam-A domain families to 24 proteomes with more sensitive domain assignments in the repeat regions. These assignments confirmed previous findings that eukaryotes, and in particular vertebrates, contain a much higher fraction of proteins with repeats compared with prokaryotes. The internal sequence similarity in each protein revealed that the domain repeats are often expanded through duplications of several domains at a time, while the duplication of one domain is less common. Many of the repeats appear to have been duplicated in the middle of the repeat region. This is in strong contrast to the evolution of other proteins that mainly works through additions of single domains at either terminus. Further, we found that some domain families show distinct duplication patterns, e.g., nebulin domains have mainly been expanded with a unit of seven domains at a time, while duplications of other domain families involve varying numbers of domains. Finally, no common mechanism for the expansion of all repeats could be detected. We found that the duplication patterns show no dependence on the size of the domains. Further, repeat expansion in some families can possibly be explained by shuffling of exons. However, exon shuffling could not have created all repeats.

Recognition of functional sites in protein structures.

Science.gov (United States)

Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J

2004-06-04

Recognition of regions on the surface of one protein, that are similar to a binding site of another is crucial for the prediction of molecular interactions and for functional classifications. We first describe a novel method, SiteEngine, that assumes no sequence or fold similarities and is able to recognize proteins that have similar binding sites and may perform similar functions. We achieve high efficiency and speed by introducing a low-resolution surface representation via chemically important surface points, by hashing triangles of physico-chemical properties and by application of hierarchical scoring schemes for a thorough exploration of global and local similarities. We proceed to rigorously apply this method to functional site recognition in three possible ways: first, we search a given functional site on a large set of complete protein structures. Second, a potential functional site on a protein of interest is compared with known binding sites, to recognize similar features. Third, a complete protein structure is searched for the presence of an a priori unknown functional site, similar to known sites. Our method is robust and efficient enough to allow computationally demanding applications such as the first and the third. From the biological standpoint, the first application may identify secondary binding sites of drugs that may lead to side-effects. The third application finds new potential sites on the protein that may provide targets for drug design. Each of the three applications may aid in assigning a function and in classification of binding patterns. We highlight the advantages and disadvantages of each type of search, provide examples of large-scale searches of the entire Protein Data Base and make functional predictions.

LiveBench-1: continuous benchmarking of protein structure prediction servers.

Science.gov (United States)

Bujnicki, J M; Elofsson, A; Fischer, D; Rychlewski, L

2001-02-01

We present a novel, continuous approach aimed at the large-scale assessment of the performance of available fold-recognition servers. Six popular servers were investigated: PDB-Blast, FFAS, T98-lib, GenTHREADER, 3D-PSSM, and INBGU. The assessment was conducted using as prediction targets a large number of selected protein structures released from October 1999 to April 2000. A target was selected if its sequence showed no significant similarity to any of the proteins previously available in the structural database. Overall, the servers were able to produce structurally similar models for one-half of the targets, but significantly accurate sequence-structure alignments were produced for only one-third of the targets. We further classified the targets into two sets: easy and hard. We found that all servers were able to find the correct answer for the vast majority of the easy targets if a structurally similar fold was present in the server's fold libraries. However, among the hard targets--where standard methods such as PSI-BLAST fail--the most sensitive fold-recognition servers were able to produce similar models for only 40% of the cases, half of which had a significantly accurate sequence-structure alignment. Among the hard targets, the presence of updated libraries appeared to be less critical for the ranking. An "ideally combined consensus" prediction, where the results of all servers are considered, would increase the percentage of correct assignments by 50%. Each server had a number of cases with a correct assignment, where the assignments of all the other servers were wrong. This emphasizes the benefits of considering more than one server in difficult prediction tasks. The LiveBench program (http://BioInfo.PL/LiveBench) is being continued, and all interested developers are cordially invited to join.

Solution structure and dynamics of melanoma inhibitory activity protein

International Nuclear Information System (INIS)

Lougheed, Julie C.; Domaille, Peter J.; Handel, Tracy M.

2002-01-01

Melanoma inhibitory activity (MIA) is a small secreted protein that is implicated in cartilage cell maintenance and melanoma metastasis. It is representative of a recently discovered family of proteins that contain a Src Homologous 3 (SH3) subdomain. While SH3 domains are normally found in intracellular proteins and mediate protein-protein interactions via recognition of polyproline helices, MIA is single-domain extracellular protein, and it probably binds to a different class of ligands.Here we report the assignments, solution structure, and dynamics of human MIA determined by heteronuclear NMR methods. The structures were calculated in a semi-automated manner without manual assignment of NOE crosspeaks, and have a backbone rmsd of 0.38 A over the ordered regions of the protein. The structure consists of an SH3-like subdomain with N- and C-terminal extensions of approximately 20 amino acids each that together form a novel fold. The rmsd between the solution structure and our recently reported crystal structure is 0.86 A over the ordered regions of the backbone, and the main differences are localized to the most dynamic regions of the protein. The similarity between the NMR and crystal structures supports the use of automated NOE assignments and ambiguous restraints to accelerate the calculation of NMR structures

1H, 15N and 13C NMR Assignments of Mouse Methionine Sulfoxide Reductase B2

Science.gov (United States)

Breivik, Åshild S.; Aachmann, Finn L.; Sal, Lena S.; Kim, Hwa-Young; Del Conte, Rebecca; Gladyshev, Vadim N.; Dikiy, Alexander

2011-01-01

A recombinant mouse methionine-r-sulfoxide reductase 2 (MsrB2ΔS) isotopically labeled with 15N and 15N/13C was generated. We report here the 1H, 15N and 13C NMR assignments of the reduced form of this protein. PMID:19636904

A collaborative filtering approach for protein-protein docking scoring functions.

Science.gov (United States)

Bourquard, Thomas; Bernauer, Julie; Azé, Jérôme; Poupon, Anne

2011-04-22

A protein-protein docking procedure traditionally consists in two successive tasks: a search algorithm generates a large number of candidate conformations mimicking the complex existing in vivo between two proteins, and a scoring function is used to rank them in order to extract a native-like one. We have already shown that using Voronoi constructions and a well chosen set of parameters, an accurate scoring function could be designed and optimized. However to be able to perform large-scale in silico exploration of the interactome, a near-native solution has to be found in the ten best-ranked solutions. This cannot yet be guaranteed by any of the existing scoring functions. In this work, we introduce a new procedure for conformation ranking. We previously developed a set of scoring functions where learning was performed using a genetic algorithm. These functions were used to assign a rank to each possible conformation. We now have a refined rank using different classifiers (decision trees, rules and support vector machines) in a collaborative filtering scheme. The scoring function newly obtained is evaluated using 10 fold cross-validation, and compared to the functions obtained using either genetic algorithms or collaborative filtering taken separately. This new approach was successfully applied to the CAPRI scoring ensembles. We show that for 10 targets out of 12, we are able to find a near-native conformation in the 10 best ranked solutions. Moreover, for 6 of them, the near-native conformation selected is of high accuracy. Finally, we show that this function dramatically enriches the 100 best-ranking conformations in near-native structures.

Exogenous spatial attention influences figure-ground assignment.

Science.gov (United States)

Vecera, Shaun P; Flevaris, Anastasia V; Filapek, Joseph C

2004-01-01

In a hierarchical stage account of vision, figure-ground assignment is thought to be completed before the operation of focal spatial attention. Results of previous studies have supported this account by showing that unpredictive, exogenous spatial precues do not influence figure-ground assignment, although voluntary attention can influence figure-ground assignment. However, in these studies, attention was not summoned directly to a region in a figure-ground display. In three experiments, we addressed the relationship between figure-ground assignment and visuospatial attention. In Experiment 1, we replicated the finding that exogenous precues do not influence figure-ground assignment when they direct attention outside of a figure-ground stimulus. In Experiment 2, we demonstrated that exogenous attention can influence figure-ground assignment if it is directed to one of the regions in a figure-ground stimulus. In Experiment 3, we demonstrated that exogenous attention can influence figure-ground assignment in displays that contain a Gestalt figure-ground cue; this result suggests that figure-ground processes are not entirely completed prior to the operation of focal spatial attention. Exogenous spatial attention acts as a cue for figure-ground assignment and can affect the outcome of figure-ground processes.

Detecting Protein-Protein Interactions in the Intact Cell of Bacillus subtilis (ATCC 6633)

OpenAIRE

Winters, Michael S.; Day, R. A.

2003-01-01

The salt bridge, paired group-specific reagent cyanogen (ethanedinitrile; C2N2) converts naturally occurring pairs of functional groups into covalently linked products. Cyanogen readily permeates cell walls and membranes. When the paired groups are shared between associated proteins, isolation of the covalently linked proteins allows their identity to be assigned. Examination of organisms of known genome sequence permits identification of the linked proteins by mass spectrometric techniques a...

K-nearest uphill clustering in the protein structure space

KAUST Repository

Cui, Xuefeng; Gao, Xin

2016-01-01

The protein structure classification problem, which is to assign a protein structure to a cluster of similar proteins, is one of the most fundamental problems in the construction and application of the protein structure space. Early manually curated

Improving the Accuracy of NMR Structures of Large Proteins Using Pseudocontact Shifts as Long-Range Restraints

Energy Technology Data Exchange (ETDEWEB)

Gaponenko, Vadim [National Cancer Institute, Structural Biophysics Laboratory (United States); Sarma, Siddhartha P. [Indian Institute of Science, Molecular Biophysics Unit (India); Altieri, Amanda S. [National Cancer Institute, Structural Biophysics Laboratory (United States); Horita, David A. [Wake Forest University School of Medicine, Department of Biochemistry (United States); Li, Jess; Byrd, R. Andrew [National Cancer Institute, Structural Biophysics Laboratory (United States)], E-mail: rabyrd@ncifcrf.gov

2004-03-15

We demonstrate improved accuracy in protein structure determination for large ({>=}30 kDa), deuterated proteins (e.g. STAT4{sub NT}) via the combination of pseudocontact shifts for amide and methyl protons with the available NOEs in methyl-protonated proteins. The improved accuracy is cross validated by Q-factors determined from residual dipolar couplings measured as a result of magnetic susceptibility alignment. The paramagnet is introduced via binding to thiol-reactive EDTA, and multiple sites can be serially engineered to obtain data from alternative orientations of the paramagnetic anisotropic susceptibility tensor. The technique is advantageous for systems where the target protein has strong interactions with known alignment media.

Phase modulated 2D HSQC-TOCSY for unambiguous assignment of overlapping spin systems

Science.gov (United States)

Singh, Amrinder; Dubey, Abhinav; Adiga, Satish K.; Atreya, Hanudatta S.

2018-01-01

We present a new method that allows one to unambiguously resolve overlapping spin systems often encountered in biomolecular systems such as peptides and proteins or in samples containing a mixture of different molecules such as in metabolomics. We address this problem using the recently proposed phase modulation approach. By evolving the 1H chemical shifts in a conventional two dimensional (2D) HSQC-TOCSY experiment for a fixed delay period, the phase/intensity of set of cross peaks belonging to one spin system are modulated differentially relative to those of its overlapping counterpart, resulting in their discrimination and recognition. The method thus accelerates the process of identification and resonance assignment of individual compounds in complex mixtures. This approach facilitated the assignment of molecules in the embryo culture medium used in human assisted reproductive technology.

WebAssign: Assessing Your Students' Understanding Continuously

Science.gov (United States)

Risley, John S.

1999-11-01

Motivating students to learn is a constant challenge for faculty. Technology can play a significant role. One such solution is WebAssign — a web-based homework system that offers new teaching and learning opportunities for educators and their students. WebAssign delivers, collects, grades, and records customized homework assignments over the Internet. Students get immediate feedback with credit and instructors can implement "Just-in-Time" teaching. In this talk, I will describe how assignments can be generated with different numerical values for each question, giving each student a unique problem to solve. This feature encourages independent thinking with the benefit of collaborative learning. Example assignments taken from textbook questions and intellectually engaging Java applet simulations will be shown. Studies and first-hand experience on the educational impact of using WebAssign will also be discussed.

Thermal motion in proteins: Large effects on the time-averaged interaction energies

International Nuclear Information System (INIS)

Goethe, Martin; Rubi, J. Miguel; Fita, Ignacio

2016-01-01

As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.

Thermal motion in proteins: Large effects on the time-averaged interaction energies

Energy Technology Data Exchange (ETDEWEB)

Goethe, Martin, E-mail: martingoethe@ub.edu; Rubi, J. Miguel [Departament de Física Fonamental, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona (Spain); Fita, Ignacio [Institut de Biologia Molecular de Barcelona, Baldiri Reixac 10, 08028 Barcelona (Spain)

2016-03-15

As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.

Identification of a third protein 4.1 tumor suppressor, protein 4.1R, in meningioma pathogenesis

Energy Technology Data Exchange (ETDEWEB)

Robb, Victoria A.; Li, Wen; Gascard, Philippe; Perry, Arie; Mohandas, Narla; Gutmann, David H.

2003-06-11

Meningiomas are common tumors of the central nervous system, however, the mechanisms under lying their pathogenesis are largely undefined. Two members of the Protein 4.1 super family, the neuro fibromatosis 2 (NF2) gene product (merlin/schwannomin) and Protein 4.1B have been implicated as meningioma tumor suppressors. In this report, we demonstrate that another Protein 4.1 family member, Protein 4.1R, also functions as a meningioma tumor suppressor. Based on the assignment of the Protein 4.1R gene to chromosome 1p32-36, a common region of deletion observed in meningiomas, we analyzed Protein 4.1R expression in meningioma cell lines and surgical tumor specimens. We observed loss of Protein 4.1R protein expression in two meningioma cell lines (IOMM-Lee, CH157-MN) by Western blotting as well as in 6 of 15 sporadic meningioma as by immuno histo chemistry (IHC). Analysis of a subset of these sporadic meningiomas by fluorescent in situ hybridization (FISH) with a Protein 4.1R specific probe demonstrated 100 percent concordance with the IHC results. In support of a meningioma tumor suppressor function, over expression of Protein 4.1R resulted in suppression of IOMM-Lee and CH157MN cell proliferation. Similar to the Protein 4.1B and merlin meningioma tumor suppressors, Protein 4.1R localization in the membrane fraction increased significantly under conditions of growth arrest in vitro. Lastly, Protein 4.1R interacted with some known merlin/Protein 4.1B interactors such as CD44 and bII-spectrin, but did not associate with the Protein 4.1B interactors 14-3-3 and PRMT3 or the merlin binding proteins SCHIP-1 and HRS. Collectively, these results suggest that Protein 4.1R functions as an important tumor suppressor important in the molecular pathogenesis of meningioma.

FindFoci: a focus detection algorithm with automated parameter training that closely matches human assignments, reduces human inconsistencies and increases speed of analysis.

Directory of Open Access Journals (Sweden)

Alex D Herbert

Full Text Available Accurate and reproducible quantification of the accumulation of proteins into foci in cells is essential for data interpretation and for biological inferences. To improve reproducibility, much emphasis has been placed on the preparation of samples, but less attention has been given to reporting and standardizing the quantification of foci. The current standard to quantitate foci in open-source software is to manually determine a range of parameters based on the outcome of one or a few representative images and then apply the parameter combination to the analysis of a larger dataset. Here, we demonstrate the power and utility of using machine learning to train a new algorithm (FindFoci to determine optimal parameters. FindFoci closely matches human assignments and allows rapid automated exploration of parameter space. Thus, individuals can train the algorithm to mirror their own assignments and then automate focus counting using the same parameters across a large number of images. Using the training algorithm to match human assignments of foci, we demonstrate that applying an optimal parameter combination from a single image is not broadly applicable to analysis of other images scored by the same experimenter or by other experimenters. Our analysis thus reveals wide variation in human assignment of foci and their quantification. To overcome this, we developed training on multiple images, which reduces the inconsistency of using a single or a few images to set parameters for focus detection. FindFoci is provided as an open-source plugin for ImageJ.

Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA

Directory of Open Access Journals (Sweden)

Malliavin Thérèse E

2008-06-01

Full Text Available Abstract Background The Ambiguous Restraints for Iterative Assignment (ARIA approach is widely used for NMR structure determination. It is based on simultaneously calculating structures and assigning NOE through an iterative protocol. The final solution consists of a set of conformers and a list of most probable assignments for the input NOE peak list. Results ARIA was extended with a series of graphical tools to facilitate a detailed analysis of the intermediate and final results of the ARIA protocol. These additional features provide (i an interactive contact map, serving as a tool for the analysis of assignments, and (ii graphical representations of structure quality scores and restraint statistics. The interactive contact map between residues can be clicked to obtain information about the restraints and their contributions. Profiles of quality scores are plotted along the protein sequence, and contact maps provide information of the agreement with the data on a residue pair level. Conclusion The graphical tools and outputs described here significantly extend the validation and analysis possibilities of NOE assignments given by ARIA as well as the analysis of the quality of the final structure ensemble. These tools are included in the latest version of ARIA, which is available at http://aria.pasteur.fr. The Web site also contains an installation guide, a user manual and example calculations.

Solving the rectangular assignment problem and applications

NARCIS (Netherlands)

Bijsterbosch, J.; Volgenant, A.

2010-01-01

The rectangular assignment problem is a generalization of the linear assignment problem (LAP): one wants to assign a number of persons to a smaller number of jobs, minimizing the total corresponding costs. Applications are, e.g., in the fields of object recognition and scheduling. Further, we show

7 CFR 900.106 - Assignment of mediator.

Science.gov (United States)

2010-01-01

... 7 Agriculture 8 2010-01-01 2010-01-01 false Assignment of mediator. 900.106 Section 900.106 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing... Assignment of mediator. The Director of the Division shall assign a mediator, from the group designated by...

A new method for protein estimation in large seeds using fast-neutron-activation analysis

International Nuclear Information System (INIS)

Gupta, U.C.; Misra, S.C.; Rao, U.S.

1974-01-01

A new method was developed for the determination of protein content of large seeds, using powders of different N content. The powders were obtained by mixing glucose with amino acids in different proportions and were irradiated with and without the seeds in the MeV neutron flux. The irradiated samples were counted under identical conditions and their activities were used to calculate the protein content of the seeds. The results were compared with those obtained by conventional activation technique and were found to be in good agreement. This new method has the advantage of being non-destructive. (author)

DNA-Directed Assembly of Capture Tools for Constitutional Studies of Large Protein Complexes.

Science.gov (United States)

Meyer, Rebecca; Faesen, Alex; Vogel, Katrin; Jeganathan, Sadasivam; Musacchio, Andrea; Niemeyer, Christof M

2015-06-10

Large supramolecular protein complexes, such as the molecular machinery involved in gene regulation, cell signaling, or cell division, are key in all fundamental processes of life. Detailed elucidation of structure and dynamics of such complexes can be achieved by reverse-engineering parts of the complexes in order to probe their interactions with distinctive binding partners in vitro. The exploitation of DNA nanostructures to mimic partially assembled supramolecular protein complexes in which the presence and state of two or more proteins are decisive for binding of additional building blocks is reported here. To this end, four-way DNA Holliday junction motifs bearing a fluorescein and a biotin tag, for tracking and affinity capture, respectively, are site-specifically functionalized with centromeric protein (CENP) C and CENP-T. The latter serves as baits for binding of the so-called KMN component, thereby mimicking early stages of the assembly of kinetochores, structures that mediate and control the attachment of microtubules to chromosomes in the spindle apparatus. Results from pull-down experiments are consistent with the hypothesis that CENP-C and CENP-T may bind cooperatively to the KMN network. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

My Favorite Assignment.

Science.gov (United States)

ABCA Bulletin, 1983

1983-01-01

Describes three assignments for enticing business communication students to undertake library research: an analysis of a Fortune 500 company, a career choice report, and a report on an organization that offers potential employment. (AEA)

Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm

Energy Technology Data Exchange (ETDEWEB)

Kuszewski, John J.; Thottungal, Robin Augustine [National Institutes of Health, Imaging Sciences Laboratory, Center for Information Technology (United States); Clore, G. Marius [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: mariusc@mail.nih.gov; Schwieters, Charles D. [National Institutes of Health, Imaging Sciences Laboratory, Center for Information Technology (United States)], E-mail: Charles.Schwieters@nih.gov

2008-08-15

We report substantial improvements to the previously introduced automated NOE assignment and structure determination protocol known as PASD (Kuszewski et al. (2004) J Am Chem Soc 26:6258-6273). The improved protocol includes extensive analysis of input spectral data to create a low-resolution contact map of residues expected to be close in space. This map is used to obtain reasonable initial guesses of NOE assignment likelihoods which are refined during subsequent structure calculations. Information in the contact map about which residues are predicted to not be close in space is applied via conservative repulsive distance restraints which are used in early phases of the structure calculations. In comparison with the previous protocol, the new protocol requires significantly less computation time. We show results of running the new PASD protocol on six proteins and demonstrate that useful assignment and structural information is extracted on proteins of more than 220 residues. We show that useful assignment information can be obtained even in the case in which a unique structure cannot be determined.

Screening and large-scale expression of membrane proteins in mammalian cells for structural studies.

Science.gov (United States)

Goehring, April; Lee, Chia-Hsueh; Wang, Kevin H; Michel, Jennifer Carlisle; Claxton, Derek P; Baconguis, Isabelle; Althoff, Thorsten; Fischer, Suzanne; Garcia, K Christopher; Gouaux, Eric

2014-11-01

Structural, biochemical and biophysical studies of eukaryotic membrane proteins are often hampered by difficulties in overexpression of the candidate molecule. Baculovirus transduction of mammalian cells (BacMam), although a powerful method to heterologously express membrane proteins, can be cumbersome for screening and expression of multiple constructs. We therefore developed plasmid Eric Gouaux (pEG) BacMam, a vector optimized for use in screening assays, as well as for efficient production of baculovirus and robust expression of the target protein. In this protocol, we show how to use small-scale transient transfection and fluorescence-detection size-exclusion chromatography (FSEC) experiments using a GFP-His8-tagged candidate protein to screen for monodispersity and expression level. Once promising candidates are identified, we describe how to generate baculovirus, transduce HEK293S GnTI(-) (N-acetylglucosaminyltransferase I-negative) cells in suspension culture and overexpress the candidate protein. We have used these methods to prepare pure samples of chicken acid-sensing ion channel 1a (cASIC1) and Caenorhabditis elegans glutamate-gated chloride channel (GluCl) for X-ray crystallography, demonstrating how to rapidly and efficiently screen hundreds of constructs and accomplish large-scale expression in 4-6 weeks.

Preparation and characterization of monodisperse large-porous silica microspheres as the matrix for protein separation.

Science.gov (United States)

Xia, Hongjun; Wan, Guangping; Zhao, Junlong; Liu, Jiawei; Bai, Quan

2016-11-04

High performance liquid chromatography (HPLC) is a kind of efficient separation technology and has been used widely in many fields. Micro-sized porous silica microspheres as the most popular matrix have been used for fast separation and analysis in HPLC. In this paper, the monodisperse large-porous silica microspheres with controllable size and structure were successfully synthesized with polymer microspheres as the templates and characterized. First, the poly(glycidyl methacrylate-co-ethyleneglycol dimethacrylate) microspheres (P GMA-EDMA ) were functionalized with tetraethylenepentamine (TEPA) to generate amino groups which act as a catalyst in hydrolysis of tetraethyl orthosilicate (TEOS) to form Si-containing low molecular weight species. Then the low molecular weight species diffused into the functionalized P GMA-EDMA microspheres by induction force of the amino groups to form polymer/silica hybrid microspheres. Finally, the organic polymer templates were removed by calcination, and the large-porous silica microspheres were obtained. The compositions, morphology, size distribution, specific surface area and pore size distribution of the porous silica microspheres were characterized by infrared analyzer, scanning-electron microscopy, dynamic laser scattering, the mercury intrusion method and thermal gravimetric analysis, respectively. The results show that the agglomeration of the hybrid microspheres can be overcome when the templates were functionalized with TEPA as amination reagent, and the yield of 95.7% of the monodisperse large-porous silica microspheres can be achieved with high concentration of polymer templates. The resulting large-porous silica microspheres were modified with octadecyltrichlorosilane (ODS) and the chromatographic evaluation was performed by separating the proteins and the digest of BSA. The baseline separation of seven kinds of protein standards was achieved, and the column delivered a better performance when separating BSA digests

The hepatitis B virus large surface protein (LHBs) is a transcriptional activator.

Science.gov (United States)

Hildt, E; Saher, G; Bruss, V; Hofschneider, P H

1996-11-01

It has been shown that a C-terminally truncated form of the middle-sized hepatitis B virus (HBV) surface protein (MHBst) functions as a transcriptional activator. This function is dependent on the cytosolic orientation of the N-terminal PreS2 domain of MHBst, but in the case of wild-type MHBs, the PreS2 domain is contranslationally translocated into the ER lumen. Recent reports demonstrated that the PreS2 domain of the large HBV surface protein (LHBs) initially remains on the cytosolic side of the ER membrane after translation. Therefore, the question arose as to whether the LHBs protein exhibits the same transcriptional activator function as MHBst. We show that LHBs, like MHBst, is indeed able to activate a variety of promoter elements. There is evidence for a PKC-dependent activation of AP-1 and NF-kappa B by LHBs. Downstream of the PKC the functionality of c-Raf-1 kinase is a prerequisite for LHBs-dependent activation of AP-1 and NF-kappa B since inhibition of c-Raf-1 kinase abolishes LHBs-dependent transcriptional activation of AP-1 and NF-kappa B.

Managing voluntary turnover through challenging assignments

NARCIS (Netherlands)

Preenen, P.T.Y.; de Pater, I.E.; van Vianen, A.E.M.; Keijzer, L.

2011-01-01

This study examines employees’ challenging assignments as manageable means to reduce turnover intentions, job search behaviors, and voluntary turnover. Results indicate that challenging assignments are negatively related to turnover intentions and job search behaviors and that these relationships

Managing voluntary turnover through challenging assignments

NARCIS (Netherlands)

Preenen, P.T.Y.; Pater, I.E. de; Vianen, A.E.M. van; Keijzer, L.

2011-01-01

This study examines employees' challenging assignments as manageable means to reduce turnover intentions, job search behaviors, and voluntary turnover. Results indicate that challenging assignments are negatively related to turnover intentions and job search behaviors and that these relationships

Mining protein function from text using term-based support vector machines

Science.gov (United States)

Rice, Simon B; Nenadic, Goran; Stapley, Benjamin J

2005-01-01

Background Text mining has spurred huge interest in the domain of biology. The goal of the BioCreAtIvE exercise was to evaluate the performance of current text mining systems. We participated in Task 2, which addressed assigning Gene Ontology terms to human proteins and selecting relevant evidence from full-text documents. We approached it as a modified form of the document classification task. We used a supervised machine-learning approach (based on support vector machines) to assign protein function and select passages that support the assignments. As classification features, we used a protein's co-occurring terms that were automatically extracted from documents. Results The results evaluated by curators were modest, and quite variable for different problems: in many cases we have relatively good assignment of GO terms to proteins, but the selected supporting text was typically non-relevant (precision spanning from 3% to 50%). The method appears to work best when a substantial set of relevant documents is obtained, while it works poorly on single documents and/or short passages. The initial results suggest that our approach can also mine annotations from text even when an explicit statement relating a protein to a GO term is absent. Conclusion A machine learning approach to mining protein function predictions from text can yield good performance only if sufficient training data is available, and significant amount of supporting data is used for prediction. The most promising results are for combined document retrieval and GO term assignment, which calls for the integration of methods developed in BioCreAtIvE Task 1 and Task 2. PMID:15960835

Aligator: A computational tool for optimizing total chemical synthesis of large proteins.

Science.gov (United States)

Jacobsen, Michael T; Erickson, Patrick W; Kay, Michael S

2017-09-15

The scope of chemical protein synthesis (CPS) continues to expand, driven primarily by advances in chemical ligation tools (e.g., reversible solubilizing groups and novel ligation chemistries). However, the design of an optimal synthesis route can be an arduous and fickle task due to the large number of theoretically possible, and in many cases problematic, synthetic strategies. In this perspective, we highlight recent CPS tool advances and then introduce a new and easy-to-use program, Aligator (Automated Ligator), for analyzing and designing the most efficient strategies for constructing large targets using CPS. As a model set, we selected the E. coli ribosomal proteins and associated factors for computational analysis. Aligator systematically scores and ranks all feasible synthetic strategies for a particular CPS target. The Aligator script methodically evaluates potential peptide segments for a target using a scoring function that includes solubility, ligation site quality, segment lengths, and number of ligations to provide a ranked list of potential synthetic strategies. We demonstrate the utility of Aligator by analyzing three recent CPS projects from our lab: TNFα (157 aa), GroES (97 aa), and DapA (312 aa). As the limits of CPS are extended, we expect that computational tools will play an increasingly important role in the efficient execution of ambitious CPS projects such as production of a mirror-image ribosome. Copyright © 2017 Elsevier Ltd. All rights reserved.

Scaffolding students’ assignments

DEFF Research Database (Denmark)

Slot, Marie Falkesgaard

2013-01-01

This article discusses scaffolding in typical student assignments in mother tongue learning materials in upper secondary education in Denmark and the United Kingdom. It has been determined that assignments do not have sufficient scaffolding end features to help pupils understand concepts and build...... objects. The article presents the results of empirical research on tasks given in Danish and British learning materials. This work is based on a further development of my PhD thesis: “Learning materials in the subject of Danish” (Slot 2010). The main focus is how cognitive models (and subsidiary explicit...... learning goals) can help students structure their argumentative and communica-tive learning processes, and how various multimodal representations can give more open-ended learning possibilities for collaboration. The article presents a short introduction of the skills for 21st century learning and defines...

Protein-transitions in and out of the dough matrix in wheat flour mixing.

Science.gov (United States)

Wang, Xiaolong; Appels, Rudi; Zhang, Xiaoke; Bekes, Ferenc; Torok, Kitti; Tomoskozi, Sandor; Diepeveen, Dean; Ma, Wujun; Islam, Shahidul

2017-02-15

Sequential protein behavior in the wheat dough matrix under continuous mixing and heating treatment has been studied using Mixolab-dough samples from two Australian wheat cultivars, Westonia and Wyalkatchem. Size exclusion high performance liquid chromatography (SE-HPLC) and two-dimensional gel electrophoresis (2-DGE) analysis indicated that 32min (80°C) was a critical time point in forming large protein complexes and loosing extractability of several protein groups like y-type high molecular weight glutenin subunits (HMW-GSs), gamma-gliadins, beta-amylases, serpins, and metabolic proteins with higher mass. Up to 32min (80°C) Westonia showed higher protein extractability compared to Wyalkatchem although it was in the opposite direction thereafter. Twenty differentially expressed proteins could be assigned to chromosomes 1D, 3A, 4A, 4B, 4D, 6A, 6B, 7A and 7B. The results expanded the range of proteins associated with changes in the gluten-complex during processing and provided targets for selecting new genetic variants associated with altered quality attributes of the flour. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tracing the geographic origin of traded leopard body parts in the indian subcontinent with DNA-based assignment tests.

Science.gov (United States)

Mondol, Samrat; Sridhar, Vanjulavalli; Yadav, Prasanjeet; Gubbi, Sanjay; Ramakrishnan, Uma

2015-04-01

Illicit trade in wildlife products is rapidly decimating many species across the globe. Such trade is often underestimated for wide-ranging species until it is too late for the survival of their remaining populations. Policing this trade could be vastly improved if one could reliably determine geographic origins of illegal wildlife products and identify areas where greater enforcement is needed. Using DNA-based assignment tests (i.e., samples are assigned to geographic locations), we addressed these factors for leopards (Panthera pardus) on the Indian subcontinent. We created geography-specific allele frequencies from a genetic reference database of 173 leopards across India to infer geographic origins of DNA samples from 40 seized leopard skins. Sensitivity analyses of samples of known geographic origins and assignments of seized skins demonstrated robust assignments for Indian leopards. We found that confiscated pelts seized in small numbers were not necessarily from local leopards. The geographic footprint of large seizures appeared to be bigger than the cumulative footprint of several smaller seizures, indicating widespread leopard poaching across the subcontinent. Our seized samples had male-biased sex ratios, especially the large seizures. From multiple seized sample assignments, we identified central India as a poaching hotspot for leopards. The techniques we applied can be used to identify origins of seized illegal wildlife products and trade routes at the subcontinent scale and beyond. © 2014 Society for Conservation Biology.

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

Energy Technology Data Exchange (ETDEWEB)

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

2009-08-15

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

Assignment of element and isotope factors

International Nuclear Information System (INIS)

Schneider, R.A.

1984-01-01

Element and isotope factors are assigned in the NICS internal accounting system at the Exxon Fuel Fabrication Facility on the basis of coded information included on the material transfer documents. This paper explains more fully the manner in which NICS assigns these factors

Spectral fitting for signal assignment and structural analysis of uniformly {sup 13}C-labeled solid proteins by simulated annealing based on chemical shifts and spin dynamics

Energy Technology Data Exchange (ETDEWEB)

Matsuki, Yoh; Akutsu, Hideo; Fujiwara, Toshimichi [Osaka University, Institute for Protein Research (Japan)], E-mail: tfjwr@protein.osaka-u.ac.jp

2007-08-15

We describe an approach for the signal assignment and structural analysis with a suite of two-dimensional {sup 13}C-{sup 13}C magic-angle-spinning solid-state NMR spectra of uniformly {sup 13}C-labeled peptides and proteins. We directly fit the calculated spectra to experimental ones by simulated annealing in restrained molecular dynamics program CNS as a function of atomic coordinates. The spectra are calculated from the conformation dependent chemical shift obtained with SHIFTX and the cross-peak intensities computed for recoupled dipolar interactions. This method was applied to a membrane-bound 14-residue peptide, mastoparan-X. The obtained C', C{sup {alpha}} and C{sup {beta}} chemical shifts agreed with those reported previously at the precisions of 0.2, 0.7 and 0.4 ppm, respectively. This spectral fitting program also provides backbone dihedral angles with a precision of about 50 deg. from the spectra even with resonance overlaps. The restraints on the angles were improved by applying protein database program TALOS to the obtained chemical shifts. The peptide structure provided by these restraints was consistent with the reported structure at the backbone RMSD of about 1 A.

From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data.

Science.gov (United States)

Vella, Danila; Zoppis, Italo; Mauri, Giancarlo; Mauri, Pierluigi; Di Silvestre, Dario

2017-12-01

The reductionist approach of dissecting biological systems into their constituents has been successful in the first stage of the molecular biology to elucidate the chemical basis of several biological processes. This knowledge helped biologists to understand the complexity of the biological systems evidencing that most biological functions do not arise from individual molecules; thus, realizing that the emergent properties of the biological systems cannot be explained or be predicted by investigating individual molecules without taking into consideration their relations. Thanks to the improvement of the current -omics technologies and the increasing understanding of the molecular relationships, even more studies are evaluating the biological systems through approaches based on graph theory. Genomic and proteomic data are often combined with protein-protein interaction (PPI) networks whose structure is routinely analyzed by algorithms and tools to characterize hubs/bottlenecks and topological, functional, and disease modules. On the other hand, co-expression networks represent a complementary procedure that give the opportunity to evaluate at system level including organisms that lack information on PPIs. Based on these premises, we introduce the reader to the PPI and to the co-expression networks, including aspects of reconstruction and analysis. In particular, the new idea to evaluate large-scale proteomic data by means of co-expression networks will be discussed presenting some examples of application. Their use to infer biological knowledge will be shown, and a special attention will be devoted to the topological and module analysis.

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

Differential protein expression, DNA binding and interaction with SV40 large tumour antigen implicate the p63-family of proteins in replicative senescence.

Science.gov (United States)

Djelloul, Siham; Tarunina, Marina; Barnouin, Karin; Mackay, Alan; Jat, Parmjit S

2002-02-07

P53 activity plays a key role in mammalian cells when they undergo replicative senescence at their Hayflick limit. To determine whether p63 proteins, members of the family of p53-related genes, are also involved in this process, we examined their expression in serially passaged rat embryo fibroblasts. Upon senescence, two truncated DeltaNp63 proteins decreased in abundance whereas two TAp63 isoforms accumulated. 2-D gel analysis showed that the DeltaNp63 proteins underwent post-translational modifications in both proliferating and senescent cells. Direct binding of DeltaNp63 proteins to a p53 consensus motif was greater in proliferating cells than senescent cells. In contrast p63alpha isoforms bound to DNA in a p53 dependent manner and this was higher in senescent cells than proliferating cells. An interaction of p63alpha proteins with SV40 large tumour antigen was also detected and ectopic expression of DeltaNp63alpha can extend the lifespan of rat embryo fibroblasts. Taken together the results indicate that p63 proteins may play a role in replicative senescence either by competition for p53 DNA binding sites or by direct interaction with p53 protein bound to DNA.

MetaboID: a graphical user interface package for assignment of 1H NMR spectra of bodyfluids and tissues.

Science.gov (United States)

MacKinnon, Neil; Somashekar, Bagganahalli S; Tripathi, Pratima; Ge, Wencheng; Rajendiran, Thekkelnaycke M; Chinnaiyan, Arul M; Ramamoorthy, Ayyalusamy

2013-01-01

Nuclear magnetic resonance based measurements of small molecule mixtures continues to be confronted with the challenge of spectral assignment. While multi-dimensional experiments are capable of addressing this challenge, the imposed time constraint becomes prohibitive, particularly with the large sample sets commonly encountered in metabolomic studies. Thus, one-dimensional spectral assignment is routinely performed, guided by two-dimensional experiments on a selected sample subset; however, a publicly available graphical interface for aiding in this process is currently unavailable. We have collected spectral information for 360 unique compounds from publicly available databases including chemical shift lists and authentic full resolution spectra, supplemented with spectral information for 25 compounds collected in-house at a proton NMR frequency of 900 MHz. This library serves as the basis for MetaboID, a Matlab-based user interface designed to aid in the one-dimensional spectral assignment process. The tools of MetaboID were built to guide resonance assignment in order of increasing confidence, starting from cursory compound searches based on chemical shift positions to analysis of authentic spike experiments. Together, these tools streamline the often repetitive task of spectral assignment. The overarching goal of the integrated toolbox of MetaboID is to centralize the one dimensional spectral assignment process, from providing access to large chemical shift libraries to providing a straightforward, intuitive means of spectral comparison. Such a toolbox is expected to be attractive to both experienced and new metabolomic researchers as well as general complex mixture analysts. Copyright © 2012 Elsevier Inc. All rights reserved.

Integral and peripheral association of proteins and protein complexes with Yersinia pestis inner and outer membranes

Directory of Open Access Journals (Sweden)

Bunai Christine L

2009-02-01

Full Text Available Abstract Yersinia pestis proteins were sequentially extracted from crude membranes with a high salt buffer (2.5 M NaBr, an alkaline solution (180 mM Na2CO3, pH 11.3 and membrane denaturants (8 M urea, 2 M thiourea and 1% amidosulfobetaine-14. Separation of proteins by 2D gel electrophoresis was followed by identification of more than 600 gene products by MS. Data from differential 2D gel display experiments, comparing protein abundances in cytoplasmic, periplasmic and all three membrane fractions, were used to assign proteins found in the membrane fractions to three protein categories: (i integral membrane proteins and peripheral membrane proteins with low solubility in aqueous solutions (220 entries; (ii peripheral membrane proteins with moderate to high solubility in aqueous solutions (127 entries; (iii cytoplasmic or ribosomal membrane-contaminating proteins (80 entries. Thirty-one proteins were experimentally associated with the outer membrane (OM. Circa 50 proteins thought to be part of membrane-localized, multi-subunit complexes were identified in high Mr fractions of membrane extracts via size exclusion chromatography. This data supported biologically meaningful assignments of many proteins to the membrane periphery. Since only 32 inner membrane (IM proteins with two or more predicted transmembrane domains (TMDs were profiled in 2D gels, we resorted to a proteomic analysis by 2D-LC-MS/MS. Ninety-four additional IM proteins with two or more TMDs were identified. The total number of proteins associated with Y. pestis membranes increased to 456 and included representatives of all six β-barrel OM protein families and 25 distinct IM transporter families.

Improved formulations and an Adaptive Large Neighborhood Search heuristic for the integrated berth allocation and quay crane assignment problem

DEFF Research Database (Denmark)

Iris, Cagatay; Pacino, Dario; Røpke, Stefan

2017-01-01

This paper focuses on the integrated berth allocation and quay crane assignment problem in container terminals. We consider the decrease in the marginal productivity of quay cranes and the increase in handling time due to deviation from the desired position. We consider a continuous berth...

Comparison of weight-loss diets with different compositions of fat, protein, and carbohydrates.

Science.gov (United States)

Sacks, Frank M; Bray, George A; Carey, Vincent J; Smith, Steven R; Ryan, Donna H; Anton, Stephen D; McManus, Katherine; Champagne, Catherine M; Bishop, Louise M; Laranjo, Nancy; Leboff, Meryl S; Rood, Jennifer C; de Jonge, Lilian; Greenway, Frank L; Loria, Catherine M; Obarzanek, Eva; Williamson, Donald A

2009-02-26

The possible advantage for weight loss of a diet that emphasizes protein, fat, or carbohydrates has not been established, and there are few studies that extend beyond 1 year. We randomly assigned 811 overweight adults to one of four diets; the targeted percentages of energy derived from fat, protein, and carbohydrates in the four diets were 20, 15, and 65%; 20, 25, and 55%; 40, 15, and 45%; and 40, 25, and 35%. The diets consisted of similar foods and met guidelines for cardiovascular health. The participants were offered group and individual instructional sessions for 2 years. The primary outcome was the change in body weight after 2 years in two-by-two factorial comparisons of low fat versus high fat and average protein versus high protein and in the comparison of highest and lowest carbohydrate content. At 6 months, participants assigned to each diet had lost an average of 6 kg, which represented 7% of their initial weight; they began to regain weight after 12 months. By 2 years, weight loss remained similar in those who were assigned to a diet with 15% protein and those assigned to a diet with 25% protein (3.0 and 3.6 kg, respectively); in those assigned to a diet with 20% fat and those assigned to a diet with 40% fat (3.3 kg for both groups); and in those assigned to a diet with 65% carbohydrates and those assigned to a diet with 35% carbohydrates (2.9 and 3.4 kg, respectively) (P>0.20 for all comparisons). Among the 80% of participants who completed the trial, the average weight loss was 4 kg; 14 to 15% of the participants had a reduction of at least 10% of their initial body weight. Satiety, hunger, satisfaction with the diet, and attendance at group sessions were similar for all diets; attendance was strongly associated with weight loss (0.2 kg per session attended). The diets improved lipid-related risk factors and fasting insulin levels. Reduced-calorie diets result in clinically meaningful weight loss regardless of which macronutrients they emphasize

Comparison of Weight-Loss Diets with Different Compositions of Fat, Protein, and Carbohydrates

Science.gov (United States)

Sacks, Frank M.; Bray, George A.; Carey, Vincent J.; Smith, Steven R.; Ryan, Donna H.; Anton, Stephen D.; McManus, Katherine; Champagne, Catherine M.; Bishop, Louise M.; Laranjo, Nancy; Leboff, Meryl S.; Rood, Jennifer C.; de Jonge, Lilian; Greenway, Frank L.; Loria, Catherine M.; Obarzanek, Eva; Williamson, Donald A.

2009-01-01

BACKGROUND The possible advantage for weight loss of a diet that emphasizes protein, fat, or carbohydrates has not been established, and there are few studies that extend beyond 1 year. METHODS We randomly assigned 811 overweight adults to one of four diets; the targeted percentages of energy derived from fat, protein, and carbohydrates in the four diets were 20, 15, and 65%; 20, 25, and 55%; 40, 15, and 45%; and 40, 25, and 35%. The diets consisted of similar foods and met guidelines for cardiovascular health. The participants were offered group and individual instructional sessions for 2 years. The primary outcome was the change in body weight after 2 years in two-by-two factorial comparisons of low fat versus high fat and average protein versus high protein and in the comparison of highest and lowest carbohydrate content. RESULTS At 6 months, participants assigned to each diet had lost an average of 6 kg, which represented 7% of their initial weight; they began to regain weight after 12 months. By 2 years, weight loss remained similar in those who were assigned to a diet with 15% protein and those assigned to a diet with 25% protein (3.0 and 3.6 kg, respectively); in those assigned to a diet with 20% fat and those assigned to a diet with 40% fat (3.3 kg for both groups); and in those assigned to a diet with 65% carbohydrates and those assigned to a diet with 35% carbohydrates (2.9 and 3.4 kg, respectively) (P>0.20 for all comparisons). Among the 80% of participants who completed the trial, the average weight loss was 4 kg; 14 to 15% of the participants had a reduction of at least 10% of their initial body weight. Satiety, hunger, satisfaction with the diet, and attendance at group sessions were similar for all diets; attendance was strongly associated with weight loss (0.2 kg per session attended). The diets improved lipid-related risk factors and fasting insulin levels. CONCLUSIONS Reduced-calorie diets result in clinically meaningful weight loss regardless of

K-nearest uphill clustering in the protein structure space

KAUST Repository

Cui, Xuefeng

2016-08-26

The protein structure classification problem, which is to assign a protein structure to a cluster of similar proteins, is one of the most fundamental problems in the construction and application of the protein structure space. Early manually curated protein structure classifications (e.g., SCOP and CATH) are very successful, but recently suffer the slow updating problem because of the increased throughput of newly solved protein structures. Thus, fully automatic methods to cluster proteins in the protein structure space have been designed and developed. In this study, we observed that the SCOP superfamilies are highly consistent with clustering trees representing hierarchical clustering procedures, but the tree cutting is very challenging and becomes the bottleneck of clustering accuracy. To overcome this challenge, we proposed a novel density-based K-nearest uphill clustering method that effectively eliminates noisy pairwise protein structure similarities and identifies density peaks as cluster centers. Specifically, the density peaks are identified based on K-nearest uphills (i.e., proteins with higher densities) and K-nearest neighbors. To our knowledge, this is the first attempt to apply and develop density-based clustering methods in the protein structure space. Our results show that our density-based clustering method outperforms the state-of-the-art clustering methods previously applied to the problem. Moreover, we observed that computational methods and human experts could produce highly similar clusters at high precision values, while computational methods also suggest to split some large superfamilies into smaller clusters. © 2016 Elsevier B.V.

MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

Directory of Open Access Journals (Sweden)

Kuczmarski Thomas A

2006-10-01

Full Text Available Abstract Background MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. Description MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. Conclusion MannDB comprises a large number of genomes and comprehensive protein

Large-scale gene function analysis with the PANTHER classification system.

Science.gov (United States)

Mi, Huaiyu; Muruganujan, Anushya; Casagrande, John T; Thomas, Paul D

2013-08-01

The PANTHER (protein annotation through evolutionary relationship) classification system (http://www.pantherdb.org/) is a comprehensive system that combines gene function, ontology, pathways and statistical analysis tools that enable biologists to analyze large-scale, genome-wide data from sequencing, proteomics or gene expression experiments. The system is built with 82 complete genomes organized into gene families and subfamilies, and their evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models or HMMs). Genes are classified according to their function in several different ways: families and subfamilies are annotated with ontology terms (Gene Ontology (GO) and PANTHER protein class), and sequences are assigned to PANTHER pathways. The PANTHER website includes a suite of tools that enable users to browse and query gene functions, and to analyze large-scale experimental data with a number of statistical tests. It is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. In the 2013 release of PANTHER (v.8.0), in addition to an update of the data content, we redesigned the website interface to improve both user experience and the system's analytical capability. This protocol provides a detailed description of how to analyze genome-wide experimental data with the PANTHER classification system.

Diversity and dispersal of a ubiquitous protein family: acyl-CoA dehydrogenases.

Science.gov (United States)

Shen, Yao-Qing; Lang, B Franz; Burger, Gertraud

2009-09-01

Acyl-CoA dehydrogenases (ACADs), which are key enzymes in fatty acid and amino acid catabolism, form a large, pan-taxonomic protein family with at least 13 distinct subfamilies. Yet most reported ACAD members have no subfamily assigned, and little is known about the taxonomic distribution and evolution of the subfamilies. In completely sequenced genomes from approximately 210 species (eukaryotes, bacteria and archaea), we detect ACAD subfamilies by rigorous ortholog identification combining sequence similarity search with phylogeny. We then construct taxonomic subfamily-distribution profiles and build phylogenetic trees with orthologous proteins. Subfamily profiles provide unparalleled insight into the organisms' energy sources based on genome sequence alone and further predict enzyme substrate specificity, thus generating explicit working hypotheses for targeted biochemical experimentation. Eukaryotic ACAD subfamilies are traditionally considered as mitochondrial proteins, but we found evidence that in fungi one subfamily is located in peroxisomes and participates in a distinct beta-oxidation pathway. Finally, we discern horizontal transfer, duplication, loss and secondary acquisition of ACAD genes during evolution of this family. Through these unorthodox expansion strategies, the ACAD family is proficient in utilizing a large range of fatty acids and amino acids-strategies that could have shaped the evolutionary history of many other ancient protein families.

32 CFR 884.2 - Assigned responsibilities.

Science.gov (United States)

2010-07-01

... OF PERSONNEL TO UNITED STATES CIVILIAN AUTHORITIES FOR TRIAL § 884.2 Assigned responsibilities. (a... 32 National Defense 6 2010-07-01 2010-07-01 false Assigned responsibilities. 884.2 Section 884.2... requests for return of members to the United States for delivery to civilian authorities when the request...

Protein restriction in chronic renal failure

NARCIS (Netherlands)

ECHTEN, JEKT; NAUTA, J; HOP, WCJ; de Jong, MCJ; REITSMABIERENS, WCC; VANAMSTEL, SLBP; VANACKER, KJ; NOORDZIJ, CM; WOLFF, ED

The aim of the study was to investigate the effect of a protein restricted diet on renal function and growth of children with chronic renal failure. In a multicentre prospective study 56 children (aged 2-18 years) with chronic renal failure were randomly assigned to the protein restricted (0.8-1.1

Large-scale analysis of intrinsic disorder flavors and associated functions in the protein sequence universe.

Science.gov (United States)

Necci, Marco; Piovesan, Damiano; Tosatto, Silvio C E

2016-12-01

Intrinsic disorder (ID) in proteins has been extensively described for the last decade; a large-scale classification of ID in proteins is mostly missing. Here, we provide an extensive analysis of ID in the protein universe on the UniProt database derived from sequence-based predictions in MobiDB. Almost half the sequences contain an ID region of at least five residues. About 9% of proteins have a long ID region of over 20 residues which are more abundant in Eukaryotic organisms and most frequently cover less than 20% of the sequence. A small subset of about 67,000 (out of over 80 million) proteins is fully disordered and mostly found in Viruses. Most proteins have only one ID, with short ID evenly distributed along the sequence and long ID overrepresented in the center. The charged residue composition of Das and Pappu was used to classify ID proteins by structural propensities and corresponding functional enrichment. Swollen Coils seem to be used mainly as structural components and in biosynthesis in both Prokaryotes and Eukaryotes. In Bacteria, they are confined in the nucleoid and in Viruses provide DNA binding function. Coils & Hairpins seem to be specialized in ribosome binding and methylation activities. Globules & Tadpoles bind antigens in Eukaryotes but are involved in killing other organisms and cytolysis in Bacteria. The Undefined class is used by Bacteria to bind toxic substances and mediate transport and movement between and within organisms in Viruses. Fully disordered proteins behave similarly, but are enriched for glycine residues and extracellular structures. © 2016 The Protein Society.

UFO: a web server for ultra-fast functional profiling of whole genome protein sequences.

Science.gov (United States)

Meinicke, Peter

2009-09-02

Functional profiling is a key technique to characterize and compare the functional potential of entire genomes. The estimation of profiles according to an assignment of sequences to functional categories is a computationally expensive task because it requires the comparison of all protein sequences from a genome with a usually large database of annotated sequences or sequence families. Based on machine learning techniques for Pfam domain detection, the UFO web server for ultra-fast functional profiling allows researchers to process large protein sequence collections instantaneously. Besides the frequencies of Pfam and GO categories, the user also obtains the sequence specific assignments to Pfam domain families. In addition, a comparison with existing genomes provides dissimilarity scores with respect to 821 reference proteomes. Considering the underlying UFO domain detection, the results on 206 test genomes indicate a high sensitivity of the approach. In comparison with current state-of-the-art HMMs, the runtime measurements show a considerable speed up in the range of four orders of magnitude. For an average size prokaryotic genome, the computation of a functional profile together with its comparison typically requires about 10 seconds of processing time. For the first time the UFO web server makes it possible to get a quick overview on the functional inventory of newly sequenced organisms. The genome scale comparison with a large number of precomputed profiles allows a first guess about functionally related organisms. The service is freely available and does not require user registration or specification of a valid email address.

UFO: a web server for ultra-fast functional profiling of whole genome protein sequences

Directory of Open Access Journals (Sweden)

Meinicke Peter

2009-09-01

Full Text Available Abstract Background Functional profiling is a key technique to characterize and compare the functional potential of entire genomes. The estimation of profiles according to an assignment of sequences to functional categories is a computationally expensive task because it requires the comparison of all protein sequences from a genome with a usually large database of annotated sequences or sequence families. Description Based on machine learning techniques for Pfam domain detection, the UFO web server for ultra-fast functional profiling allows researchers to process large protein sequence collections instantaneously. Besides the frequencies of Pfam and GO categories, the user also obtains the sequence specific assignments to Pfam domain families. In addition, a comparison with existing genomes provides dissimilarity scores with respect to 821 reference proteomes. Considering the underlying UFO domain detection, the results on 206 test genomes indicate a high sensitivity of the approach. In comparison with current state-of-the-art HMMs, the runtime measurements show a considerable speed up in the range of four orders of magnitude. For an average size prokaryotic genome, the computation of a functional profile together with its comparison typically requires about 10 seconds of processing time. Conclusion For the first time the UFO web server makes it possible to get a quick overview on the functional inventory of newly sequenced organisms. The genome scale comparison with a large number of precomputed profiles allows a first guess about functionally related organisms. The service is freely available and does not require user registration or specification of a valid email address.

The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

Energy Technology Data Exchange (ETDEWEB)

Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States); Petit, Chad M. [University of Alabama at Birmingham, Department of Biochemistry and Molecular Genetics (United States); Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States)

2016-06-15

We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27–98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

International Nuclear Information System (INIS)

Lee, Woonghee; Petit, Chad M.; Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L.

2016-01-01

We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27–98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

Personnel dose assignment practices

International Nuclear Information System (INIS)

Fix, J.J.

1993-04-01

Implementation of DOE N 5480.6 Radiological Control Manual Article 511(3) requirements, to minimize the assignment of personnel dosimeters, should be done only under a broader context ensuring that capabilities are in place to monitor and record personnel exposure both for compliance and for potential litigation. As noted in NCRP Report No. 114, personnel dosimetry programs are conducted to meet four major objectives: radiation safety program control and evaluation; regulatory compliance; epidemiological research; and litigation. A change to Article 511(3) is proposed that would require that minimizing the assignment of personnel dosimeters take place only following full evaluation of overall capabilities (e.g., access control, area dosimetry, etc.) to meet the NCRP objectives

Computational Aspects of Assigning Agents to a Line

DEFF Research Database (Denmark)

Aziz, Haris; Hougaard, Jens Leth; Moreno-Ternero, Juan D.

2017-01-01

-egalitarian assignments. The approach relies on an algorithm which is shown to be faster than general purpose algorithms for the assignment problem. We also extend the approach to probabilistic assignments and explore the computational features of existing, as well as new, methods for this setting....

Computational aspects of assigning agents to a line

DEFF Research Database (Denmark)

Aziz, Haris; Hougaard, Jens Leth; Moreno-Ternero, Juan D.

2017-01-01

-egalitarian assignments. The approach relies on an algorithm which is shown to be faster than general purpose algorithms for the assignment problem. We also extend the approach to probabilistic assignments and explore the computational features of existing, as well as new, methods for this setting....

Quadratic partial eigenvalue assignment in large-scale stochastic dynamic systems for resilient and economic design

Energy Technology Data Exchange (ETDEWEB)

Das, Sonjoy; Goswami, Kundan [University at Buffalo, NY (United States); Datta, Biswa N. [Northern Illinois University, IL (United States)

2014-12-10

Failure of structural systems under dynamic loading can be prevented via active vibration control which shifts the damped natural frequencies of the systems away from the dominant range of loading spectrum. The damped natural frequencies and the dynamic load typically show significant variations in practice. A computationally efficient methodology based on quadratic partial eigenvalue assignment technique and optimization under uncertainty has been formulated in the present work that will rigorously account for these variations and result in an economic and resilient design of structures. A novel scheme based on hierarchical clustering and importance sampling is also developed in this work for accurate and efficient estimation of probability of failure to guarantee the desired resilience level of the designed system. Numerical examples are presented to illustrate the proposed methodology.

Quadratic partial eigenvalue assignment in large-scale stochastic dynamic systems for resilient and economic design

International Nuclear Information System (INIS)

Das, Sonjoy; Goswami, Kundan; Datta, Biswa N.

2014-01-01

Failure of structural systems under dynamic loading can be prevented via active vibration control which shifts the damped natural frequencies of the systems away from the dominant range of loading spectrum. The damped natural frequencies and the dynamic load typically show significant variations in practice. A computationally efficient methodology based on quadratic partial eigenvalue assignment technique and optimization under uncertainty has been formulated in the present work that will rigorously account for these variations and result in an economic and resilient design of structures. A novel scheme based on hierarchical clustering and importance sampling is also developed in this work for accurate and efficient estimation of probability of failure to guarantee the desired resilience level of the designed system. Numerical examples are presented to illustrate the proposed methodology

A Computerized Approach to Trickle-Process, Random Assignment.

Science.gov (United States)

Braucht, G. Nicholas; Reichardt, Charles S.

1993-01-01

Procedures for implementing random assignment with trickle processing and ways they can be corrupted are described. A computerized method for implementing random assignment with trickle processing is presented as a desirable alternative in many situations and a way of protecting against threats to assignment validity. (SLD)

Writing Assignments that Promote Active Learning

Science.gov (United States)

Narayanan, M.

2014-12-01

Encourage students to write a detailed, analytical report correlating classroom discussions to an important historical event or a current event. Motivate students interview an expert from industry on a topic that was discussed in class. Ask the students to submit a report with supporting sketches, drawings, circuit diagrams and graphs. Propose that the students generate a complete a set of reading responses pertaining to an assigned topic. Require each student to bring in one comment or one question about an assigned reading. The assignment should be a recent publication in an appropriate journal. Have the students conduct a web search on an assigned topic. Ask them to generate a set of ideas that can relate to classroom discussions. Provide the students with a study guide. The study guide should provide about 10 or 15 short topics. Quiz the students on one or two of the topics. Encourage the students to design or develop some creative real-world examples based on a chapter discussed or a topic of interest. Require that students originate, develop, support and defend a viewpoint using a specifically assigned material. Make the students practice using or utilizing a set of new technical terms they have encountered in an assigned chapter. Have students develop original examples explaining the different terms. Ask the students to select one important terminology from the previous classroom discussions. Encourage the students to explain why they selected that particular word. Ask them to talk about the importance of the terminology from the point of view of their educational objectives and future career. Angelo, T. A. (1991). Ten easy pieces: Assessing higher learning in four dimensions. In T. A. Angelo (Ed.), Classroom research: Early lessons from success (pp. 17-31). New Directions for Teaching and Learning, No. 46. San Francisco: Jossey-Bass.

METHODOLOGY & CALCULATIONS FOR THE ASSIGNMENT OF WASTE FOR THE LARGE UNDERGROUND WASTE STORAGE TANKS AT THE HANFORD SITE

Energy Technology Data Exchange (ETDEWEB)

TU, T.A.

2007-01-04

Waste stored within tank farm double-shell tanks (DST) and single-shell tanks (SST) generates flammable gas (principally hydrogen) to varying degrees depending on the type, amount, geometry, and condition of the waste. The waste generates hydrogen through the radiolysis of water and organic compounds, thermolytic decomposition of organic compounds, and corrosion of a tank's carbon steel walls. Radiolysis and thermolytic decomposition also generates ammonia. Nonflammable gases, which act as dilutents (such as nitrous oxide), are also produced. Additional flammable gases (e.g., methane) are generated by chemical reactions between various degradation products of organic chemicals present in the tanks. Volatile and semi-volatile organic chemicals in tanks also produce organic vapors. The generated gases in tank waste are either released continuously to the tank headspace or are retained in the waste matrix. Retained gas may be released in a spontaneous or induced gas release event (GRE) that can significantly increase the flammable gas concentration in the tank headspace as described in RPP-7771, Flammable Gas Safety Isme Resolution. Appendices A through I provide supporting information. The document categorizes each of the large waste storage tanks into one of several categories based on each tank's waste and characteristics. These waste group assignments reflect a tank's propensity to retain a significant volume of flammable gases and the potential of the waste to release retained gas by a buoyant displacement event. Revision 6 is the annual update of the flammable gas Waste Groups for DSTs and SSTs.

Structural study of the membrane protein MscL using cell-free expression and solid-state NMR

Science.gov (United States)

Abdine, Alaa; Verhoeven, Michiel A.; Park, Kyu-Ho; Ghazi, Alexandre; Guittet, Eric; Berrier, Catherine; Van Heijenoort, Carine; Warschawski, Dror E.

2010-05-01

High-resolution structures of membrane proteins have so far been obtained mostly by X-ray crystallography, on samples where the protein is surrounded by detergent. Recent developments of solid-state NMR have opened the way to a new approach for the study of integral membrane proteins inside a membrane. At the same time, the extension of cell-free expression to the production of membrane proteins allows for the production of proteins tailor made for NMR. We present here an in situ solid-state NMR study of a membrane protein selectively labeled through the use of cell-free expression. The sample consists of MscL (mechano-sensitive channel of large conductance), a 75 kDa pentameric α-helical ion channel from Escherichia coli, reconstituted in a hydrated lipid bilayer. Compared to a uniformly labeled protein sample, the spectral crowding is greatly reduced in the cell-free expressed protein sample. This approach may be a decisive step required for spectral assignment and structure determination of membrane proteins by solid-state NMR.

Identifying and Remediating Student Misconceptions in Introductory Biology via Writing-to-Learn Assignments and Peer Review.

Science.gov (United States)

Halim, Audrey S; Finkenstaedt-Quinn, Solaire A; Olsen, Laura J; Gere, Anne Ruggles; Shultz, Ginger V

2018-06-01

Student misconceptions are an obstacle in science, technology, engineering, and mathematics courses and unless remediated may continue causing difficulties in learning as students advance in their studies. Writing-to-learn assignments (WTL) are characterized by their ability to promote in-depth conceptual learning by allowing students to explore their understanding of a topic. This study sought to determine whether and what types of misconceptions are elicited by WTL assignments and how the process of peer review and revision leads to remediation or propagation of misconceptions. We examined four WTL assignments in an introductory biology course in which students first wrote about content by applying it to a realistic scenario, then participated in a peer-review process before revising their work. Misconceptions were identified in all four assignments, with the greatest number pertaining to protein structure and function. Additionally, in certain contexts, students used scientific terminology incorrectly. Analysis of the drafts and peer-review comments generated six profiles by which misconceptions were addressed through the peer-review process. The prevalent mode of remediation arose through directed peer-review comments followed by correction during revision. It was also observed that additional misconceptions were elicited as students revised their writing in response to general peer-review suggestions.

Maternal Obesity Induces Sustained Inflammation in Both Fetal and Offspring Large Intestine of Sheep

Science.gov (United States)

Yan, Xu; Huang, Yan; Wang, Hui; Du, Min; Hess, Bret W.; Ford, Stephen P.; Nathanielsz, Peter W.; Zhu, Mei-Jun

2010-01-01

Background Both maternal obesity and inflammatory bowel diseases (IBDs) are increasing. It was hypothesized that maternal obesity induces an inflammatory response in the fetal large intestine, predisposing offspring to IBDs. Methods Nonpregnant ewes were assigned to a control (Con, 100% of National Research Council [NRC] recommendations) or obesogenic (OB, 150% of NRC) diet from 60 days before conception. The large intestine was sampled from fetuses at 135 days (term 150 days) after conception and from offspring lambs at 22.5 ± 0.5 months of age. Results Maternal obesity enhanced mRNA expression tumor necrosis factor (TNF)α, interleukin (IL)1α, IL1β, IL6, IL8, and monocyte/macrophage chemotactic protein-1 (MCP1), as well as macrophage markers, CD11b, CD14, and CD68 in fetal gut. mRNA expression of Toll-like receptor (TLR) 2 and TLR4 was increased in OB versus Con fetuses; correspondingly, inflammatory NF-κB and JNK signaling pathways were also upregulated. Both mRNA expression and protein content of transforming growth factor (TGF) β was increased. The IL-17A mRNA expression and protein content was higher in OB compared to Con samples, which was associated with fibrosis in the large intestine of OB fetuses. Similar inflammatory responses and enhanced fibrosis were detected in OB compared to Con offspring. Conclusions Maternal obesity induced inflammation and enhanced expression of proinflammatory cytokines in fetal and offspring large intestine, which correlated with increased TGFβ and IL17 expression. These data show that maternal obesity may predispose offspring gut to IBDs. PMID:21674707

Rapamycin-binding FKBP25 associates with diverse proteins that form large intracellular entities

International Nuclear Information System (INIS)

Galat, Andrzej; Thai, Robert

2014-01-01

Highlights: • The hFKBP25 interacts with diverse components of macromolecular entities. • We show that the endogenous human FKBP25 is bound to polyribosomes. • The endogenous hFKBP25 co-immunoprecipitated with nucleosomal proteins. • FKBP25 could induce conformational switch in macromolecular complexes. - Abstract: In this paper, we show some evidence that a member of the FK506-binding proteins, FKBP25 is associated to diverse components that are part of several different intracellular large-molecular mass entities. The FKBP25 is a high-affinity rapamycin-binding immunophilin, which has nuclear translocation signals present in its PPIase domain but it was detected both in the cytoplasm compartment and in the nuclear proteome. Analyses of antiFKBP25-immunoprecipitated proteins have revealed that the endogenous FKBP25 is associated to the core histones of the nucleosome, and with several proteins forming spliceosomal complexes and ribosomal subunits. Using polyclonal antiFKBP25 we have detected FKBP25 associated with polyribosomes. Added RNAs or 0.5 M NaCl release FKBP25 that was associated with the polyribosomes indicating that the immunophilin has an intrinsic capacity to form complexes with polyribonucleotides via its charged surface patches. Rapamycin or FK506 treatments of the polyribosomes isolated from porcine brain, HeLa and K568 cells caused a residual release of the endogenous FKBP25, which suggests that the immunophilin also binds to some proteins via its PPIase cavity. Our proteomics study indicates that the nuclear pool of the FKBP25 targets various nuclear proteins that are crucial for packaging of DNA, chromatin remodeling and pre-mRNA splicing whereas the cytosolic pool of this immunophilin is bound to some components of the ribosome

Rapamycin-binding FKBP25 associates with diverse proteins that form large intracellular entities

Energy Technology Data Exchange (ETDEWEB)

Galat, Andrzej, E-mail: galat@dsvidf.cea.fr; Thai, Robert

2014-08-08

Highlights: • The hFKBP25 interacts with diverse components of macromolecular entities. • We show that the endogenous human FKBP25 is bound to polyribosomes. • The endogenous hFKBP25 co-immunoprecipitated with nucleosomal proteins. • FKBP25 could induce conformational switch in macromolecular complexes. - Abstract: In this paper, we show some evidence that a member of the FK506-binding proteins, FKBP25 is associated to diverse components that are part of several different intracellular large-molecular mass entities. The FKBP25 is a high-affinity rapamycin-binding immunophilin, which has nuclear translocation signals present in its PPIase domain but it was detected both in the cytoplasm compartment and in the nuclear proteome. Analyses of antiFKBP25-immunoprecipitated proteins have revealed that the endogenous FKBP25 is associated to the core histones of the nucleosome, and with several proteins forming spliceosomal complexes and ribosomal subunits. Using polyclonal antiFKBP25 we have detected FKBP25 associated with polyribosomes. Added RNAs or 0.5 M NaCl release FKBP25 that was associated with the polyribosomes indicating that the immunophilin has an intrinsic capacity to form complexes with polyribonucleotides via its charged surface patches. Rapamycin or FK506 treatments of the polyribosomes isolated from porcine brain, HeLa and K568 cells caused a residual release of the endogenous FKBP25, which suggests that the immunophilin also binds to some proteins via its PPIase cavity. Our proteomics study indicates that the nuclear pool of the FKBP25 targets various nuclear proteins that are crucial for packaging of DNA, chromatin remodeling and pre-mRNA splicing whereas the cytosolic pool of this immunophilin is bound to some components of the ribosome.

Detecting Plagiarism in MS Access Assignments

Science.gov (United States)

Singh, Anil

2013-01-01

Assurance of individual effort from students in computer-based assignments is a challenge. Due to digitization, students can easily use a copy of their friend's work and submit it as their own. Plagiarism in assignments puts students who cheat at par with those who work honestly and this compromises the learning evaluation process. Using a…

Four signature motifs define the first class of structurally related large coiled-coil proteins in plants.

Directory of Open Access Journals (Sweden)

Meier Iris

2002-04-01

Full Text Available Abstract Background Animal and yeast proteins containing long coiled-coil domains are involved in attaching other proteins to the large, solid-state components of the cell. One subgroup of long coiled-coil proteins are the nuclear lamins, which are involved in attaching chromatin to the nuclear envelope and have recently been implicated in inherited human diseases. In contrast to other eukaryotes, long coiled-coil proteins have been barely investigated in plants. Results We have searched the completed Arabidopsis genome and have identified a family of structurally related long coiled-coil proteins. Filament-like plant proteins (FPP were identified by sequence similarity to a tomato cDNA that encodes a coiled-coil protein which interacts with the nuclear envelope-associated protein, MAF1. The FPP family is defined by four novel unique sequence motifs and by two clusters of long coiled-coil domains separated by a non-coiled-coil linker. All family members are expressed in a variety of Arabidopsis tissues. A homolog sharing the structural features was identified in the monocot rice, indicating conservation among angiosperms. Conclusion Except for myosins, this is the first characterization of a family of long coiled-coil proteins in plants. The tomato homolog of the FPP family binds in a yeast two-hybrid assay to a nuclear envelope-associated protein. This might suggest that FPP family members function in nuclear envelope biology. Because the full Arabidopsis genome does not appear to contain genes for lamins, it is of interest to investigate other long coiled-coil proteins, which might functionally replace lamins in the plant kingdom.

Unveiling protein functions through the dynamics of the interaction network.

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Irene Sendiña-Nadal

Full Text Available Protein interaction networks have become a tool to study biological processes, either for predicting molecular functions or for designing proper new drugs to regulate the main biological interactions. Furthermore, such networks are known to be organized in sub-networks of proteins contributing to the same cellular function. However, the protein function prediction is not accurate and each protein has traditionally been assigned to only one function by the network formalism. By considering the network of the physical interactions between proteins of the yeast together with a manual and single functional classification scheme, we introduce a method able to reveal important information on protein function, at both micro- and macro-scale. In particular, the inspection of the properties of oscillatory dynamics on top of the protein interaction network leads to the identification of misclassification problems in protein function assignments, as well as to unveil correct identification of protein functions. We also demonstrate that our approach can give a network representation of the meta-organization of biological processes by unraveling the interactions between different functional classes.

The pepATTRACT web server for blind, large-scale peptide-protein docking.

Science.gov (United States)

de Vries, Sjoerd J; Rey, Julien; Schindler, Christina E M; Zacharias, Martin; Tuffery, Pierre

2017-07-03

Peptide-protein interactions are ubiquitous in the cell and form an important part of the interactome. Computational docking methods can complement experimental characterization of these complexes, but current protocols are not applicable on the proteome scale. pepATTRACT is a novel docking protocol that is fully blind, i.e. it does not require any information about the binding site. In various stages of its development, pepATTRACT has participated in CAPRI, making successful predictions for five out of seven protein-peptide targets. Its performance is similar or better than state-of-the-art local docking protocols that do require binding site information. Here we present a novel web server that carries out the rigid-body stage of pepATTRACT. On the peptiDB benchmark, the web server generates a correct model in the top 50 in 34% of the cases. Compared to the full pepATTRACT protocol, this leads to some loss of performance, but the computation time is reduced from ∼18 h to ∼10 min. Combined with the fact that it is fully blind, this makes the web server well-suited for large-scale in silico protein-peptide docking experiments. The rigid-body pepATTRACT server is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/pepATTRACT. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Batch metadata assignment to archival photograph collections using facial recognition software

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Kyle Banerjee

2013-07-01

Full Text Available Useful metadata is essential to giving individual meaning and value within the context of a greater image collection as well as making them more discoverable. However, often little information is available about the photos themselves, so adding consistent metadata to large collections of digital and digitized photographs is a time consuming process requiring highly experienced staff. By using facial recognition software, staff can identify individuals more quickly and reliably. Knowledge of individuals in photos helps staff determine when and where photos are taken and also improves understanding of the subject matter. This article demonstrates simple techniques for using facial recognition software and command line tools to assign, modify, and read metadata for large archival photograph collections.

METHODOLOGY & CALCULATIONS FOR THE ASSIGNMENT OF WASTE GROUPS FOR THE LARGE UNDERGROUND WASTE STORAGE TANKS AT THE HANFORD SITE

Energy Technology Data Exchange (ETDEWEB)

BARKER, S.A.

2006-07-27

Waste stored within tank farm double-shell tanks (DST) and single-shell tanks (SST) generates flammable gas (principally hydrogen) to varying degrees depending on the type, amount, geometry, and condition of the waste. The waste generates hydrogen through the radiolysis of water and organic compounds, thermolytic decomposition of organic compounds, and corrosion of a tank's carbon steel walls. Radiolysis and thermolytic decomposition also generates ammonia. Nonflammable gases, which act as dilutents (such as nitrous oxide), are also produced. Additional flammable gases (e.g., methane) are generated by chemical reactions between various degradation products of organic chemicals present in the tanks. Volatile and semi-volatile organic chemicals in tanks also produce organic vapors. The generated gases in tank waste are either released continuously to the tank headspace or are retained in the waste matrix. Retained gas may be released in a spontaneous or induced gas release event (GRE) that can significantly increase the flammable gas concentration in the tank headspace as described in RPP-7771. The document categorizes each of the large waste storage tanks into one of several categories based on each tank's waste characteristics. These waste group assignments reflect a tank's propensity to retain a significant volume of flammable gases and the potential of the waste to release retained gas by a buoyant displacement event. Revision 5 is the annual update of the methodology and calculations of the flammable gas Waste Groups for DSTs and SSTs.

Milk yield, feed efficiency and metabolic profiles in Jersey and Holstein cows assigned to different fat supplementation strategies

DEFF Research Database (Denmark)

Alstrup, Lene; Nielsen, M.O.; Lund, Peter

2015-01-01

, compared to their lowest recorded weight after calving. Subsequently, the cows were randomly assigned to one of the four treatments until the end of lactation. There was no effect of feeding strategy on DM intake during week 9–40 of lactation. Fat supplemented rations (WCR; RPF) increased yield of milk...... energy efficiency in Jersey cows but increased energy efficiency in Holstein cows. Because fat supplementation reduced dietary protein concentration and increased milk production, protein intake was lower and N efficiency was higher on WCR and RPF than on CON. Metabolite concentrations in jugular vein...

Flexible taxonomic assignment of ambiguous sequencing reads

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Jansson Jesper

2011-01-01

Full Text Available Abstract Background To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it. Results We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed. Conclusions The assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the q parameter. Validation of our results in an artificial dataset confirm that a combination of values of q produces the most accurate results.

First Trimester Fetal Gender Assignment by Ultrasound

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Sabahattin Altunyurt

2010-03-01

Full Text Available Objective: To investigate the efficiency of genital tubercule angle on detecting fetal gender in first trimester by ultrasonography. Material-Method: Fetal sex assignment by ultrasound was carried out in 172 pregnancies at 11-13+6 weeks between 2007 June and 2007 December. Gestational age was determined by the measurement of crown-rump length (CRL. The ultrasound predictions were compared with actual sex at birth. Mid-sagittal planes of a section of the fetal genital tubercle were performed to identify the gender. Results: 155 of 172 patients’ data were achieved. The overall success rate was 92.3 % in sonographic assignment of fetal sex. The correct assignment rate in female fetuses was significantly higher than males (95.9 % - 88.8 % [p=0,001]. The correct identification of fetal sex improved with advancing gestational age from 89.3 % between 11-11+6 weeks, 92.5 % between 12-12+6 weeks and 93.4 % between 13-13+6 weeks (p=0,96. Conclusion: The fetal sex assignment by ultrasonography between 11-13+6 weeks had high success rate. The sensitivity of fetal sex assignment was not affected with fetus position and gestational age.

Probabilistic Cross-identification in Crowded Fields as an Assignment Problem

Science.gov (United States)

Budavári, Tamás; Basu, Amitabh

2016-10-01

One of the outstanding challenges of cross-identification is multiplicity: detections in crowded regions of the sky are often linked to more than one candidate associations of similar likelihoods. We map the resulting maximum likelihood partitioning to the fundamental assignment problem of discrete mathematics and efficiently solve the two-way catalog-level matching in the realm of combinatorial optimization using the so-called Hungarian algorithm. We introduce the method, demonstrate its performance in a mock universe where the true associations are known, and discuss the applicability of the new procedure to large surveys.

PROBABILISTIC CROSS-IDENTIFICATION IN CROWDED FIELDS AS AN ASSIGNMENT PROBLEM

Energy Technology Data Exchange (ETDEWEB)

Budavári, Tamás; Basu, Amitabh, E-mail: budavari@jhu.edu, E-mail: basu.amitabh@jhu.edu [Dept. of Applied Mathematics and Statistics, Johns Hopkins University, 3400 N. Charles St., MD 21218 (United States)

2016-10-01

One of the outstanding challenges of cross-identification is multiplicity: detections in crowded regions of the sky are often linked to more than one candidate associations of similar likelihoods. We map the resulting maximum likelihood partitioning to the fundamental assignment problem of discrete mathematics and efficiently solve the two-way catalog-level matching in the realm of combinatorial optimization using the so-called Hungarian algorithm. We introduce the method, demonstrate its performance in a mock universe where the true associations are known, and discuss the applicability of the new procedure to large surveys.

PROBABILISTIC CROSS-IDENTIFICATION IN CROWDED FIELDS AS AN ASSIGNMENT PROBLEM

International Nuclear Information System (INIS)

Budavári, Tamás; Basu, Amitabh

2016-01-01

One of the outstanding challenges of cross-identification is multiplicity: detections in crowded regions of the sky are often linked to more than one candidate associations of similar likelihoods. We map the resulting maximum likelihood partitioning to the fundamental assignment problem of discrete mathematics and efficiently solve the two-way catalog-level matching in the realm of combinatorial optimization using the so-called Hungarian algorithm. We introduce the method, demonstrate its performance in a mock universe where the true associations are known, and discuss the applicability of the new procedure to large surveys.

Historical WBAN ID Assignments

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — 4"x6" index cards represent the first written assignments of Weather Bureau Army Navy (WBAN) station identifier numbers by the National Climatic Data Center....

SCRAED - Simple and Complex Random Assignment in Experimental Designs

OpenAIRE

Alferes, Valentim R.

2009-01-01

SCRAED is a package of 37 self-contained SPSS syntax files that performs simple and complex random assignment in experimental designs. For between-subjects designs, SCRAED includes simple random assignment (no restrictions, forced equal sizes, forced unequal sizes, and unequal probabilities), block random assignment (simple and generalized blocks), and stratified random assignment (no restrictions, forced equal sizes, forced unequal sizes, and unequal probabilities). For within-subject...

Structure based modification of Bluetongue virus helicase protein VP6 to produce a viable VP6-truncated BTV

Energy Technology Data Exchange (ETDEWEB)

Matsuo, Eiko [Microbiology and Immunology, Division of Animal Science, Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1, Rokkodai, Nada-ku, Kobe-City 657-8501 (Japan); Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT (United Kingdom); Leon, Esther; Matthews, Steve J. [Division of Molecular Biosciences, Centre for Structural Biology, Imperial College London, South Kensington, London SW7 2AZ (United Kingdom); Roy, Polly, E-mail: polly.roy@lshtm.ac.uk [Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT (United Kingdom)

2014-09-05

Highlights: • NMR analysis on BTV VP6 reveals two large loop regions. • The loss of a loop (aa 34–130) does not affect the overall fold of the protein. • A region of VP6 (aa 34–92) is not required for BTV replication. • A region of VP6 (aa 93–130) plays an essential role in the virus replication. - Abstract: Bluetongue virus core protein VP6 is an ATP hydrolysis dependent RNA helicase. However, despite much study, the precise role of VP6 within the viral capsid and its structure remain unclear. To investigate the requirement of VP6 in BTV replication, we initiated a structural and biological study. Multinuclear nuclear magnetic resonance spectra were assigned on his-tagged full-length VP6 (329 amino acid residues) as well as several truncated VP6 variants. The analysis revealed a large structured domain with two large loop regions that exhibit significant conformational exchange. One of the loops (amino acid position 34–130) could be removed without affecting the overall fold of the protein. Moreover, using a BTV reverse genetics system, it was possible to demonstrate that the VP6-truncated BTV was viable in BHK cells in the absence of any helper VP6 protein, suggesting that a large portion of this loop region is not absolutely required for BTV replication.

GENERAL ISSUES CONCERNING THE ASSIGNMENT OF SOCIAL PARTS

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Stela Mihăilescu

2012-11-01

Full Text Available By means of the present study, we try to offer a thorough image and an analysis concerning the assignment mode of social parts within a company having limited liability. The assignment of social parts is free and unrestricted except for the cases provided by article 202, paragraph 2 from Law no. 31/ 1990- the law of commercial companies with further modifications and completions and the ones provided in OUG no. 54/ 2010 concerning some measures for fighting fiscal evasion. By means of the assignment operation a transmission is made up by an assignment of social parts contract towards one or more already associated persons in the company or towards other individual or legal persons who are going to obtain the associate quality. The principle governing any assignment is the one of goods circulation freedom, a freedom restricted only by the public order and imperative judicial norms.

Assignment of uncertainties to scientific data

International Nuclear Information System (INIS)

Froehner, F.H.

1994-01-01

Long-standing problems of uncertainty assignment to scientific data came into a sharp focus in recent years when uncertainty information ('covariance files') had to be added to application-oriented large libraries of evaluated nuclear data such as ENDF and JEF. Question arouse about the best way to express uncertainties, the meaning of statistical and systematic errors, the origin of correlation and construction of covariance matrices, the combination of uncertain data from different sources, the general usefulness of results that are strictly valid only for Gaussian or only for linear statistical models, etc. Conventional statistical theory is often unable to give unambiguous answers, and tends to fail when statistics is bad so that prior information becomes crucial. Modern probability theory, on the other hand, incorporating decision information becomes group-theoretic results, is shown to provide straight and unique answers to such questions, and to deal easily with prior information and small samples. (author). 10 refs

Stress Assignment in Reading Italian Polysyllabic Pseudowords

Science.gov (United States)

Sulpizio, Simone; Arduino, Lisa S.; Paizi, Despina; Burani, Cristina

2013-01-01

In 4 naming experiments we investigated how Italian readers assign stress to pseudowords. We assessed whether participants assign stress following distributional information such as stress neighborhood (the proportion and number of existent words sharing orthographic ending and stress pattern) and whether such distributional information affects…

A casein-kinase-2-related protein kinase is tightly associated with the large T antigen of simian virus 40

DEFF Research Database (Denmark)

Götz, C; Koenig, M G; Issinger, O G

1995-01-01

by the addition of protein kinase CK2 suggest that at least one of the T-antigen-associated protein kinases is CK2 or a protein-kinase-CK2-related enzyme. The association of recombinant CK2 with T antigen was strongly confirmed by in vitro binding studies. Experiments with temperature-sensitive SV40-transformed......The simian virus 40 (SV40) large T antigen is a multifunctional protein involved in SV40 cell transformation and lytic virus infection. Some of its activities are regulated by interaction with cellular proteins and/or by phosphorylation of T antigen by various protein kinases. In this study, we...... show that immuno-purified T antigen from SV40-transformed cells and from baculovirus-infected insect cells is tightly associated with a protein kinase that phosphorylates T antigen in vitro. In the presence of heparin or a peptide resembling a protein kinase CK2 recognition site, the phosphorylation...

Assigning breed origin to alleles in crossbred animals.

Science.gov (United States)

Vandenplas, Jérémie; Calus, Mario P L; Sevillano, Claudia A; Windig, Jack J; Bastiaansen, John W M

2016-08-22

For some species, animal production systems are based on the use of crossbreeding to take advantage of the increased performance of crossbred compared to purebred animals. Effects of single nucleotide polymorphisms (SNPs) may differ between purebred and crossbred animals for several reasons: (1) differences in linkage disequilibrium between SNP alleles and a quantitative trait locus; (2) differences in genetic backgrounds (e.g., dominance and epistatic interactions); and (3) differences in environmental conditions, which result in genotype-by-environment interactions. Thus, SNP effects may be breed-specific, which has led to the development of genomic evaluations for crossbred performance that take such effects into account. However, to estimate breed-specific effects, it is necessary to know breed origin of alleles in crossbred animals. Therefore, our aim was to develop an approach for assigning breed origin to alleles of crossbred animals (termed BOA) without information on pedigree and to study its accuracy by considering various factors, including distance between breeds. The BOA approach consists of: (1) phasing genotypes of purebred and crossbred animals; (2) assigning breed origin to phased haplotypes; and (3) assigning breed origin to alleles of crossbred animals based on a library of assigned haplotypes, the breed composition of crossbred animals, and their SNP genotypes. The accuracy of allele assignments was determined for simulated datasets that include crosses between closely-related, distantly-related and unrelated breeds. Across these scenarios, the percentage of alleles of a crossbred animal that were correctly assigned to their breed origin was greater than 90 %, and increased with increasing distance between breeds, while the percentage of incorrectly assigned alleles was always less than 2 %. For the remaining alleles, i.e. 0 to 10 % of all alleles of a crossbred animal, breed origin could not be assigned. The BOA approach accurately assigns

Simulation-Based Dynamic Passenger Flow Assignment Modelling for a Schedule-Based Transit Network

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Xiangming Yao

2017-01-01

Full Text Available The online operation management and the offline policy evaluation in complex transit networks require an effective dynamic traffic assignment (DTA method that can capture the temporal-spatial nature of traffic flows. The objective of this work is to propose a simulation-based dynamic passenger assignment framework and models for such applications in the context of schedule-based rail transit systems. In the simulation framework, travellers are regarded as individual agents who are able to obtain complete information on the current traffic conditions. A combined route selection model integrated with pretrip route selection and entrip route switch is established for achieving the dynamic network flow equilibrium status. The train agent is operated strictly with the timetable and its capacity limitation is considered. A continuous time-driven simulator based on the proposed framework and models is developed, whose performance is illustrated through a large-scale network of Beijing subway. The results indicate that more than 0.8 million individual passengers and thousands of trains can be simulated simultaneously at a speed ten times faster than real time. This study provides an efficient approach to analyze the dynamic demand-supply relationship for large schedule-based transit networks.

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

Science.gov (United States)

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

2011-06-15

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

Integer Linear Programming for Constrained Multi-Aspect Committee Review Assignment

Science.gov (United States)

Karimzadehgan, Maryam; Zhai, ChengXiang

2011-01-01

Automatic review assignment can significantly improve the productivity of many people such as conference organizers, journal editors and grant administrators. A general setup of the review assignment problem involves assigning a set of reviewers on a committee to a set of documents to be reviewed under the constraint of review quota so that the reviewers assigned to a document can collectively cover multiple topic aspects of the document. No previous work has addressed such a setup of committee review assignments while also considering matching multiple aspects of topics and expertise. In this paper, we tackle the problem of committee review assignment with multi-aspect expertise matching by casting it as an integer linear programming problem. The proposed algorithm can naturally accommodate any probabilistic or deterministic method for modeling multiple aspects to automate committee review assignments. Evaluation using a multi-aspect review assignment test set constructed using ACM SIGIR publications shows that the proposed algorithm is effective and efficient for committee review assignments based on multi-aspect expertise matching. PMID:22711970

COMe: the ontology of bioinorganic proteins

Directory of Open Access Journals (Sweden)

Contrino Sergio

2004-02-01

Full Text Available Abstract Background Many characterised proteins contain metal ions, small organic molecules or modified residues. In contrast, the huge amount of data generated by genome projects consists exclusively of sequences with almost no annotation. One of the goals of the structural genomics initiative is to provide representative three-dimensional (3-D structures for as many protein/domain folds as possible to allow successful homology modelling. However, important functional features such as metal co-ordination or a type of prosthetic group are not always conserved in homologous proteins. So far, the problem of correct annotation of bioinorganic proteins has been largely ignored by the bioinformatics community and information on bioinorganic centres obtained by methods other than crystallography or NMR is only available in literature databases. Results COMe (Co-Ordination of Metals represents the ontology for bioinorganic and other small molecule centres in complex proteins. COMe consists of three types of entities: 'bioinorganic motif' (BIM, 'molecule' (MOL, and 'complex proteins' (PRX, with each entity being assigned a unique identifier. A BIM consists of at least one centre (metal atom, inorganic cluster, organic molecule and two or more endogenous and/or exogenous ligands. BIMs are represented as one-dimensional (1-D strings and 2-D diagrams. A MOL entity represents a 'small molecule' which, when in complex with one or more polypeptides, forms a functional protein. The PRX entities refer to the functional proteins as well as to separate protein domains and subunits. The complex proteins in COMe are subdivided into three categories: (i metalloproteins, (ii organic prosthetic group proteins and (iii modified amino acid proteins. The data are currently stored in both XML format and a relational database and are available at http://www.ebi.ac.uk/come/. Conclusion COMe provides the classification of proteins according to their 'bioinorganic' features

Methyl CpG–binding proteins induce large-scale chromatin reorganization during terminal differentiation

Science.gov (United States)

Brero, Alessandro; Easwaran, Hariharan P.; Nowak, Danny; Grunewald, Ingrid; Cremer, Thomas; Leonhardt, Heinrich; Cardoso, M. Cristina

2005-01-01

Pericentric heterochromatin plays an important role in epigenetic gene regulation. We show that pericentric heterochromatin aggregates during myogenic differentiation. This clustering leads to the formation of large chromocenters and correlates with increased levels of the methyl CpG–binding protein MeCP2 and pericentric DNA methylation. Ectopic expression of fluorescently tagged MeCP2 mimicked this effect, causing a dose-dependent clustering of chromocenters in the absence of differentiation. MeCP2-induced rearrangement of heterochromatin occurred throughout interphase, did not depend on the H3K9 histone methylation pathway, and required the methyl CpG–binding domain (MBD) only. Similar to MeCP2, another methyl CpG–binding protein, MBD2, also increased during myogenic differentiation and could induce clustering of pericentric regions, arguing for functional redundancy. This MeCP2- and MBD2-mediated chromatin reorganization may thus represent a molecular link between nuclear genome topology and the epigenetic maintenance of cellular differentiation. PMID:15939760

istar: a web platform for large-scale protein-ligand docking.

Directory of Open Access Journals (Sweden)

Hongjian Li

Full Text Available Protein-ligand docking is a key computational method in the design of starting points for the drug discovery process. We are motivated by the desire to automate large-scale docking using our popular docking engine idock and thus have developed a publicly-accessible web platform called istar. Without tedious software installation, users can submit jobs using our website. Our istar website supports 1 filtering ligands by desired molecular properties and previewing the number of ligands to dock, 2 monitoring job progress in real time, and 3 visualizing ligand conformations and outputting free energy and ligand efficiency predicted by idock, binding affinity predicted by RF-Score, putative hydrogen bonds, and supplier information for easy purchase, three useful features commonly lacked on other online docking platforms like DOCK Blaster or iScreen. We have collected 17,224,424 ligands from the All Clean subset of the ZINC database, and revamped our docking engine idock to version 2.0, further improving docking speed and accuracy, and integrating RF-Score as an alternative rescoring function. To compare idock 2.0 with the state-of-the-art AutoDock Vina 1.1.2, we have carried out a rescoring benchmark and a redocking benchmark on the 2,897 and 343 protein-ligand complexes of PDBbind v2012 refined set and CSAR NRC HiQ Set 24Sept2010 respectively, and an execution time benchmark on 12 diverse proteins and 3,000 ligands of different molecular weight. Results show that, under various scenarios, idock achieves comparable success rates while outperforming AutoDock Vina in terms of docking speed by at least 8.69 times and at most 37.51 times. When evaluated on the PDBbind v2012 core set, our istar platform combining with RF-Score manages to reproduce Pearson's correlation coefficient and Spearman's correlation coefficient of as high as 0.855 and 0.859 respectively between the experimental binding affinity and the predicted binding affinity of the docked

istar: a web platform for large-scale protein-ligand docking.

Science.gov (United States)

Li, Hongjian; Leung, Kwong-Sak; Ballester, Pedro J; Wong, Man-Hon

2014-01-01

Protein-ligand docking is a key computational method in the design of starting points for the drug discovery process. We are motivated by the desire to automate large-scale docking using our popular docking engine idock and thus have developed a publicly-accessible web platform called istar. Without tedious software installation, users can submit jobs using our website. Our istar website supports 1) filtering ligands by desired molecular properties and previewing the number of ligands to dock, 2) monitoring job progress in real time, and 3) visualizing ligand conformations and outputting free energy and ligand efficiency predicted by idock, binding affinity predicted by RF-Score, putative hydrogen bonds, and supplier information for easy purchase, three useful features commonly lacked on other online docking platforms like DOCK Blaster or iScreen. We have collected 17,224,424 ligands from the All Clean subset of the ZINC database, and revamped our docking engine idock to version 2.0, further improving docking speed and accuracy, and integrating RF-Score as an alternative rescoring function. To compare idock 2.0 with the state-of-the-art AutoDock Vina 1.1.2, we have carried out a rescoring benchmark and a redocking benchmark on the 2,897 and 343 protein-ligand complexes of PDBbind v2012 refined set and CSAR NRC HiQ Set 24Sept2010 respectively, and an execution time benchmark on 12 diverse proteins and 3,000 ligands of different molecular weight. Results show that, under various scenarios, idock achieves comparable success rates while outperforming AutoDock Vina in terms of docking speed by at least 8.69 times and at most 37.51 times. When evaluated on the PDBbind v2012 core set, our istar platform combining with RF-Score manages to reproduce Pearson's correlation coefficient and Spearman's correlation coefficient of as high as 0.855 and 0.859 respectively between the experimental binding affinity and the predicted binding affinity of the docked conformation. istar

Assignment and Correspondence Tracking System - Tactical / Operational Reporting

Data.gov (United States)

Social Security Administration — Reporting data store for the Assignment and Correspondence Tracking System (ACT). ACT automates the assignment and tracking of correspondence processing within the...

Statistical aspects of optimal treatment assignment

OpenAIRE

van der Linden, Willem J.

1980-01-01

The issues of treatment assignment is ordinarily dealt with within the framework of testing aptitude treatment interaction (ATI) hypothesis. ATI research mostly uses linear regression techniques, and an ATI exists when the aptitude treatment (AT) regression lines cross each other within the relevant interval of the aptitude variable. Consistent with this approach is the use of the points of interaction of AT regression lines as treatment-assignment rule. The replacement of such rules by monot...

One of My Favorite Assignments: Automated Teller Machine Simulation.

Science.gov (United States)

Oberman, Paul S.

2001-01-01

Describes an assignment for an introductory computer science class that requires the student to write a software program that simulates an automated teller machine. Highlights include an algorithm for the assignment; sample file contents; language features used; assignment variations; and discussion points. (LRW)

Probing the Mechanism of pH-Induced Large-Scale Conformational Changes in Dengue Virus Envelope Protein Using Atomistic Simulations

Science.gov (United States)

Prakash, Meher K.; Barducci, Alessandro; Parrinello, Michele

2010-01-01

Abstract One of the key steps in the infection of the cell by dengue virus is a pH-induced conformational change of the viral envelope proteins. These envelope proteins undergo a rearrangement from a dimer to a trimer, with large conformational changes in the monomeric unit. In this article, metadynamics simulations were used to enable us to understand the mechanism of these large-scale changes in the monomer. By using all-atom, explicit solvent simulations of the monomers, the stability of the protein structure is studied under low and high pH conditions. Free energy profiles obtained along appropriate collective coordinates demonstrate that pH affects the domain interface in both the conformations of E monomer, stabilizing one and destabilizing the other. These simulations suggest a mechanism with an intermediate detached state between the two monomeric structures. Using further analysis, we comment on the key residue interactions responsible for the instability and the pH-sensing role of a histidine that could not otherwise be studied experimentally. The insights gained from this study and methodology can be extended for studying similar mechanisms in the E proteins of the other members of class II flavivirus family. PMID:20643078

7 CFR 1900.5 - Assignment of cases.

Science.gov (United States)

2010-01-01

... 7 Agriculture 12 2010-01-01 2010-01-01 false Assignment of cases. 1900.5 Section 1900.5 Agriculture Regulations of the Department of Agriculture (Continued) RURAL HOUSING SERVICE, RURAL BUSINESS... REGULATIONS GENERAL Delegations of Authority § 1900.5 Assignment of cases. The State Director may, in writing...

METHOD FOR SOLVING FUZZY ASSIGNMENT PROBLEM USING MAGNITUDE RANKING TECHNIQUE

OpenAIRE

D. Selvi; R. Queen Mary; G. Velammal

2017-01-01

Assignment problems have various applications in the real world because of their wide applicability in industry, commerce, management science, etc. Traditional classical assignment problems cannot be successfully used for real life problem, hence the use of fuzzy assignment problems is more appropriate. In this paper, the fuzzy assignment problem is formulated to crisp assignment problem using Magnitude Ranking technique and Hungarian method has been applied to find an optimal solution. The N...

Detecting protein-protein interactions in the intact cell of Bacillus subtilis (ATCC 6633).

Science.gov (United States)

Winters, Michael S; Day, R A

2003-07-01

The salt bridge, paired group-specific reagent cyanogen (ethanedinitrile; C(2)N(2)) converts naturally occurring pairs of functional groups into covalently linked products. Cyanogen readily permeates cell walls and membranes. When the paired groups are shared between associated proteins, isolation of the covalently linked proteins allows their identity to be assigned. Examination of organisms of known genome sequence permits identification of the linked proteins by mass spectrometric techniques applied to peptides derived from them. The cyanogen-linked proteins were isolated by polyacrylamide gel electrophoresis. Digestion of the isolated proteins with proteases of known specificity afforded sets of peptides that could be analyzed by mass spectrometry. These data were compared with those derived theoretically from the Swiss Protein Database by computer-based comparisons (Protein Prospector; http://prospector.ucsf.edu). Identification of associated proteins in the ribosome of Bacillus subtilis strain ATCC 6633 showed that there is an association homology with the association patterns of the ribosomal proteins of Haloarcula marismortui and Thermus thermophilus. In addition, other proteins involved in protein biosynthesis were shown to be associated with ribosomal proteins.

MYC protein expression and genetic alterations have prognostic impact in patients with diffuse large B-cell lymphoma treated with immunochemotherapy.

Science.gov (United States)

Valera, Alexandra; López-Guillermo, Armando; Cardesa-Salzmann, Teresa; Climent, Fina; González-Barca, Eva; Mercadal, Santiago; Espinosa, Iñigo; Novelli, Silvana; Briones, Javier; Mate, José L; Salamero, Olga; Sancho, Juan M; Arenillas, Leonor; Serrano, Sergi; Erill, Nadina; Martínez, Daniel; Castillo, Paola; Rovira, Jordina; Martínez, Antonio; Campo, Elias; Colomo, Luis

2013-10-01

MYC alterations influence the survival of patients with diffuse large B-cell lymphoma. Most studies have focused on MYC translocations but there is little information regarding the impact of numerical alterations and protein expression. We analyzed the genetic alterations and protein expression of MYC, BCL2, BCL6, and MALT1 in 219 cases of diffuse large B-cell lymphoma. MYC rearrangement occurred as the sole abnormality (MYC single-hit) in 3% of cases, MYC and concurrent BCL2 and/or BCL6 rearrangements (MYC double/triple-hit) in 4%, MYC amplifications in 2% and MYC gains in 19%. MYC single-hit, MYC double/triple-hit and MYC amplifications, but not MYC gains or other gene rearrangements, were associated with unfavorable progression-free survival and overall survival. MYC protein expression, evaluated using computerized image analysis, captured the unfavorable prognosis of MYC translocations/amplifications and identified an additional subset of patients without gene alterations but with similar poor prognosis. Patients with tumors expressing both MYC/BCL2 had the worst prognosis, whereas those with double-negative tumors had the best outcome. High MYC expression was associated with shorter overall survival irrespectively of the International Prognostic Index and BCL2 expression. In conclusion, MYC protein expression identifies a subset of diffuse large B-cell lymphoma with very poor prognosis independently of gene alterations and other prognostic parameters.

Using sound to solve syntactic problems: the role of phonology in grammatical category assignments.

Science.gov (United States)

Kelly, M H

1992-04-01

One ubiquitous problem in language processing involves the assignment of words to the correct grammatical category, such as noun or verb. In general, semantic and syntactic cues have been cited as the principal information for grammatical category assignment, to the neglect of possible phonological cues. This neglect is unwarranted, and the following claims are made: (a) Numerous correlations between phonology and grammatical class exist, (b) some of these correlations are large and can pervade the entire lexicon of a language and hence can involve thousands of words, (c) experiments have repeatedly found that adults and children have learned these correlations, and (d) explanations for how these correlations arose can be proposed and evaluated. Implications of these phenomena for language representation and processing are discussed.

Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index

Directory of Open Access Journals (Sweden)

Zomaya Albert Y

2006-12-01

Full Text Available Abstract Background Knowledge of protein domain boundaries is critical for the characterisation and understanding of protein function. The ability to identify domains without the knowledge of the structure – by using sequence information only – is an essential step in many types of protein analyses. In this present study, we demonstrate that the performance of DomainDiscovery is improved significantly by including the inter-domain linker index value for domain identification from sequence-based information. Improved DomainDiscovery uses a Support Vector Machine (SVM approach and a unique training dataset built on the principle of consensus among experts in defining domains in protein structure. The SVM was trained using a PSSM (Position Specific Scoring Matrix, secondary structure, solvent accessibility information and inter-domain linker index to detect possible domain boundaries for a target sequence. Results Improved DomainDiscovery is compared with other methods by benchmarking against a structurally non-redundant dataset and also CASP5 targets. Improved DomainDiscovery achieves 70% accuracy for domain boundary identification in multi-domains proteins. Conclusion Improved DomainDiscovery compares favourably to the performance of other methods and excels in the identification of domain boundaries for multi-domain proteins as a result of introducing support vector machine with benchmark_2 dataset.

Protein Annotators' Assistant: A Novel Application of Information Retrieval Techniques.

Science.gov (United States)

Wise, Michael J.

2000-01-01

Protein Annotators' Assistant (PAA) is a software system which assists protein annotators in assigning functions to newly sequenced proteins. PAA employs a number of information retrieval techniques in a novel setting and is thus related to text categorization, where multiple categories may be suggested, except that in this case none of the…

Database proton NMR chemical shifts for RNA signal assignment and validation

Energy Technology Data Exchange (ETDEWEB)

Barton, Shawn; Heng Xiao [University of Maryland, Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce@onemoonscientific.com [University of Maryland, Baltimore County, Department of Chemistry and Biochemistry (United States); Summers, Michael F., E-mail: summers@hhmi.umbc.edu [University of Maryland, Baltimore County, Howard Hughes Medical Institute (United States)

2013-01-15

The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central base pair within a stretch of three adjacent base pairs (BP triplets), and included both Watson-Crick (WC; G:C, A:U) and G:U wobble pairs. Chemical shift values were included for all 4{sup 3} possible WC-BP triplets, as well as 137 additional triplets that contain one or more G:U wobbles. Sequence-dependent chemical shift correlations were identified, including correlations involving terminating base pairs within the triplets and canonical and non-canonical structures adjacent to the BP triplets (i.e. bulges, loops, WC and non-WC BPs), despite the fact that the NMR data were obtained under different conditions of pH, buffer, ionic strength, and temperature. A computer program (RNAShifts) was developed that enables convenient comparison of RNA {sup 1}H NMR assignments with database predictions, which should facilitate future signal assignment/validation efforts and enable rapid identification of non-canonical RNA structures and RNA-ligand/protein interaction sites.

Testing the Effectiveness of Online Assignments in Theory of Finance

Science.gov (United States)

Batu, Michael; Bower, Nancy; Lun, Esmond; Sadanand, Asha

2018-01-01

The authors investigated the effectiveness of online versus paper assignments using final examination scores in three cohorts of theory of finance. In particular, two cohorts were exposed to online assignments while another cohort was exposed to traditional assignments. The central result is that exposure to online assignments robustly leads to…

3D complex: a structural classification of protein complexes.

Directory of Open Access Journals (Sweden)

Emmanuel D Levy

2006-11-01

Full Text Available Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

NMRNet: A deep learning approach to automated peak picking of protein NMR spectra.

Science.gov (United States)

Klukowski, Piotr; Augoff, Michal; Zieba, Maciej; Drwal, Maciej; Gonczarek, Adam; Walczak, Michal J

2018-03-14

Automated selection of signals in protein NMR spectra, known as peak picking, has been studied for over 20 years, nevertheless existing peak picking methods are still largely deficient. Accurate and precise automated peak picking would accelerate the structure calculation, and analysis of dynamics and interactions of macromolecules. Recent advancement in handling big data, together with an outburst of machine learning techniques, offer an opportunity to tackle the peak picking problem substantially faster than manual picking and on par with human accuracy. In particular, deep learning has proven to systematically achieve human-level performance in various recognition tasks, and thus emerges as an ideal tool to address automated identification of NMR signals. We have applied a convolutional neural network for visual analysis of multidimensional NMR spectra. A comprehensive test on 31 manually-annotated spectra has demonstrated top-tier average precision (AP) of 0.9596, 0.9058 and 0.8271 for backbone, side-chain and NOESY spectra, respectively. Furthermore, a combination of extracted peak lists with automated assignment routine, FLYA, outperformed other methods, including the manual one, and led to correct resonance assignment at the levels of 90.40%, 89.90% and 90.20% for three benchmark proteins. The proposed model is a part of a Dumpling software (platform for protein NMR data analysis), and is available at https://dumpling.bio/. michaljerzywalczak@gmail.compiotr.klukowski@pwr.edu.pl. Supplementary data are available at Bioinformatics online.

12 CFR 563e.28 - Assigned ratings.

Science.gov (United States)

2010-01-01

... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Assigned ratings. 563e.28 Section 563e.28 Banks... for Assessing Performance § 563e.28 Assigned ratings. (a) Ratings in general. Subject to paragraphs (b... performance under the lending, investment and service tests, the community development test, the small savings...

The PMDB Protein Model Database

Science.gov (United States)

Castrignanò, Tiziana; De Meo, Paolo D'Onorio; Cozzetto, Domenico; Talamo, Ivano Giuseppe; Tramontano, Anna

2006-01-01

The Protein Model Database (PMDB) is a public resource aimed at storing manually built 3D models of proteins. The database is designed to provide access to models published in the scientific literature, together with validating experimental data. It is a relational database and it currently contains >74 000 models for ∼240 proteins. The system is accessible at and allows predictors to submit models along with related supporting evidence and users to download them through a simple and intuitive interface. Users can navigate in the database and retrieve models referring to the same target protein or to different regions of the same protein. Each model is assigned a unique identifier that allows interested users to directly access the data. PMID:16381873

Large scale identification and categorization of protein sequences using structured logistic regression.

Directory of Open Access Journals (Sweden)

Bjørn P Pedersen

Full Text Available BACKGROUND: Structured Logistic Regression (SLR is a newly developed machine learning tool first proposed in the context of text categorization. Current availability of extensive protein sequence databases calls for an automated method to reliably classify sequences and SLR seems well-suited for this task. The classification of P-type ATPases, a large family of ATP-driven membrane pumps transporting essential cations, was selected as a test-case that would generate important biological information as well as provide a proof-of-concept for the application of SLR to a large scale bioinformatics problem. RESULTS: Using SLR, we have built classifiers to identify and automatically categorize P-type ATPases into one of 11 pre-defined classes. The SLR-classifiers are compared to a Hidden Markov Model approach and shown to be highly accurate and scalable. Representing the bulk of currently known sequences, we analysed 9.3 million sequences in the UniProtKB and attempted to classify a large number of P-type ATPases. To examine the distribution of pumps on organisms, we also applied SLR to 1,123 complete genomes from the Entrez genome database. Finally, we analysed the predicted membrane topology of the identified P-type ATPases. CONCLUSIONS: Using the SLR-based classification tool we are able to run a large scale study of P-type ATPases. This study provides proof-of-concept for the application of SLR to a bioinformatics problem and the analysis of P-type ATPases pinpoints new and interesting targets for further biochemical characterization and structural analysis.

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.

Science.gov (United States)

Brown, Peter; Pullan, Wayne; Yang, Yuedong; Zhou, Yaoqi

2016-02-01

The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org yaoqi.zhou@griffith.edu.au. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Dual earners’ willingness to accept an international assignment.

NARCIS (Netherlands)

van der Velde, E.G.; Bossink, C.J.H.; Jansen, P.G.W.

2005-01-01

Multinational organisations experience difficulties in finding managers willing to accept international assignments. This study has therefore focused on factors that can predict males' and females' willingness to accept international assignments, or to follow their partners on international

Task assignment and coaching

NARCIS (Netherlands)

Dominguez-Martinez, S.

2009-01-01

An important task of a manager is to motivate her subordinates. One way in which a manager can give incentives to junior employees is through the assignment of tasks. How a manager allocates tasks in an organization, provides information to the junior employees about his ability. Without coaching

Assigning probability gain for precursors of four large Chinese earthquakes

Energy Technology Data Exchange (ETDEWEB)

Cao, T.; Aki, K.

1983-03-10

We extend the concept of probability gain associated with a precursor (Aki, 1981) to a set of precursors which may be mutually dependent. Making use of a new formula, we derive a criterion for selecting precursors from a given data set in order to calculate the probability gain. The probabilities per unit time immediately before four large Chinese earthquakes are calculated. They are approximately 0.09, 0.09, 0.07 and 0.08 per day for 1975 Haicheng (M = 7.3), 1976 Tangshan (M = 7.8), 1976 Longling (M = 7.6), and Songpan (M = 7.2) earthquakes, respectively. These results are encouraging because they suggest that the investigated precursory phenomena may have included the complete information for earthquake prediction, at least for the above earthquakes. With this method, the step-by-step approach to prediction used in China may be quantified in terms of the probability of earthquake occurrence. The ln P versus t curve (where P is the probability of earthquake occurrence at time t) shows that ln P does not increase with t linearly but more rapidly as the time of earthquake approaches.

dFOXO Activates Large and Small Heat Shock Protein Genes in Response to Oxidative Stress to Maintain Proteostasis in Drosophila.

Science.gov (United States)

Donovan, Marissa R; Marr, Michael T

2016-09-02

Maintaining protein homeostasis is critical for survival at the cellular and organismal level (Morimoto, R. I. (2011) Cold Spring Harb. Symp. Quant. Biol. 76, 91-99). Cells express a family of molecular chaperones, the heat shock proteins, during times of oxidative stress to protect against proteotoxicity. We have identified a second stress responsive transcription factor, dFOXO, that works alongside the heat shock transcription factor to activate transcription of both the small heat shock protein and the large heat shock protein genes. This expression likely protects cells from protein misfolding associated with oxidative stress. Here we identify the regions of the Hsp70 promoter essential for FOXO-dependent transcription using in vitro methods and find a physiological role for FOXO-dependent expression of heat shock proteins in vivo. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Chaperonin Structure - The Large Multi-Subunit Protein Complex

Directory of Open Access Journals (Sweden)

Irena Roterman

2009-03-01

Full Text Available The multi sub-unit protein structure representing the chaperonins group is analyzed with respect to its hydrophobicity distribution. The proteins of this group assist protein folding supported by ATP. The specific axial symmetry GroEL structure (two rings of seven units stacked back to back - 524 aa each and the GroES (single ring of seven units - 97 aa each polypeptide chains are analyzed using the hydrophobicity distribution expressed as excess/deficiency all over the molecule to search for structure-to-function relationships. The empirically observed distribution of hydrophobic residues is confronted with the theoretical one representing the idealized hydrophobic core with hydrophilic residues exposure on the surface. The observed discrepancy between these two distributions seems to be aim-oriented, determining the structure-to-function relation. The hydrophobic force field structure generated by the chaperonin capsule is presented. Its possible influence on substrate folding is suggested.

Expatriate Assignments: Understanding the Skill, Ability, Personality, and Behavioral Requirements of Working Abroad

OpenAIRE

Shin, Shung J.; Morgeson, Frederick P.; Campion, Michael A.

2003-01-01

It is often assumed that adjustment to the local working environment is essential for expatriate assignments. As such, it is surprising there is little empirical research identifying how skill, ability, and personality requirements might differ between expatriate and domestic jobs and how cultural values are related to expatriate behaviors. In a large sample of professionals (N = 1,312) working in comparable jobs in 156 different countries, we found higher social and perceptual skill requirem...

On Maximizing the Lifetime of Wireless Sensor Networks by Optimally Assigning Energy Supplies

Science.gov (United States)

Asorey-Cacheda, Rafael; García-Sánchez, Antonio Javier; García-Sánchez, Felipe; García-Haro, Joan; Gonzalez-Castaño, Francisco Javier

2013-01-01

The extension of the network lifetime of Wireless Sensor Networks (WSN) is an important issue that has not been appropriately solved yet. This paper addresses this concern and proposes some techniques to plan an arbitrary WSN. To this end, we suggest a hierarchical network architecture, similar to realistic scenarios, where nodes with renewable energy sources (denoted as primary nodes) carry out most message delivery tasks, and nodes equipped with conventional chemical batteries (denoted as secondary nodes) are those with less communication demands. The key design issue of this network architecture is the development of a new optimization framework to calculate the optimal assignment of renewable energy supplies (primary node assignment) to maximize network lifetime, obtaining the minimum number of energy supplies and their node assignment. We also conduct a second optimization step to additionally minimize the number of packet hops between the source and the sink. In this work, we present an algorithm that approaches the results of the optimization framework, but with much faster execution speed, which is a good alternative for large-scale WSN networks. Finally, the network model, the optimization process and the designed algorithm are further evaluated and validated by means of computer simulation under realistic conditions. The results obtained are discussed comparatively. PMID:23939582

On Maximizing the Lifetime of Wireless Sensor Networks by Optimally Assigning Energy Supplies

Directory of Open Access Journals (Sweden)

Francisco Javier González-Castano

2013-08-01

Full Text Available The extension of the network lifetime of Wireless Sensor Networks (WSN is an important issue that has not been appropriately solved yet. This paper addresses this concern and proposes some techniques to plan an arbitrary WSN. To this end, we suggest a hierarchical network architecture, similar to realistic scenarios, where nodes with renewable energy sources (denoted as primary nodes carry out most message delivery tasks, and nodes equipped with conventional chemical batteries (denoted as secondary nodes are those with less communication demands. The key design issue of this network architecture is the development of a new optimization framework to calculate the optimal assignment of renewable energy supplies (primary node assignment to maximize network lifetime, obtaining the minimum number of energy supplies and their node assignment. We also conduct a second optimization step to additionally minimize the number of packet hops between the source and the sink. In this work, we present an algorithm that approaches the results of the optimization framework, but with much faster execution speed, which is a good alternative for large-scale WSN networks. Finally, the network model, the optimization process and the designed algorithm are further evaluated and validated by means of computer simulation under realistic conditions. The results obtained are discussed comparatively.

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

Science.gov (United States)

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

2017-01-04

The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Water-Protein Hydrogen Exchange in the Micro-Crystalline Protein Crh as Observed by Solid State NMR Spectroscopy

International Nuclear Information System (INIS)

Boeckmann, Anja; Juy, Michel; Bettler, Emmanuel; Emsley, Lyndon; Galinier, Anne; Penin, Francois; Lesage, Anne

2005-01-01

We report site-resolved observation of hydrogen exchange in the micro-crystalline protein Crh. Our approach is based on the use of proton T 2 ' -selective 1 H- 13 C- 13 C correlation spectra for site-specific assignments of carbons nearby labile protein protons. We compare the proton T 2 ' selective scheme to frequency selective water observation in deuterated proteins, and discuss the impacts of deuteration on 13 C linewidths in Crh. We observe that in micro-crystalline proteins, solvent accessible hydroxyl and amino protons show comparable exchange rates with water protons as for proteins in solution, and that structural constraints, such as hydrogen bonding or solvent accessibility, more significantly reduce exchange rates

NMR experiments for resonance assignments of 13C, 15N doubly-labeled flexible polypeptides: Application to the human prion protein hPrP(23-230)

International Nuclear Information System (INIS)

Liu Aizhuo; Riek, Roland; Wider, Gerhard; Schroetter, Christine von; Zahn, Ralph; Wuethrich, Kurt

2000-01-01

A combination of three heteronuclear three-dimensional NMR experiments tailored for sequential resonance assignments in uniformly 15 N, 13 C-labeled flexible polypeptide chains is described. The 3D (H)N(CO-TOCSY)NH, 3D (H)CA(CO-TOCSY)NH and 3D (H)CBCA(CO-TOCSY)NH schemes make use of the favorable 15 N chemical shift dispersion in unfolded polypeptides, exploit the slow transverse 15 N relaxation rates of unfolded polypeptides in high resolution constant-time [ 1 H, 15 N]-correlation experiments, and use carbonyl carbon homonuclear isotropic mixing to transfer magnetization sequentially along the amino acid sequence. Practical applications are demonstrated with the 100-residue flexible tail of the recombinant human prion protein, making use of spectral resolution up to 0.6 Hz in the 15 N dimension, simultaneous correlation with the two adjacent amino acid residues to overcome problems associated with spectral overlap, and the potential of the presently described experiments to establish nearest-neighbor correlations across proline residues in the amino acid sequence

Learning Gains from a Recurring "Teach and Question" Homework Assignment in a General Biology Course: Using Reciprocal Peer Tutoring Outside Class.

Science.gov (United States)

Bailey, E G; Baek, D; Meiling, J; Morris, C; Nelson, N; Rice, N S; Rose, S; Stockdale, P

2018-06-01

Providing students with one-on-one interaction with instructors is a big challenge in large courses. One solution is to have students interact with their peers during class. Reciprocal peer tutoring (RPT) is a more involved interaction that requires peers to alternate the roles of "teacher" and "student." Theoretically, advantages for peer tutoring include the verbalization and questioning of information and the scaffolded exploration of material through social and cognitive interaction. Studies on RPT vary in their execution, but most require elaborate planning and take up valuable class time. We tested the effectiveness of a "teach and question" (TQ) assignment that required student pairs to engage in RPT regularly outside class. A quasi-experimental design was implemented: one section of a general biology course completed TQ assignments, while another section completed a substitute assignment requiring individuals to review course material. The TQ section outperformed the other section by ∼6% on exams. Session recordings were coded to investigate correlation between TQ quality and student performance. Asking more questions was the characteristic that best predicted exam performance, and this was more predictive than most aspects of the course. We propose the TQ as an easy assignment to implement with large performance gains.

Efficient large-scale protein production of larvae and pupae of silkworm by Bombyx mori nuclear polyhedrosis virus bacmid system

International Nuclear Information System (INIS)

Motohashi, Tomoko; Shimojima, Tsukasa; Fukagawa, Tatsuo; Maenaka, Katsumi; Park, Enoch Y.

2005-01-01

Silkworm is one of the most attractive hosts for large-scale production of eukaryotic proteins as well as recombinant baculoviruses for gene transfer to mammalian cells. The bacmid system of Autographa californica nuclear polyhedrosis virus (AcNPV) has already been established and widely used. However, the AcNPV does not have a potential to infect silkworm. We developed the first practical Bombyx mori nuclear polyhedrosis virus bacmid system directly applicable for the protein expression of silkworm. By using this system, the green fluorescence protein was successfully expressed in silkworm larvae and pupae not only by infection of its recombinant virus but also by direct injection of its bacmid DNA. This method provides the rapid protein production in silkworm as long as 10 days, is free from biohazard, thus will be a powerful tool for the future production factory of recombinant eukaryotic proteins and baculoviruses

Subcarrier Group Assignment for MC-CDMA Wireless Networks

Directory of Open Access Journals (Sweden)

Le-Ngoc Tho

2007-01-01

Full Text Available Two interference-based subcarrier group assignment strategies in dynamic resource allocation are proposed for MC-CDMA wireless systems to achieve high throughput in a multicell environment. Least interfered group assignment (LIGA selects for each session the subcarrier group on which the user receives the minimum interference, while best channel ratio group assignment (BCRGA chooses the subcarrier group with the largest channel response-to-interference ratio. Both analytical framework and simulation model are developed for evaluation of throughput distribution of the proposed schemes. An iterative approach is devised to handle the complex interdependency between multicell interference profiles in the throughput analysis. Illustrative results show significant throughput improvement offered by the interference-based assignment schemes for MC-CDMA multicell wireless systems. In particular, under low loading conditions, LIGA renders the best performance. However, as the load increases BCRGA tends to offer superior performance.

Subcarrier Group Assignment for MC-CDMA Wireless Networks

Directory of Open Access Journals (Sweden)

Tho Le-Ngoc

2007-12-01

Full Text Available Two interference-based subcarrier group assignment strategies in dynamic resource allocation are proposed for MC-CDMA wireless systems to achieve high throughput in a multicell environment. Least interfered group assignment (LIGA selects for each session the subcarrier group on which the user receives the minimum interference, while best channel ratio group assignment (BCRGA chooses the subcarrier group with the largest channel response-to-interference ratio. Both analytical framework and simulation model are developed for evaluation of throughput distribution of the proposed schemes. An iterative approach is devised to handle the complex interdependency between multicell interference profiles in the throughput analysis. Illustrative results show significant throughput improvement offered by the interference-based assignment schemes for MC-CDMA multicell wireless systems. In particular, under low loading conditions, LIGA renders the best performance. However, as the load increases BCRGA tends to offer superior performance.

Alternative SAIL-Trp for robust aromatic signal assignment and determination of the χ2 conformation by intra-residue NOEs

International Nuclear Information System (INIS)

Miyanoiri, Yohei; Takeda, Mitsuhiro; Jee, JunGoo; Ono, Akira M.; Okuma, Kosuke; Terauchi, Tsutomu; Kainosho, Masatsune

2011-01-01

Tryptophan (Trp) residues are frequently found in the hydrophobic cores of proteins, and therefore, their side-chain conformations, especially the precise locations of the bulky indole rings, are critical for determining structures by NMR. However, when analyzing [U– 13 C, 15 N]-proteins, the observation and assignment of the ring signals are often hampered by excessive overlaps and tight spin couplings. These difficulties have been greatly alleviated by using stereo-array isotope labeled (SAIL) proteins, which are composed of isotope-labeled amino acids optimized for unambiguous side-chain NMR assignment, exclusively through the 13 C– 13 C and 13 C– 1 H spin coupling networks (Kainosho et al. in Nature 440:52–57, 2006). In this paper, we propose an alternative type of SAIL-Trp with the [ζ2,ζ3- 2 H 2 ; δ1,ε3,η2- 13 C 3 ; ε1- 15 N]-indole ring ([ 12 C γ, 12 C ε2 ] SAIL-Trp), which provides a more robust way to correlate the 1 H β , 1 H α , and 1 H N to the 1 H δ1 and 1 H ε3 through the intra-residue NOEs. The assignment of the 1 H δ1 / 13 C δ1 and 1 H ε3 / 13 C ε3 signals can thus be transferred to the 1 H ε1 / 15 N ε1 and 1 H η2 / 13 C η2 signals, as with the previous type of SAIL-Trp, which has an extra 13 C at the C γ of the ring. By taking advantage of the stereospecific deuteration of one of the prochiral β-methylene protons, which was 1 H β2 in this experiment, one can determine the side-chain conformation of the Trp residue including the χ 2 angle, which is especially important for Trp residues, as they can adopt three preferred conformations. We demonstrated the usefulness of [ 12 C γ , 12 C ε2 ] SAIL-Trp for the 12 kDa DNA binding domain of mouse c-Myb protein (Myb-R2R3), which contains six Trp residues.

Alternative SAIL-Trp for robust aromatic signal assignment and determination of the χ(2) conformation by intra-residue NOEs.

Science.gov (United States)

Miyanoiri, Yohei; Takeda, Mitsuhiro; Jee, JunGoo; Ono, Akira M; Okuma, Kosuke; Terauchi, Tsutomu; Kainosho, Masatsune

2011-12-01

Tryptophan (Trp) residues are frequently found in the hydrophobic cores of proteins, and therefore, their side-chain conformations, especially the precise locations of the bulky indole rings, are critical for determining structures by NMR. However, when analyzing [U-(13)C,(15)N]-proteins, the observation and assignment of the ring signals are often hampered by excessive overlaps and tight spin couplings. These difficulties have been greatly alleviated by using stereo-array isotope labeled (SAIL) proteins, which are composed of isotope-labeled amino acids optimized for unambiguous side-chain NMR assignment, exclusively through the (13)C-(13)C and (13)C-(1)H spin coupling networks (Kainosho et al. in Nature 440:52-57, 2006). In this paper, we propose an alternative type of SAIL-Trp with the [ζ2,ζ3-(2)H(2); δ1,ε3,η2-(13)C(3); ε1-(15)N]-indole ring ([(12)C (γ,) ( 12) C(ε2)] SAIL-Trp), which provides a more robust way to correlate the (1)H(β), (1)H(α), and (1)H(N) to the (1)H(δ1) and (1)H(ε3) through the intra-residue NOEs. The assignment of the (1)H(δ1)/(13)C(δ1) and (1)H(ε3)/(13)C(ε3) signals can thus be transferred to the (1)H(ε1)/(15)N(ε1) and (1)H(η2)/(13)C(η2) signals, as with the previous type of SAIL-Trp, which has an extra (13)C at the C(γ) of the ring. By taking advantage of the stereospecific deuteration of one of the prochiral β-methylene protons, which was (1)H(β2) in this experiment, one can determine the side-chain conformation of the Trp residue including the χ(2) angle, which is especially important for Trp residues, as they can adopt three preferred conformations. We demonstrated the usefulness of [(12)C(γ),(12)C(ε2)] SAIL-Trp for the 12 kDa DNA binding domain of mouse c-Myb protein (Myb-R2R3), which contains six Trp residues.

RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

International Nuclear Information System (INIS)

Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E.; Eghbalnia, Hamid R.

2012-01-01

The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ( 1 H– 15 N 2D HMQC) and proton–proton nuclear Overhauser enhancement spectroscopy ( 1 H– 1 H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino resonances for a

RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

Energy Technology Data Exchange (ETDEWEB)

Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E. [National Magnetic Resonance Facility at Madison (United States); Eghbalnia, Hamid R., E-mail: eghbalhd@uc.edu [University of Cincinnati, Department of Molecular and Cellular Physiology (United States)

2012-04-15

The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ({sup 1}H-{sup 15}N 2D HMQC) and proton-proton nuclear Overhauser enhancement spectroscopy ({sup 1}H-{sup 1}H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino

Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR)

Science.gov (United States)

Laszlo, Kenneth J.; Bush, Matthew F.

2015-12-01

Mass spectra of native-like protein complexes often exhibit narrow charge-state distributions, broad peaks, and contributions from multiple, coexisting species. These factors can make it challenging to interpret those spectra, particularly for mixtures with significant heterogeneity. Here we demonstrate the use of ion/ion proton transfer reactions to reduce the charge states of m/ z-selected, native-like ions of proteins and protein complexes, a technique that we refer to as cation to anion proton transfer reactions (CAPTR). We then demonstrate that CAPTR can increase the accuracy of charge state assignments and the resolution of interfering species in native mass spectrometry. The CAPTR product ion spectra for pyruvate kinase exhibit ~30 peaks and enable unambiguous determination of the charge state of each peak, whereas the corresponding precursor spectra exhibit ~6 peaks and the assigned charge states have an uncertainty of ±3%. 15+ bovine serum albumin and 21+ yeast enolase dimer both appear near m/ z 4450 and are completely unresolved in a mixture. After a single CAPTR event, the resulting product ions are baseline resolved. The separation of the product ions increases dramatically after each subsequent CAPTR event; 12 events resulted in a 3000-fold improvement in separation relative to the precursor ions. Finally, we introduce a framework for interpreting and predicting the figures of merit for CAPTR experiments. More generally, these results suggest that CAPTR strongly complements other mass spectrometry tools for analyzing proteins and protein complexes, particularly those in mixtures.

1H NMR studies of plastocyanin from Scenedesmus obliquus: Complete sequence-specific assignment, secondary structure analysis, and global fold

International Nuclear Information System (INIS)

Moore, J.M.; Chazin, W.J.; Wright, P.E.; Powls, R.

1988-01-01

Two-dimensional 1 H NMR methods have been used to make sequence-specific resonance assignments for the 97 amino acid residues of the plastocyanin from the green alga Scenedesmus obliquus. Assignments were obtained for all backbone protons and the majority of the side-chain protons. Spin system identification relied heavily on the observation of relayed connectivities to the backbone amide proton. Sequence-specific assignments were made by using the sequential assignment procedure. During this process, an extra valine residue was identified that had not been detected in the original amino acid sequence. Elements of regular secondary structure were identified from characteristic NOE connectivities between backbone protons, coupling constant values, and the observation of slowly exchanging amide protons. The protein in solution contains eight β-strands, one short segment of helix, five reverse turns, and five loops. The β-strands may be arranged into two βsheets on the basis of extensive cross-strand NOE connectivities. The chain-folding topology determined from the NMR experiments is that of a Greek key β-barrel and is similar to that observed for French bean plastocyanin in solution and poplar plastocyanin in the crystalline state. While the overall structures are similar, several differences in local structure between the S. obliquus and higher plant plastocyanins have been identified

Student generated assignments about electrical circuits in a computer simulation

NARCIS (Netherlands)

Vreman-de Olde, Cornelise; de Jong, Anthonius J.M.

2004-01-01

In this study we investigated the design of assignments by students as a knowledge-generating activity. Students were required to design assignments for 'other students' in a computer simulation environment about electrical circuits. Assignments consisted of a question, alternatives, and feedback on

A large-scale evaluation of computational protein function prediction

NARCIS (Netherlands)

Radivojac, P.; Clark, W.T.; Oron, T.R.; Schnoes, A.M.; Wittkop, T.; Kourmpetis, Y.A.I.; Dijk, van A.D.J.; Friedberg, I.

2013-01-01

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be

On pole structure assignment in linear systems

Czech Academy of Sciences Publication Activity Database

Loiseau, J.-J.; Zagalak, Petr

2009-01-01

Roč. 82, č. 7 (2009), s. 1179-1192 ISSN 0020-7179 R&D Projects: GA ČR(CZ) GA102/07/1596 Institutional research plan: CEZ:AV0Z10750506 Keywords : linear systems * linear state feedback * pole structure assignment Subject RIV: BC - Control Systems Theory Impact factor: 1.124, year: 2009 http://library.utia.cas.cz/separaty/2009/AS/zagalak-on pole structure assignment in linear systems.pdf

An Approach to Function Annotation for Proteins of Unknown Function (PUFs in the Transcriptome of Indian Mulberry.

Directory of Open Access Journals (Sweden)

K H Dhanyalakshmi

Full Text Available The modern sequencing technologies are generating large volumes of information at the transcriptome and genome level. Translation of this information into a biological meaning is far behind the race due to which a significant portion of proteins discovered remain as proteins of unknown function (PUFs. Attempts to uncover the functional significance of PUFs are limited due to lack of easy and high throughput functional annotation tools. Here, we report an approach to assign putative functions to PUFs, identified in the transcriptome of mulberry, a perennial tree commonly cultivated as host of silkworm. We utilized the mulberry PUFs generated from leaf tissues exposed to drought stress at whole plant level. A sequence and structure based computational analysis predicted the probable function of the PUFs. For rapid and easy annotation of PUFs, we developed an automated pipeline by integrating diverse bioinformatics tools, designated as PUFs Annotation Server (PUFAS, which also provides a web service API (Application Programming Interface for a large-scale analysis up to a genome. The expression analysis of three selected PUFs annotated by the pipeline revealed abiotic stress responsiveness of the genes, and hence their potential role in stress acclimation pathways. The automated pipeline developed here could be extended to assign functions to PUFs from any organism in general. PUFAS web server is available at http://caps.ncbs.res.in/pufas/ and the web service is accessible at http://capservices.ncbs.res.in/help/pufas.

Personnel shift assignment: Existence conditions and network models

NARCIS (Netherlands)

van den Berg, Jeroen P.; van den Berg, J.P.; Panton, David M.

1994-01-01

The personnel scheduling problem is known to be a five-stage process in which the final stage involves the assignment of shifts to the days worked in the schedule. This paper discusses the existence conditions for both continuous and forward rotating shift assignments and heuristic network

75 FR 55355 - Delegation of Authority and Assignment of Responsibility

Science.gov (United States)

2010-09-10

... DEPARTMENT OF LABOR Office of the Secretary Delegation of Authority and Assignment of Responsibility Secretary's Order 4-2010 Subject: Delegation of Authority and Assignment of Responsibility to the... delegations and assignments in full force and effect, except as expressly modified herein. 4. Delegation of...

Staff assignment practices in nursing homes: review of the literature.

Science.gov (United States)

Rahman, Anna; Straker, Jane K; Manning, Lydia

2009-01-01

Consistent assignment, whereby nursing home staff members, particularly certified nurse aides, are assigned to the same residents on most shifts, is increasingly viewed as a cornerstone of culture change in nursing homes. It has been advocated as a best-care model that increases residents' quality of life while contributing to a more stable frontline staff. Given these potential benefits, consistent assignment is now widely viewed as superior to rotating assignment, an alternative staffing model that aims to distribute care burden more fairly among staff and ensure that workers are familiar with most residents. Despite favorable anecdotal reports about the benefits of consistent assignment, the research literature reports mixed and sometimes contradictory findings for this staffing practice. This article reviews the research pertaining to staff assignment practices in nursing homes. Reviewed here are 13 reports on experimental trials (6 reports), evaluation research (4 reports), and nursing home surveys (3 reports). The review reveals broad diversity in staffing practices and raises questions that challenge popular assumptions about consistent assignment. The article closes with a discussion of the research, policy, and practice implications of the research findings.

Learning to assign binary weights to binary descriptor

Science.gov (United States)

Huang, Zhoudi; Wei, Zhenzhong; Zhang, Guangjun

2016-10-01

Constructing robust binary local feature descriptors are receiving increasing interest due to their binary nature, which can enable fast processing while requiring significantly less memory than their floating-point competitors. To bridge the performance gap between the binary and floating-point descriptors without increasing the computational cost of computing and matching, optimal binary weights are learning to assign to binary descriptor for considering each bit might contribute differently to the distinctiveness and robustness. Technically, a large-scale regularized optimization method is applied to learn float weights for each bit of the binary descriptor. Furthermore, binary approximation for the float weights is performed by utilizing an efficient alternatively greedy strategy, which can significantly improve the discriminative power while preserve fast matching advantage. Extensive experimental results on two challenging datasets (Brown dataset and Oxford dataset) demonstrate the effectiveness and efficiency of the proposed method.

75 FR 55354 - Delegation of Authority and Assignment of Responsibilities

Science.gov (United States)

2010-09-10

... DEPARTMENT OF LABOR Office of the Secretary Delegation of Authority and Assignment of Responsibilities Secretary's Order 3-2010 Subject: Delegation of Authority and Assignment of Responsibilities to... Secretary to enforce sections 18A and 18B of the FLSA. 4. Delegation of Authority and Assignment of...

25 CFR 225.33 - Assignment of minerals agreements.

Science.gov (United States)

2010-04-01

... 25 Indians 1 2010-04-01 2010-04-01 false Assignment of minerals agreements. 225.33 Section 225.33 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ENERGY AND MINERALS OIL AND GAS, GEOTHERMAL, AND SOLID MINERALS AGREEMENTS Minerals Agreements § 225.33 Assignment of minerals agreements. An...

Automating Formative and Summative Feedback for Individualised Assignments

Science.gov (United States)

Hamilton, Ian Robert

2009-01-01

Purpose: The purpose of this paper is to report on the rationale behind the use of a unique paper-based individualised accounting assignment, which automated the provision to students of immediate formative and timely summative feedback. Design/methodology/approach: As students worked towards completing their assignment, the package provided…

submission of art studio-based assignments: students experience

African Journals Online (AJOL)

PUBLICATIONS1

are reluctant to complete their studio assignments on time are critically ... tative and qualitative data, derived from survey and interviews were used to ... is therefore exploratory and studio based. It ... mogenous group of students who report pro- ... Assignment management .... The analyses in this study are based on data.

Heuristic for Task-Worker Assignment with Varying Learning Slopes

Directory of Open Access Journals (Sweden)

Wipawee Tharmmaphornphilas

2010-04-01

Full Text Available Fashion industry has variety products, so the multi-skilled workers are required to improve flexibility in production and assignment. Generally the supervisor will assign task to the workers based on skill and skill levels of worker. Since in fashion industry new product styles are launched more frequently and the order size tends to be smaller, the workers always learn when the raw material and the production process changes. Consequently they require less time to produce the succeeding units of a task based on their learning ability. Since the workers have both experience and inexperience workers, so each worker has different skill level and learning ability. Consequently, the assignment which assumed constant skill level is not proper to use. This paper proposes a task-worker assignment considering worker skill levels and learning abilities. Processing time of each worker changes along production period due to a worker learning ability. We focus on a task-worker assignment in a fashion industry where tasks are ordered in series; the number of tasks is greater than the number of workers. Therefore, workers can perform multiple assignments followed the precedence restriction as an assembly line balancing problem. The problem is formulated in an integer linear programming model with objective to minimize makespan. A heuristic is proposed to determine the lower bound (LB and the upper bound (UB of the problem and the best assignment is determined. The performance of the heuristic method is tested by comparing quality of solution and computational time to optimal solutions.

Assignment Procedures in the Air Force Procurement Management Information System.

Science.gov (United States)

Ward, Joe H., Jr.; And Others

An overview is presented of the procedure for offering jobs in the Air Force Procurement Management Information System (PROMIS), an assignment system which makes possible the use of human resources research findings to improve individual personnel assignments. A general framework for viewing personnel assignment systems is presented; then job…

A property of assignment type mixed integer linear programming problems

NARCIS (Netherlands)

Benders, J.F.; van Nunen, J.A.E.E.

1982-01-01

In this paper we will proof that rather tight upper bounds can be given for the number of non-unique assignments that are achieved after solving the linear programming relaxation of some types of mixed integer linear assignment problems. Since in these cases the number of splitted assignments is

41 CFR 105-8.152 - Program accessibility: Assignment of space.

Science.gov (United States)

2010-07-01

... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false Program accessibility: Assignment of space. 105-8.152 Section 105-8.152 Public Contracts and Property Management Federal Property...-8.152 Program accessibility: Assignment of space. (a) When GSA assigns or reassigns space to an...

Detection of C',Cα correlations in proteins using a new time- and sensitivity-optimal experiment

International Nuclear Information System (INIS)

Lee, Donghan; Voegeli, Beat; Pervushin, Konstantin

2005-01-01

Sensitivity- and time-optimal experiment, called COCAINE (CO-CA In- and aNtiphase spectra with sensitivity Enhancement), is proposed to correlate chemical shifts of 13 C' and 13 C α spins in proteins. A comparison of the sensitivity and duration of the experiment with the corresponding theoretical unitary bounds shows that the COCAINE experiment achieves maximum possible transfer efficiency in the shortest possible time, and in this sense the sequence is optimal. Compared to the standard HSQC, the COCAINE experiment delivers a 2.7-fold gain in sensitivity. This newly proposed experiment can be used for assignment of backbone resonances in large deuterated proteins effectively bridging 13 C' and 13 C α resonances in adjacent amino acids. Due to the spin-state selection employed, the COCAINE experiment can also be used for efficient measurements of one-bond couplings (e.g. scalar and residual dipolar couplings) in any two-spin system (e.g. the N/H in the backbone of protein)

Socially-assigned race, healthcare discrimination and preventive healthcare services.

Directory of Open Access Journals (Sweden)

Tracy Macintosh

Full Text Available Race and ethnicity, typically defined as how individuals self-identify, are complex social constructs. Self-identified racial/ethnic minorities are less likely to receive preventive care and more likely to report healthcare discrimination than self-identified non-Hispanic whites. However, beyond self-identification, these outcomes may vary depending on whether racial/ethnic minorities are perceived by others as being minority or white; this perception is referred to as socially-assigned race.To examine the associations between socially-assigned race and healthcare discrimination and receipt of selected preventive services.Cross-sectional analysis of the 2004 Behavioral Risk Factor Surveillance System "Reactions to Race" module. Respondents from seven states and the District of Columbia were categorized into 3 groups, defined by a composite of self-identified race/socially-assigned race: Minority/Minority (M/M, n = 6,837, Minority/White (M/W, n = 929, and White/White (W/W, n = 25,913. Respondents were 18 years or older, with 61.7% under age 60; 51.8% of respondents were female. Measures included reported healthcare discrimination and receipt of vaccinations and cancer screenings.Racial/ethnic minorities who reported being socially-assigned as minority (M/M were more likely to report healthcare discrimination compared with those who reported being socially-assigned as white (M/W (8.9% vs. 5.0%, p = 0.002. Those reporting being socially-assigned as white (M/W and W/W had similar rates for past-year influenza (73.1% vs. 74.3% and pneumococcal (69.3% vs. 58.6% vaccinations; however, rates were significantly lower among M/M respondents (56.2% and 47.6%, respectively, p-values<0.05. There were no significant differences between the M/M and M/W groups in the receipt of cancer screenings.Racial/ethnic minorities who reported being socially-assigned as white are more likely to receive preventive vaccinations and less likely to report

A high quality nuclear magnetic resonance solution structure of peptide deformylase from Escherichia coli: application of an automated assignment strategy using GARANT.

Science.gov (United States)

O'Connell, J F; Pryor, K D; Grant, S K; Leiting, B

1999-04-01

The NMR structure of the peptide deformylase (PDF) (1-150) from Escherichia coli, which is an essential enzyme that removes the formyl group from nascent polypeptides and represents a potential target for drug discovery, was determined using 15N/13C doubly labeled protein. Nearly completely automated assignment routines were employed to assign three-dimensional triple resonance, 15N-resolved and 13C-resolved NOESY spectra using the program GARANT. This assignment strategy, demonstrated on a 17 kDa protein, is a significant advance in the automation of NMR data assignment and structure determination that will accelerate future work. A total of 2302 conformational constraints were collected as input for the distance geometry program DYANA. After restrained energy minimization with the program X-PLOR the 20 best conformers characterize a high quality structure with an average of 0.43 A for the root-mean-square deviation calculated from the backbone atoms N, C alpha and C', and 0.81 A for all heavy atoms of the individual conformers relative to the mean coordinates for residues 1 to 150. The globular fold of PDF contains two alpha-helices comprising residues 25-40, 125-138, six beta-strands 57-60, 70-77, 85-88, 98-101, 105-111, 117-123 and one 3(10) helix comprising residues 49-51. The C-terminal helix contains the HEXXH motif positioning a zinc ligand in a similar fashion to other metalloproteases, with the third ligand being cysteine and the fourth presumably a water. The three-dimensional structure of PDF affords insight into the substrate recognition and specificity for N-formylated over N-acetylated substrates and is compared to other PDF structures.

A high quality nuclear magnetic resonance solution structure of peptide deformylase from Escherichia coli: Application of an automated assignment strategy using GARANT

International Nuclear Information System (INIS)

O'Connell, John F.; Pryor, KellyAnn D.; Grant, Stephan K.; Leiting, Barbara

1999-01-01

The NMR structure of the peptide deformylase (PDF) (1-150) from Escherichia coli, which is an essential enzyme that removes the formyl group from nascent polypeptides and represents a potential target for drug discovery, was determined using 15N/13C doubly labeled protein. Nearly completely automated assignment routines were employed to assign three-dimensional triple resonance, 15N-resolved and 13C-resolved NOESY spectra using the program GARANT. This assignment strategy, demonstrated on a 17 kDa protein, is a significant advance in the automation of NMR data assignment and structure determination that will accelerate future work. A total of 2302 conformational constraints were collected as input for the distance geometry program DYANA. After restrained energy minimization with the program X-PLOR the 20 best conformers characterize a high quality structure with an average of 0.43 A for the root-mean-square deviation calculated from the backbone atoms N, Cα and C', and 0.81 A for all heavy atoms of the individual conformers relative to the mean coordinates for residues 1 to 150. The globular fold of PDF contains two α-helices comprising residues 25-40, 125-138, six β-strands 57-60, 70-77, 85-88, 98-101, 105-111, 117-123 and one 310 helix comprising residues 49-51. The C-terminal helix contains the HEXXH motif positioning a zinc ligand in a similar fashion to other metalloproteases, with the third ligand being cysteine and the fourth presumably a water. The three-dimensional structure of PDF affords insight into the substrate recognition and specificity for N-formylated over N-acetylated substrates and is compared to other PDF structures

The Presentation Assignment: Creating Learning Opportunities for Diverse Student Populations.

Science.gov (United States)

Spencer, Brenda H.; Bartle-Angus, Kathryn

2000-01-01

Finds the presentation assignment to be an effective method of providing students with the opportunity to apply the literacy skills they are learning in ways that are personally meaningful. Describes the presentation assignment framework and provides an example of an assignment that required students to analyze and interpret works of literature…

Triage level assignment and nurse characteristics and experience.

Science.gov (United States)

Gómez-Angelats, Elisenda; Miró, Òscar; Bragulat Baur, Ernesto; Antolín Santaliestra, Alberto; Sánchez Sánchez, Miquel

2018-06-01

To study the relation between nursing staff demographics and experience and their assignment of triage level in the emergency department. One-year retrospective observational study in the triage area of a tertiary care urban university hospital that applies the Andorran-Spanish triage model. Variables studied were age, gender, nursing experience, triage experience, shift, usual level of emergency work the nurse undertakes, number of triage decisions made, and percentage of patients assigned to each level. Fifty nurses (5 men, 45 women) with a mean (SD) age of 45 (9) years triaged 67 803 patients during the year. Nurses classified more patients in level 5 on the morning shift (7.9%) than on the afternoon shift (5.5%) (P=.003). The difference in the rate of level-5 triage classification became significant when nurses were older (β = 0.092, P=.037) and experience was greater (β = 0.103, P=.017). The number of triages recorded by a nurse was significantly and directly related to the percentage of patients assigned to level 3 (β = 0.003, P=.006) and inversely related to the percentages assigned to level 4 (β = -0.002, P=.008) and level 5 (β = -0.001, P=.017). We found that triage level assignments were related to age, experience, shift, and total number of patients triaged by a nurse.

Visual words assignment via information-theoretic manifold embedding.

Science.gov (United States)

Deng, Yue; Li, Yipeng; Qian, Yanjun; Ji, Xiangyang; Dai, Qionghai

2014-10-01

Codebook-based learning provides a flexible way to extract the contents of an image in a data-driven manner for visual recognition. One central task in such frameworks is codeword assignment, which allocates local image descriptors to the most similar codewords in the dictionary to generate histogram for categorization. Nevertheless, existing assignment approaches, e.g., nearest neighbors strategy (hard assignment) and Gaussian similarity (soft assignment), suffer from two problems: 1) too strong Euclidean assumption and 2) neglecting the label information of the local descriptors. To address the aforementioned two challenges, we propose a graph assignment method with maximal mutual information (GAMI) regularization. GAMI takes the power of manifold structure to better reveal the relationship of massive number of local features by nonlinear graph metric. Meanwhile, the mutual information of descriptor-label pairs is ultimately optimized in the embedding space for the sake of enhancing the discriminant property of the selected codewords. According to such objective, two optimization models, i.e., inexact-GAMI and exact-GAMI, are respectively proposed in this paper. The inexact model can be efficiently solved with a closed-from solution. The stricter exact-GAMI nonparametrically estimates the entropy of descriptor-label pairs in the embedding space and thus leads to a relatively complicated but still trackable optimization. The effectiveness of GAMI models are verified on both the public and our own datasets.

28 CFR 545.23 - Inmate work/program assignment.

Science.gov (United States)

2010-07-01

... community living area, unless the pretrial inmate has signed a waiver of his or her right not to work (see... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Inmate work/program assignment. 545.23... WORK AND COMPENSATION Inmate Work and Performance Pay Program § 545.23 Inmate work/program assignment...

"Why bother so incredibly much?": student perspectives on PISA science assignments

Science.gov (United States)

Serder, Margareta; Jakobsson, Anders

2015-09-01

Large-scale assessment, such as the Programme for International Assessment (PISA), plays an increasingly important role in current educational practice and politics. However, many scholars have questioned the validity and reliability of the tests and the extent to which they actually constitute trustworthy representations of students' knowledge. In the light of such critical voices the present article adopts a sociocultural perspective of human knowledge and action in order to explore the encounters between students and the science test assignments with which their knowledge is tested. Of particular interest in this study are the described "real-life situations" presented as the relevant background in which scientific literacy is assessed in PISA. According to the sociocultural theoretical onset the methodology used to approach the students' meaning making of the image of science as portrayed in the test were collaborative situations in which students work in small groups with units of PISA assignments, enabling a study of student-assignment encounters in action. The data we worked with consists of video-recordings from 71 Swedish 15-year-old students working with three released units from the PISA science test. According to our analysis, the "real-life situations" described in the test emerge as problematic in the students' meaning-making. This is demonstrated for instance by the students' positioning themselves as being different from and opposed to the fictional pictured students who appear in the backstories of the test. This article provides examples of how the scientific and academic language used by the fictional students in the assignments mediates distance and resistance among the students. The fictional students' use of strict scientific language and methods in day-to-day life situations leads them to be perceived as "little scientists" and as elite stereotypes of the scientific culture. We conclude that, by using assignments of this type, measurements of

Optimal assignment of incoming flights to baggage carousels at airports

DEFF Research Database (Denmark)

Barth, Torben C.

The problem considered in this report is an assignment problem occurring at airports. This problem concerns the assignment of baggage carousels in baggage claim halls to arriving aircraft (baggage carousel assignment problem). This is a highly dynamic problem since disruptions frequently occur du...... and in general is a substantial support in decision making....

PARETO OPTIMAL SOLUTIONS FOR MULTI-OBJECTIVE GENERALIZED ASSIGNMENT PROBLEM

Directory of Open Access Journals (Sweden)

S. Prakash

2012-01-01

Full Text Available

ENGLISH ABSTRACT: The Multi-Objective Generalized Assignment Problem (MGAP with two objectives, where one objective is linear and the other one is non-linear, has been considered, with the constraints that a job is assigned to only one worker – though he may be assigned more than one job, depending upon the time available to him. An algorithm is proposed to find the set of Pareto optimal solutions of the problem, determining assignments of jobs to workers with two objectives without setting priorities for them. The two objectives are to minimise the total cost of the assignment and to reduce the time taken to complete all the jobs.

AFRIKAANSE OPSOMMING: ‘n Multi-doelwit veralgemeende toekenningsprobleem (“multi-objective generalised assignment problem – MGAP” met twee doelwitte, waar die een lineêr en die ander nielineêr is nie, word bestudeer, met die randvoorwaarde dat ‘n taak slegs toegedeel word aan een werker – alhoewel meer as een taak aan hom toegedeel kan word sou die tyd beskikbaar wees. ‘n Algoritme word voorgestel om die stel Pareto-optimale oplossings te vind wat die taaktoedelings aan werkers onderhewig aan die twee doelwitte doen sonder dat prioriteite toegeken word. Die twee doelwitte is om die totale koste van die opdrag te minimiseer en om die tyd te verminder om al die take te voltooi.

Peakr: simulating solid-state NMR spectra of proteins

International Nuclear Information System (INIS)

Schneider, Robert; Odronitz, Florian; Hammesfahr, Bjorn; Hellkamp, Marcel; Kollmar, Martin

2013-01-01

When analyzing solid-state nuclear magnetic resonance (NMR) spectra of proteins, assignment of resonances to nuclei and derivation of restraints for 3D structure calculations are challenging and time-consuming processes. Simulated spectra that have been calculated based on, for example, chemical shift predictions and structural models can be of considerable help. Existing solutions are typically limited in the type of experiment they can consider and difficult to adapt to different settings. Here, we present Peakr, a software to simulate solid-state NMR spectra of proteins. It can generate simulated spectra based on numerous common types of internuclear correlations relevant for assignment and structure elucidation, can compare simulated and experimental spectra and produces lists and visualizations useful for analyzing measured spectra. Compared with other solutions, it is fast, versatile and user friendly. (authors)

Game theory and traffic assignment.

Science.gov (United States)

2013-09-01

Traffic assignment is used to determine the number of users on roadway links in a network. While this problem has : been widely studied in transportation literature, its use of the concept of equilibrium has attracted considerable interest : in the f...

Protein Structure Determination Using Chemical Shifts

DEFF Research Database (Denmark)

Christensen, Anders Steen

is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

Membrane-localized extra-large G proteins and Gbg of the heterotrimeric G proteins form functional complexes engaged in plant immunity in Arabidopsis.

Science.gov (United States)

Maruta, Natsumi; Trusov, Yuri; Brenya, Eric; Parekh, Urvi; Botella, José Ramón

2015-03-01

In animals, heterotrimeric G proteins, comprising Ga, Gb, and Gg subunits, are molecular switches whose function tightly depends on Ga and Gbg interaction. Intriguingly, in Arabidopsis (Arabidopsis thaliana), multiple defense responses involve Gbg, but not Ga. We report here that the Gbg dimer directly partners with extra-large G proteins (XLGs) to mediate plant immunity. Arabidopsis mutants deficient in XLGs, Gb, and Gg are similarly compromised in several pathogen defense responses, including disease development and production of reactive oxygen species. Genetic analysis of double, triple, and quadruple mutants confirmed that XLGs and Gbg functionally interact in the same defense signaling pathways. In addition, mutations in XLG2 suppressed the seedling lethal and cell death phenotypes of BRASSINOSTEROID INSENSITIVE1-associated receptor kinase1-interacting receptor-like kinase1 mutants in an identical way as reported for Arabidopsis Gb-deficient mutants. Yeast (Saccharomyces cerevisiae) three-hybrid and bimolecular fluorescent complementation assays revealed that XLG2 physically interacts with all three possible Gbg dimers at the plasma membrane. Phylogenetic analysis indicated a close relationship between XLGs and plant Ga subunits, placing the divergence point at the dawn of land plant evolution. Based on these findings, we conclude that XLGs form functional complexes with Gbg dimers, although the mechanism of action of these complexes, including activation/deactivation, must be radically different form the one used by the canonical Ga subunit and are not likely to share the same receptors. Accordingly, XLGs expand the repertoire of heterotrimeric G proteins in plants and reveal a higher level of diversity in heterotrimeric G protein signaling.

Simulated annealing algorithm for solving chambering student-case assignment problem

Science.gov (United States)

Ghazali, Saadiah; Abdul-Rahman, Syariza

2015-12-01

The problem related to project assignment problem is one of popular practical problem that appear nowadays. The challenge of solving the problem raise whenever the complexity related to preferences, the existence of real-world constraints and problem size increased. This study focuses on solving a chambering student-case assignment problem by using a simulated annealing algorithm where this problem is classified under project assignment problem. The project assignment problem is considered as hard combinatorial optimization problem and solving it using a metaheuristic approach is an advantage because it could return a good solution in a reasonable time. The problem of assigning chambering students to cases has never been addressed in the literature before. For the proposed problem, it is essential for law graduates to peruse in chambers before they are qualified to become legal counselor. Thus, assigning the chambering students to cases is a critically needed especially when involving many preferences. Hence, this study presents a preliminary study of the proposed project assignment problem. The objective of the study is to minimize the total completion time for all students in solving the given cases. This study employed a minimum cost greedy heuristic in order to construct a feasible initial solution. The search then is preceded with a simulated annealing algorithm for further improvement of solution quality. The analysis of the obtained result has shown that the proposed simulated annealing algorithm has greatly improved the solution constructed by the minimum cost greedy heuristic. Hence, this research has demonstrated the advantages of solving project assignment problem by using metaheuristic techniques.

A branch-and-price algorithm to solve the integrated berth allocation and yard assignment problem in bulk ports

DEFF Research Database (Denmark)

Robenek, Tomáš; Umang, Nitish; Bierlaire, Michel

2014-01-01

In this research, two crucial optimization problems of berth allocation and yard assignment in the context of bulk ports are studied. We discuss how these problems are interrelated and can be combined and solved as a single large scale optimization problem. More importantly we highlight the diffe...

Insights into SCP/TAPS proteins of liver flukes based on large-scale bioinformatic analyses of sequence datasets.

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Cinzia Cantacessi

Full Text Available BACKGROUND: SCP/TAPS proteins of parasitic helminths have been proposed to play key roles in fundamental biological processes linked to the invasion of and establishment in their mammalian host animals, such as the transition from free-living to parasitic stages and the modulation of host immune responses. Despite the evidence that SCP/TAPS proteins of parasitic nematodes are involved in host-parasite interactions, there is a paucity of information on this protein family for parasitic trematodes of socio-economic importance. METHODOLOGY/PRINCIPAL FINDINGS: We conducted the first large-scale study of SCP/TAPS proteins of a range of parasitic trematodes of both human and veterinary importance (including the liver flukes Clonorchis sinensis, Opisthorchis viverrini, Fasciola hepatica and F. gigantica as well as the blood flukes Schistosoma mansoni, S. japonicum and S. haematobium. We mined all current transcriptomic and/or genomic sequence datasets from public databases, predicted secondary structures of full-length protein sequences, undertook systematic phylogenetic analyses and investigated the differential transcription of SCP/TAPS genes in O. viverrini and F. hepatica, with an emphasis on those that are up-regulated in the developmental stages infecting the mammalian host. CONCLUSIONS: This work, which sheds new light on SCP/TAPS proteins, guides future structural and functional explorations of key SCP/TAPS molecules associated with diseases caused by flatworms. Future fundamental investigations of these molecules in parasites and the integration of structural and functional data could lead to new approaches for the control of parasitic diseases.

Effect of dietary protein source on piglet meat quality characteristics

Directory of Open Access Journals (Sweden)

Panagiotis E Simitzis

2014-03-01

Full Text Available An experiment was conducted to examine the effects of different dietary protein sources (soybean meal vs whey protein on piglet meat quality characteristics. Eighteen castrated male Large White × Duroc × Landrace piglets were randomly assigned to 2 groups. Piglets were kept in individual metabolic cages and fed ad libitum over a period of 38 days the following 2 diets: diet SB, which was formulated to meet the nutrient requirements of piglets using soybean meal as the main crude protein source and diet WP, where SB was totally replaced by a mixture of whey proteins on equal digestible energy and crude protein basis. At the end of the experiment, piglets were weighed and slaughtered. After overnight chilling, samples of Longissimus dorsi muscle were taken and were used for meat quality measurements.          No significant differences were observed in the values of pH, colour, water holding capacity, shear force and intramuscular fat content of L. dorsi muscle between the dietary treatments. Measurement of lipid oxidation values showed that dietary supplementation with different protein sources did not influence meat antioxidant properties during refrigerated storage. The SB piglets had lower 14:0 (P<0.01 and higher 18:3n-3 (P<0.001 levels in intramuscular fat in comparison with WP piglets. However, these changes were attributed to background differences in the dietary FA profile and not to a direct protein source effect. The results of this preliminary study indicate that the examined dietary protein sources (soybean meal or whey protein do not have a significant effect on meat quality characteristics of piglets.

Efficient Mechanisms to Allocate Assignment Incentives in the Navy

National Research Council Canada - National Science Library

Nimon, R. W; Hall, Ricky D; Zaki, Hossam

2005-01-01

.... All assignments, however, may not necessarily be voluntary. These assignments (jobs) have been labeled as "hard to fill" by Navy leadership, and the Navy has implemented market-based, cash stipends to attract Sailors to these jobs...

Ant Colony Algorithm and Simulation for Robust Airport Gate Assignment

Directory of Open Access Journals (Sweden)

Hui Zhao

2014-01-01

Full Text Available Airport gate assignment is core task for airport ground operations. Due to the fact that the departure and arrival time of flights may be influenced by many random factors, the airport gate assignment scheme may encounter gate conflict and many other problems. This paper aims at finding a robust solution for airport gate assignment problem. A mixed integer model is proposed to formulate the problem, and colony algorithm is designed to solve this model. Simulation result shows that, in consideration of robustness, the ability of antidisturbance for airport gate assignment scheme has much improved.

Non-uniform tube representation of proteins

DEFF Research Database (Denmark)

Hansen, Mikael Sonne

Treating the full protein structure is often neither computationally nor physically possible. Instead one is forced to consider various reduced models capturing the properties of interest. Previous work have used tubular neighborhoods of the C-alpha backbone. However, assigning a unique radius...... might not correctly capture volume exclusion - of crucial importance when trying to understand a proteins $3$d-structure. We propose a new reduced model treating the protein as a non-uniform tube with a radius reflecting the positions of atoms. The tube representation is well suited considering X......-ray crystallographic resolution ~ 3Å while a varying radius accounts for the different sizes of side chains. Such a non-uniform tube better capture the protein geometry and has numerous applications in structural/computational biology from the classification of protein structures to sequence-structure prediction....

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 .

Potential Mediators between Fibromyalgia and C-Reactive protein: Results from a Large U.S. Community Survey

OpenAIRE

Feinberg, Termeh; Sambamoorthi, Usha; Lilly, Christa; Innes, Kim Karen

2017-01-01

Background Fibromyalgia, a potentially debilitating chronic pain syndrome of unknown etiology, may be characterized by inflammation. In this study, we investigated the relation of FMS to serum C-reactive protein (CRP) in a large population of adults (18+) and investigated the influence of other factors on this relationship, including BMI, comorbidities, as well as mood and sleep disturbance. Methods Participants were 52,535 Ohio Valley residents (Fibromyalgia n?=?1125). All participants compl...

Assigning agents to a line

DEFF Research Database (Denmark)

Hougaard, Jens Leth; Moreno-Ternero, Juan D.; Østerdal, Lars Peter Raahave

2014-01-01

minimizing modification of the classic random priority method to solve this class of problems. We also provide some logical relations in our setting among standard axioms in the literature on assignment problems, and explore the robustness of our results to several extensions of our setting....

The ICAP (Interactive Course Assignment Pages Publishing System

Directory of Open Access Journals (Sweden)

Kim Griggs

2008-03-01

Full Text Available The ICAP publishing system is an open source custom content management system that enables librarians to easily and quickly create and manage library help pages for course assignments (ICAPs, without requiring knowledge of HTML or other web technologies. The system's unique features include an emphasis on collaboration and content reuse and an easy-to-use interface that includes in-line help, simple forms and drag and drop functionality. The system generates dynamic, attractive course assignment pages that blend Web 2.0 features with traditional library resources, and makes the pages easier to find by providing a central web page for the course assignment pages. As of December 2007, the code is available as free, open-source software under the GNU General Public License.

Large-scale purification and crystallization of the endoribonuclease XendoU: troubleshooting with His-tagged proteins

International Nuclear Information System (INIS)

Renzi, Fabiana; Panetta, Gianna; Vallone, Beatrice; Brunori, Maurizio; Arceci, Massimo; Bozzoni, Irene; Laneve, Pietro; Caffarelli, Elisa

2006-01-01

Recombinant His-tagged XendoU, a eukaryotic endoribonuclease, appeared to aggregate in the presence of divalent cations. Monodisperse protein which yielded crystals diffracting to 2.2 Å was obtained by addition of EDTA. XendoU is the first endoribonuclease described in higher eukaryotes as being involved in the endonucleolytic processing of intron-encoded small nucleolar RNAs. It is conserved among eukaryotes and its viral homologue is essential in SARS replication and transcription. The large-scale purification and crystallization of recombinant XendoU are reported. The tendency of the recombinant enzyme to aggregate could be reversed upon the addition of chelating agents (EDTA, imidazole): aggregation is a potential drawback when purifying and crystallizing His-tagged proteins, which are widely used, especially in high-throughput structural studies. Purified monodisperse XendoU crystallized in two different space groups: trigonal P3 1 21, diffracting to low resolution, and monoclinic C2, diffracting to higher resolution

Artificial membrane-binding proteins stimulate oxygenation of stem cells during engineering of large cartilage tissue

Science.gov (United States)

Armstrong, James P. K.; Shakur, Rameen; Horne, Joseph P.; Dickinson, Sally C.; Armstrong, Craig T.; Lau, Katherine; Kadiwala, Juned; Lowe, Robert; Seddon, Annela; Mann, Stephen; Anderson, J. L. Ross; Perriman, Adam W.; Hollander, Anthony P.

2015-06-01

Restricted oxygen diffusion can result in central cell necrosis in engineered tissue, a problem that is exacerbated when engineering large tissue constructs for clinical application. Here we show that pre-treating human mesenchymal stem cells (hMSCs) with synthetic membrane-active myoglobin-polymer-surfactant complexes can provide a reservoir of oxygen capable of alleviating necrosis at the centre of hyaline cartilage. This is achieved through the development of a new cell functionalization methodology based on polymer-surfactant conjugation, which allows the delivery of functional proteins to the hMSC membrane. This new approach circumvents the need for cell surface engineering using protein chimerization or genetic transfection, and we demonstrate that the surface-modified hMSCs retain their ability to proliferate and to undergo multilineage differentiation. The functionalization technology is facile, versatile and non-disruptive, and in addition to tissue oxygenation, it should have far-reaching application in a host of tissue engineering and cell-based therapies.

A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.

Directory of Open Access Journals (Sweden)

Shannon M Clarke

Full Text Available Accurate pedigree information is critical to animal breeding systems to ensure the highest rate of genetic gain and management of inbreeding. The abundance of available genomic data, together with development of high throughput genotyping platforms, means that single nucleotide polymorphisms (SNPs are now the DNA marker of choice for genomic selection studies. Furthermore the superior qualities of SNPs compared to microsatellite markers allows for standardization between laboratories; a property that is crucial for developing an international set of markers for traceability studies. The objective of this study was to develop a high throughput SNP assay for use in the New Zealand sheep industry that gives accurate pedigree assignment and will allow a reduction in breeder input over lambing. This required two phases of development--firstly, a method of extracting quality DNA from ear-punch tissue performed in a high throughput cost efficient manner and secondly a SNP assay that has the ability to assign paternity to progeny resulting from mob mating. A likelihood based approach to infer paternity was used where sires with the highest LOD score (log of the ratio of the likelihood given parentage to likelihood given non-parentage are assigned. An 84 "parentage SNP panel" was developed that assigned, on average, 99% of progeny to a sire in a problem where there were 3,000 progeny from 120 mob mated sires that included numerous half sib sires. In only 6% of those cases was there another sire with at least a 0.02 probability of paternity. Furthermore dam information (either recorded, or by genotyping possible dams was absent, highlighting the SNP test's suitability for paternity testing. Utilization of this parentage SNP assay will allow implementation of progeny testing into large commercial farms where the improved accuracy of sire assignment and genetic evaluations will increase genetic gain in the sheep industry.

Genetics of traffic assignment models for strategic transport planning

NARCIS (Netherlands)

Bliemer, M.C.J.; Raadsen, M.P.H.; Brederode, L.J.N.; Bell, M.G.H.; Wismans, Luc Johannes Josephus; Smith, M.J.

2016-01-01

This paper presents a review and classification of traffic assignment models for strategic transport planning purposes by using concepts analogous to genetics in biology. Traffic assignment models share the same theoretical framework (DNA), but differ in capability (genes). We argue that all traffic

Epstein-Barr virus large tegument protein BPLF1 contributes to innate immune evasion through interference with toll-like receptor signaling.

Directory of Open Access Journals (Sweden)

Michiel van Gent

2014-02-01

Full Text Available Viral infection triggers an early host response through activation of pattern recognition receptors, including Toll-like receptors (TLR. TLR signaling cascades induce production of type I interferons and proinflammatory cytokines involved in establishing an anti-viral state as well as in orchestrating ensuing adaptive immunity. To allow infection, replication, and persistence, (herpesviruses employ ingenious strategies to evade host immunity. The human gamma-herpesvirus Epstein-Barr virus (EBV is a large, enveloped DNA virus persistently carried by more than 90% of adults worldwide. It is the causative agent of infectious mononucleosis and is associated with several malignant tumors. EBV activates TLRs, including TLR2, TLR3, and TLR9. Interestingly, both the expression of and signaling by TLRs is attenuated during productive EBV infection. Ubiquitination plays an important role in regulating TLR signaling and is controlled by ubiquitin ligases and deubiquitinases (DUBs. The EBV genome encodes three proteins reported to exert in vitro deubiquitinase activity. Using active site-directed probes, we show that one of these putative DUBs, the conserved herpesvirus large tegument protein BPLF1, acts as a functional DUB in EBV-producing B cells. The BPLF1 enzyme is expressed during the late phase of lytic EBV infection and is incorporated into viral particles. The N-terminal part of the large BPLF1 protein contains the catalytic site for DUB activity and suppresses TLR-mediated activation of NF-κB at, or downstream of, the TRAF6 signaling intermediate. A catalytically inactive mutant of this EBV protein did not reduce NF-κB activation, indicating that DUB activity is essential for attenuating TLR signal transduction. Our combined results show that EBV employs deubiquitination of signaling intermediates in the TLR cascade as a mechanism to counteract innate anti-viral immunity of infected hosts.

The PAS fold: A redefinition of the PAS domain based upon structural prediction. A large-scale homology modelling study

NARCIS (Netherlands)

Hefti, M.H.; Francoijs, C.J.J.; Vries, de S.C.; Dixon, R.; Vervoort, J.J.M.

2004-01-01

In the postgenomic era it is essential that protein sequences are annotated correctly in order to help in the assignment of their putative functions. Over 1300 proteins in current protein sequence databases are predicted to contain a PAS domain based upon amino acid sequence alignments. One of the

An Active-Learning Approach to Fostering Understanding of Research Methods in Large Classes

Science.gov (United States)

LaCosse, Jennifer; Ainsworth, Sarah E.; Shepherd, Melissa A.; Ent, Michael; Klein, Kelly M.; Holland-Carter, Lauren A.; Moss, Justin H.; Licht, Mark; Licht, Barbara

2017-01-01

The current investigation tested the effectiveness of an online student research project designed to supplement traditional methods (e.g., lectures, discussions, and assigned readings) of teaching research methods in a large-enrollment Introduction to Psychology course. Over the course of the semester, students completed seven assignments, each…